N E X T F L O W ~ version 21.04.1 Launching `nf-core/sarek` [friendly_northcutt] - revision: 68b9930a74 [master] WARN: It appears you have never run this project before -- Option `-resume` is ignored ------------------------------------------------------ ,--./,-. ___ __ __ __ ___ /,-._.--~' |\ | |__ __ / ` / \ |__) |__ } { | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,' ____ .´ _ `. / |\`-_ \ __ __ ___ | | \ `-| |__` /\ |__) |__ |__/ \ | \ / .__| /¯¯\ | \ |___ | \ `|____\´ nf-core/sarek v2.7.1 ------------------------------------------------------ WARN: Found unexpected parameters: * --saveReference: true - Ignore this warning: params.schema_ignore_params = "saveReference" Core Nextflow options revision : master runName : friendly_northcutt containerEngine : singularity container : nfcore/sarek:2.7.1 launchDir : /work2/project/sigenae/Formation_Aln-SNP_chr25-26 workDir : /work2/project/sigenae/Formation_Aln-SNP_chr25-26/work projectDir : /home/sigenae/.nextflow/assets/nf-core/sarek userName : sigenae profile : standard configFiles : /home/sigenae/.nextflow/assets/nf-core/sarek/nextflow.config, /work2/project/sigenae/Formation_Aln-SNP_chr25-26/./genotoul_1.config Input/output options input : /work2/project/sigenae/Formation_Aln-SNP_chr25-26/input.tsv Main options tools : HaplotypeCaller,FreeBayes,mpileup skip_qc : null Trim/split FASTQ clip_r1 : 0 clip_r2 : 0 three_prime_clip_r1 : 0 three_prime_clip_r2 : 0 trim_nextseq : 0 Preprocessing markdup_java_options : "-Xms4000m -Xmx7g" Variant Calling ascat_ploidy : null ascat_purity : null cf_contamination : null cf_ploidy : 2 generate_gvcf : true read_structure1 : null read_structure2 : null Annotation annotate_tools : null cadd_indels : false cadd_indels_tbi : false cadd_wg_snvs : false cadd_wg_snvs_tbi : false snpeff_cache : null vep_cache : null Reference genome options genome : Gallus_gallus-5.0_25-26 bwa : /work2/project/sigenae/Formation_Aln-SNP_chr25-26/Data/Gallus_gallus.Gallus_gallus-5.0.dna.toplevel_chr25-26.fa.{amb,ann,bwt,pac,sa} dict : /work2/project/sigenae/Formation_Aln-SNP_chr25-26/Data/Gallus_gallus.Gallus_gallus-5.0.dna.toplevel_chr25-26.dict fasta : /work2/project/sigenae/Formation_Aln-SNP_chr25-26/Data/Gallus_gallus.Gallus_gallus-5.0.dna.toplevel_chr25-26.fa known_indels : /work2/project/sigenae/Formation_Aln-SNP_chr25-26/Data/Gallus_gallus_incl_consequences_chr25-26.vcf known_indels_index : /work2/project/sigenae/Formation_Aln-SNP_chr25-26/Data/Gallus_gallus_incl_consequences_chr25-26.vcf.idx igenomes_base : s3://ngi-igenomes/igenomes/ genomes_base : /work2/project/sigenae/Formation_Aln-SNP_chr25-26/Data Generic options max_multiqc_email_size : 25 MB sequencing_center : null Max job request options single_cpu_mem : 7 GB max_cpus : 10 max_memory : 120 GB max_time : 4d Institutional config options config_profile_description: The Genotoul cluster profile config_profile_contact : support.bioinfo.genotoul@inra.fr config_profile_url : http://bioinfo.genotoul.fr/ ------------------------------------------------------ Only displaying parameters that differ from defaults. ------------------------------------------------------ Pipeline Release : master Run Name : friendly_northcutt Max Resources : 120 GB memory, 10 cpus, 4d time per job Container : singularity - nfcore/sarek:2.7.1 Output dir : ./results Launch dir : /work2/project/sigenae/Formation_Aln-SNP_chr25-26 Working dir : /work2/project/sigenae/Formation_Aln-SNP_chr25-26/work Script dir : /home/sigenae/.nextflow/assets/nf-core/sarek User : sigenae Input : /work2/project/sigenae/Formation_Aln-SNP_chr25-26/input.tsv Step : mapping Genome : Gallus_gallus-5.0_25-26 Nucleotides/s : 1000 Tools : haplotypecaller, freebayes, mpileup MarkDuplicates : Options Java options : "-Xms4000m -Xmx7g" GATK Spark : No Save BAMs mapped : No Skip MarkDuplicates: No GVCF : Yes AWS iGenomes base : s3://ngi-igenomes/igenomes/ Genomes base : /work2/project/sigenae/Formation_Aln-SNP_chr25-26/Data Save Reference : No BWA indexes : /work2/project/sigenae/Formation_Aln-SNP_chr25-26/Data/Gallus_gallus.Gallus_gallus-5.0.dna.toplevel_chr25-26.fa.{amb,ann,bwt,pac,sa} dict : /work2/project/sigenae/Formation_Aln-SNP_chr25-26/Data/Gallus_gallus.Gallus_gallus-5.0.dna.toplevel_chr25-26.dict fasta reference : /work2/project/sigenae/Formation_Aln-SNP_chr25-26/Data/Gallus_gallus.Gallus_gallus-5.0.dna.toplevel_chr25-26.fa known indels : /work2/project/sigenae/Formation_Aln-SNP_chr25-26/Data/Gallus_gallus_incl_consequences_chr25-26.vcf known indels index: /work2/project/sigenae/Formation_Aln-SNP_chr25-26/Data/Gallus_gallus_incl_consequences_chr25-26.vcf.idx Publish dir mode : copy Config Profile : standard Config Description: The Genotoul cluster profile Config Contact : support.bioinfo.genotoul@inra.fr Config URL : http://bioinfo.genotoul.fr/ Config Files : /home/sigenae/.nextflow/assets/nf-core/sarek/nextflow.config, /work2/project/sigenae/Formation_Aln-SNP_chr25-26/./genotoul_1.config ---------------------------------------------------- [- ] process > get_software_versions - [- ] process > get_software_versions - [- ] process > BuildBWAindexes - [- ] process > BuildDict - [- ] process > BuildFastaFai - [- ] process > BuildDbsnpIndex - [- ] process > get_software_versions - [- ] process > BuildBWAindexes - [- ] process > BuildDict - [- ] process > BuildFastaFai - [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > get_software_versions - [- ] process > BuildBWAindexes - [- ] process > BuildDict - [- ] process > BuildFastaFai - [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > get_software_versions - [- ] process > BuildBWAindexes - [- ] process > BuildDict - [- ] process > BuildFastaFai - [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > get_software_versions - [- ] process > BuildBWAindexes - [- ] process > BuildDict - [- ] process > BuildFastaFai [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [- ] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [- ] process > BuildFastaFai [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [- ] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - executor > slurm (1) [- ] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [- ] process > FastQCFQ [ 0%] 0 of 2 executor > slurm (2) [33/5dda4f] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [- ] process > FastQCFQ [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - executor > slurm (3) [33/5dda4f] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [c0/ec3341] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - executor > slurm (4) [33/5dda4f] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - executor > slurm (4) [33/5dda4f] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - executor > slurm (4) [33/5dda4f] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - executor > slurm (4) [33/5dda4f] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - executor > slurm (4) [33/5dda4f] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - executor > slurm (4) [33/5dda4f] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - executor > slurm (4) [33/5dda4f] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - executor > slurm (4) [33/5dda4f] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - executor > slurm (4) [33/5dda4f] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - executor > slurm (4) [33/5dda4f] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - executor > slurm (4) [33/5dda4f] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - executor > slurm (4) [33/5dda4f] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - executor > slurm (4) [33/5dda4f] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - executor > slurm (4) [33/5dda4f] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - executor > slurm (4) [33/5dda4f] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - executor > slurm (4) [33/5dda4f] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - executor > slurm (4) [33/5dda4f] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - executor > slurm (4) [33/5dda4f] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - executor > slurm (4) [33/5dda4f] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - executor > slurm (4) [33/5dda4f] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - executor > slurm (4) [33/5dda4f] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - executor > slurm (4) [33/5dda4f] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - executor > slurm (4) [33/5dda4f] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - executor > slurm (4) [33/5dda4f] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - executor > slurm (4) [33/5dda4f] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - executor > slurm (4) [33/5dda4f] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - executor > slurm (4) [33/5dda4f] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [- ] process > Output_documentation [ 0%] 0 of 1 executor > slurm (5) [33/5dda4f] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [ 0%] 0 of 1 executor > slurm (5) [33/5dda4f] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [ 0%] 0 of 1 [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals - [- ] process > CreateIntervalBeds - [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads - [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [ 0%] 0 of 1 executor > slurm (5) [33/5dda4f] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [- ] process > BuildIntervals [ 0%] 0 of 1 [- ] process > CreateIntervalBeds - [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [- ] process > MapReads [ 0%] 0 of 2 [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [ 0%] 0 of 1 executor > slurm (7) [33/5dda4f] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [ 0%] 0 of 1 [- ] process > CreateIntervalBeds - [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [10/51e619] process > MapReads (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [ 0%] 0 of 1 ✔ executor > slurm (8) [33/5dda4f] process > get_software_versions [ 0%] 0 of 1 [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [ 0%] 0 of 1 [- ] process > CreateIntervalBeds - [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (8) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [ 0%] 0 of 1 [- ] process > CreateIntervalBeds - [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (8) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [ 0%] 0 of 1 [- ] process > CreateIntervalBeds - [c0/ec3341] process > FastQCFQ (F_Aln-SNP-1) [ 50%] 1 of 2 [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (8) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [ 0%] 0 of 1 [- ] process > CreateIntervalBeds - [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (8) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [- ] process > CreateIntervalBeds [ 0%] 0 of 1 [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (9) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [ 0%] 0 of 1 [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [ 0%] 0 of 2 [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC - [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (9) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [ 0%] 0 of 1 [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [- ] process > MarkDuplicates - [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [- ] process > BamQC [ 0%] 0 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (12) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [ 0%] 0 of 1 [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [78/92896f] process > MarkDuplicates (F_Aln-SNP-S... [ 0%] 0 of 2 [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [a1/f08544] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 0%] 0 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (13) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [ 0%] 0 of 1 [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [ 0%] 0 of 2 [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [a1/f08544] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 0%] 0 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (13) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [ 0%] 0 of 2 [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [a1/f08544] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 0%] 0 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (13) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [ 0%] 0 of 2 [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [a1/f08544] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 0%] 0 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (13) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [ 0%] 0 of 2 [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [a1/f08544] process > BamQC (F_Aln-SNP-SRR7062655_1) [ 50%] 1 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (13) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [ 0%] 0 of 2 [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [4b/ec97de] process > BamQC (F_Aln-SNP-SRR7062654_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (13) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [78/92896f] process > MarkDuplicates (F_Aln-SNP-S... [ 50%] 1 of 2 [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator - [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [4b/ec97de] process > BamQC (F_Aln-SNP-SRR7062654_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (13) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [- ] process > BaseRecalibrator [ 0%] 0 of 3 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [4b/ec97de] process > BamQC (F_Aln-SNP-SRR7062654_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (14) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [ 0%] 0 of 4 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [4b/ec97de] process > BamQC (F_Aln-SNP-SRR7062654_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (16) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2d/36e485] process > BaseRecalibrator (F_Aln-SNP... [ 0%] 0 of 4 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [4b/ec97de] process > BamQC (F_Aln-SNP-SRR7062654_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (17) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [80/5f6296] process > BaseRecalibrator (F_Aln-SNP... [ 0%] 0 of 4 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [4b/ec97de] process > BamQC (F_Aln-SNP-SRR7062654_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (17) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [80/5f6296] process > BaseRecalibrator (F_Aln-SNP... [ 0%] 0 of 4 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [4b/ec97de] process > BamQC (F_Aln-SNP-SRR7062654_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (17) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [b0/059aaf] process > BaseRecalibrator (F_Aln-SNP... [ 25%] 1 of 4 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [4b/ec97de] process > BamQC (F_Aln-SNP-SRR7062654_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (17) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [80/5f6296] process > BaseRecalibrator (F_Aln-SNP... [ 75%] 3 of 4 [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [4b/ec97de] process > BamQC (F_Aln-SNP-SRR7062654_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (17) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [- ] process > GatherBQSRReports - [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [4b/ec97de] process > BamQC (F_Aln-SNP-SRR7062654_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (19) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [ 0%] 0 of 2 [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [4b/ec97de] process > BamQC (F_Aln-SNP-SRR7062654_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (19) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [ 0%] 0 of 2 [- ] process > ApplyBQSR - [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [4b/ec97de] process > BamQC (F_Aln-SNP-SRR7062654_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (19) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [- ] process > ApplyBQSR [ 0%] 0 of 3 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [4b/ec97de] process > BamQC (F_Aln-SNP-SRR7062654_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (22) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [6e/663e29] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 0%] 0 of 4 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [4b/ec97de] process > BamQC (F_Aln-SNP-SRR7062654_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (23) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [38/efae1a] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 0%] 0 of 4 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [4b/ec97de] process > BamQC (F_Aln-SNP-SRR7062654_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (23) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [38/efae1a] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 0%] 0 of 4 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [4b/ec97de] process > BamQC (F_Aln-SNP-SRR7062654_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (23) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [38/efae1a] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 0%] 0 of 4 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [4b/ec97de] process > BamQC (F_Aln-SNP-SRR7062654_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (23) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7c/cac295] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 25%] 1 of 4 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [4b/ec97de] process > BamQC (F_Aln-SNP-SRR7062654_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (23) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [6e/663e29] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 50%] 2 of 4 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [4b/ec97de] process > BamQC (F_Aln-SNP-SRR7062654_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (23) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [38/efae1a] process > ApplyBQSR (F_Aln-SNP-SRR706... [ 75%] 3 of 4 [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal - [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [4b/ec97de] process > BamQC (F_Aln-SNP-SRR7062654_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (23) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [- ] process > MergeBamRecal [ 0%] 0 of 2 [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [4b/ec97de] process > BamQC (F_Aln-SNP-SRR7062654_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (25) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [ 0%] 0 of 2 [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [4b/ec97de] process > BamQC (F_Aln-SNP-SRR7062654_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (25) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [ 0%] 0 of 2 [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [4b/ec97de] process > BamQC (F_Aln-SNP-SRR7062654_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (25) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [2b/4e1fe1] process > MergeBamRecal (F_Aln-SNP-SR... [ 50%] 1 of 2 [- ] process > IndexBamRecal - [- ] process > SamtoolsStats - [4b/ec97de] process > BamQC (F_Aln-SNP-SRR7062654_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle - [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (26) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [e7/912ebd] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 1 [4b/ec97de] process > BamQC (F_Aln-SNP-SRR7062654_1) [100%] 2 of 2 [- ] process > HaplotypeCaller - [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle [ 0%] 0 of 2 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup - [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (26) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [e7/912ebd] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [4b/ec97de] process > BamQC (F_Aln-SNP-SRR7062654_1) [ 67%] 2 of 3 [- ] process > HaplotypeCaller [ 0%] 0 of 1 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle [ 0%] 0 of 2 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 2 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (26) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [e7/912ebd] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [4b/ec97de] process > BamQC (F_Aln-SNP-SRR7062654_1) [ 67%] 2 of 3 [- ] process > HaplotypeCaller [ 0%] 0 of 2 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [- ] process > FreebayesSingle [ 0%] 0 of 2 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 4 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (27) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [e7/912ebd] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [4b/ec97de] process > BamQC (F_Aln-SNP-SRR7062654_1) [ 50%] 2 of 4 [- ] process > HaplotypeCaller [ 0%] 0 of 4 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [7d/2f0fea] process > FreebayesSingle (SRR7062654... [ 0%] 0 of 4 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > Mpileup [ 0%] 0 of 4 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (29) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [e7/912ebd] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [4b/ec97de] process > BamQC (F_Aln-SNP-SRR7062654_1) [ 50%] 2 of 4 [- ] process > HaplotypeCaller [ 0%] 0 of 4 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [7d/2f0fea] process > FreebayesSingle (SRR7062654... [ 0%] 0 of 4 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [e4/3d40c1] process > Mpileup (SRR7062654-25_1-29... [ 0%] 0 of 4 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (31) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [e7/912ebd] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [4b/ec97de] process > BamQC (F_Aln-SNP-SRR7062654_1) [ 50%] 2 of 4 [a5/6d6b32] process > HaplotypeCaller (SRR7062654... [ 0%] 0 of 4 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [7d/2f0fea] process > FreebayesSingle (SRR7062654... [ 0%] 0 of 4 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [3e/51b42a] process > Mpileup (SRR7062654-26_1-53... [ 0%] 0 of 4 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (32) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [e7/912ebd] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [9d/72de5d] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [a5/6d6b32] process > HaplotypeCaller (SRR7062654... [ 0%] 0 of 4 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [7d/2f0fea] process > FreebayesSingle (SRR7062654... [ 0%] 0 of 4 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [3e/51b42a] process > Mpileup (SRR7062654-26_1-53... [ 0%] 0 of 4 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (34) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [ac/90fa6d] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [9d/72de5d] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [a5/6d6b32] process > HaplotypeCaller (SRR7062654... [ 0%] 0 of 4 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [7d/2f0fea] process > FreebayesSingle (SRR7062654... [ 0%] 0 of 4 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [48/bc0d9d] process > Mpileup (SRR7062655-26_1-53... [ 0%] 0 of 4 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (36) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [ac/90fa6d] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [9d/72de5d] process > BamQC (F_Aln-SNP-SRR7062654) [ 50%] 2 of 4 [01/fb211b] process > HaplotypeCaller (SRR7062654... [ 0%] 0 of 4 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [7d/2f0fea] process > FreebayesSingle (SRR7062654... [ 0%] 0 of 4 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [62/f6aa59] process > Mpileup (SRR7062655-25_1-29... [ 0%] 0 of 4 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (39) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [ac/90fa6d] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [cf/1f7770] process > BamQC (F_Aln-SNP-SRR7062655) [ 50%] 2 of 4 [af/efa05e] process > HaplotypeCaller (SRR7062655... [ 0%] 0 of 4 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [c5/606882] process > FreebayesSingle (SRR7062655... [ 0%] 0 of 4 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [62/f6aa59] process > Mpileup (SRR7062655-25_1-29... [ 0%] 0 of 4 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (41) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [ac/90fa6d] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [cf/1f7770] process > BamQC (F_Aln-SNP-SRR7062655) [ 50%] 2 of 4 [b8/155e80] process > HaplotypeCaller (SRR7062655... [ 0%] 0 of 4 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [98/eb47b7] process > FreebayesSingle (SRR7062655... [ 0%] 0 of 4 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [62/f6aa59] process > Mpileup (SRR7062655-25_1-29... [ 0%] 0 of 4 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (41) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [ac/90fa6d] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [cf/1f7770] process > BamQC (F_Aln-SNP-SRR7062655) [ 50%] 2 of 4 [b8/155e80] process > HaplotypeCaller (SRR7062655... [ 0%] 0 of 4 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [98/eb47b7] process > FreebayesSingle (SRR7062655... [ 0%] 0 of 4 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [62/f6aa59] process > Mpileup (SRR7062655-25_1-29... [ 0%] 0 of 4 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (41) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [ac/90fa6d] process > SamtoolsStats (F_Aln-SNP-SR... [ 0%] 0 of 2 [cf/1f7770] process > BamQC (F_Aln-SNP-SRR7062655) [ 50%] 2 of 4 [b8/155e80] process > HaplotypeCaller (SRR7062655... [ 0%] 0 of 4 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [98/eb47b7] process > FreebayesSingle (SRR7062655... [ 0%] 0 of 4 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [62/f6aa59] process > Mpileup (SRR7062655-25_1-29... [ 0%] 0 of 4 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (41) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [ac/90fa6d] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [cf/1f7770] process > BamQC (F_Aln-SNP-SRR7062655) [ 50%] 2 of 4 [b8/155e80] process > HaplotypeCaller (SRR7062655... [ 0%] 0 of 4 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [98/eb47b7] process > FreebayesSingle (SRR7062655... [ 0%] 0 of 4 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [62/f6aa59] process > Mpileup (SRR7062655-25_1-29... [ 0%] 0 of 4 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (41) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [ac/90fa6d] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [cf/1f7770] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [b8/155e80] process > HaplotypeCaller (SRR7062655... [ 0%] 0 of 4 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [98/eb47b7] process > FreebayesSingle (SRR7062655... [ 0%] 0 of 4 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [62/f6aa59] process > Mpileup (SRR7062655-25_1-29... [ 0%] 0 of 4 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (41) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [ac/90fa6d] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [cf/1f7770] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [b8/155e80] process > HaplotypeCaller (SRR7062655... [ 0%] 0 of 4 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [98/eb47b7] process > FreebayesSingle (SRR7062655... [ 0%] 0 of 4 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [e4/3d40c1] process > Mpileup (SRR7062654-25_1-29... [ 25%] 1 of 4 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (41) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [ac/90fa6d] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [cf/1f7770] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [b8/155e80] process > HaplotypeCaller (SRR7062655... [ 0%] 0 of 4 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [98/eb47b7] process > FreebayesSingle (SRR7062655... [ 25%] 1 of 4 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [e4/3d40c1] process > Mpileup (SRR7062654-25_1-29... [ 25%] 1 of 4 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (41) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [ac/90fa6d] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [cf/1f7770] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [b8/155e80] process > HaplotypeCaller (SRR7062655... [ 0%] 0 of 4 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [7d/2f0fea] process > FreebayesSingle (SRR7062654... [ 50%] 2 of 4 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [e4/3d40c1] process > Mpileup (SRR7062654-25_1-29... [ 25%] 1 of 4 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (41) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [ac/90fa6d] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [cf/1f7770] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [b8/155e80] process > HaplotypeCaller (SRR7062655... [ 0%] 0 of 4 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [7d/2f0fea] process > FreebayesSingle (SRR7062654... [ 50%] 2 of 4 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [62/f6aa59] process > Mpileup (SRR7062655-25_1-29... [ 50%] 2 of 4 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (41) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [ac/90fa6d] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [cf/1f7770] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [b8/155e80] process > HaplotypeCaller (SRR7062655... [ 0%] 0 of 4 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [7d/2f0fea] process > FreebayesSingle (SRR7062654... [ 50%] 2 of 4 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [3e/51b42a] process > Mpileup (SRR7062654-26_1-53... [ 75%] 3 of 4 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (41) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [ac/90fa6d] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [cf/1f7770] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [b8/155e80] process > HaplotypeCaller (SRR7062655... [ 0%] 0 of 4 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [c5/606882] process > FreebayesSingle (SRR7062655... [ 75%] 3 of 4 [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [3e/51b42a] process > Mpileup (SRR7062654-26_1-53... [ 75%] 3 of 4 [- ] process > MergeMpileup - [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (41) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [ac/90fa6d] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [cf/1f7770] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [b8/155e80] process > HaplotypeCaller (SRR7062655... [ 0%] 0 of 4 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [13/9b80df] process > FreebayesSingle (SRR7062654... [100%] 4 of 4 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [- ] process > ConcatVCF - [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [48/bc0d9d] process > Mpileup (SRR7062655-26_1-53... [100%] 4 of 4 ✔ [- ] process > MergeMpileup [ 0%] 0 of 1 [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (44) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [ac/90fa6d] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [cf/1f7770] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [b8/155e80] process > HaplotypeCaller (SRR7062655... [ 0%] 0 of 4 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [13/9b80df] process > FreebayesSingle (SRR7062654... [100%] 4 of 4 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [56/145c72] process > ConcatVCF (FreeBayes-SRR706... [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [48/bc0d9d] process > Mpileup (SRR7062655-26_1-53... [100%] 4 of 4 ✔ [a9/333cdc] process > MergeMpileup (SRR7062655) [ 0%] 0 of 2 [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (45) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [ac/90fa6d] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [cf/1f7770] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [b8/155e80] process > HaplotypeCaller (SRR7062655... [ 0%] 0 of 4 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [13/9b80df] process > FreebayesSingle (SRR7062654... [100%] 4 of 4 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [56/8fbd8b] process > ConcatVCF (FreeBayes-SRR706... [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [48/bc0d9d] process > Mpileup (SRR7062655-26_1-53... [100%] 4 of 4 ✔ [a9/333cdc] process > MergeMpileup (SRR7062655) [ 0%] 0 of 2 [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (45) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [ac/90fa6d] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [cf/1f7770] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [b8/155e80] process > HaplotypeCaller (SRR7062655... [ 0%] 0 of 4 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [13/9b80df] process > FreebayesSingle (SRR7062654... [100%] 4 of 4 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [56/8fbd8b] process > ConcatVCF (FreeBayes-SRR706... [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [48/bc0d9d] process > Mpileup (SRR7062655-26_1-53... [100%] 4 of 4 ✔ [a9/333cdc] process > MergeMpileup (SRR7062655) [ 0%] 0 of 2 [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (45) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [ac/90fa6d] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [cf/1f7770] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [b8/155e80] process > HaplotypeCaller (SRR7062655... [ 0%] 0 of 4 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [13/9b80df] process > FreebayesSingle (SRR7062654... [100%] 4 of 4 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [56/8fbd8b] process > ConcatVCF (FreeBayes-SRR706... [ 0%] 0 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [48/bc0d9d] process > Mpileup (SRR7062655-26_1-53... [100%] 4 of 4 ✔ [a9/333cdc] process > MergeMpileup (SRR7062655) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats - [- ] process > Vcftools - [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (45) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [ac/90fa6d] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [cf/1f7770] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [b8/155e80] process > HaplotypeCaller (SRR7062655... [ 0%] 0 of 4 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [13/9b80df] process > FreebayesSingle (SRR7062654... [100%] 4 of 4 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [56/8fbd8b] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [48/bc0d9d] process > Mpileup (SRR7062655-26_1-53... [100%] 4 of 4 ✔ [a9/333cdc] process > MergeMpileup (SRR7062655) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [- ] process > BcftoolsStats [ 0%] 0 of 2 [- ] process > Vcftools [ 0%] 0 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (47) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [ac/90fa6d] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [cf/1f7770] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [b8/155e80] process > HaplotypeCaller (SRR7062655... [ 0%] 0 of 4 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [13/9b80df] process > FreebayesSingle (SRR7062654... [100%] 4 of 4 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [56/8fbd8b] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [48/bc0d9d] process > Mpileup (SRR7062655-26_1-53... [100%] 4 of 4 ✔ [a9/333cdc] process > MergeMpileup (SRR7062655) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [b1/671ee1] process > BcftoolsStats (FreeBayes - ... [ 0%] 0 of 2 [93/002b39] process > Vcftools (FreeBayes - FreeB... [ 0%] 0 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (49) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [ac/90fa6d] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [cf/1f7770] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [b8/155e80] process > HaplotypeCaller (SRR7062655... [ 0%] 0 of 4 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [13/9b80df] process > FreebayesSingle (SRR7062654... [100%] 4 of 4 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [56/8fbd8b] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [48/bc0d9d] process > Mpileup (SRR7062655-26_1-53... [100%] 4 of 4 ✔ [a9/333cdc] process > MergeMpileup (SRR7062655) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [9c/91b996] process > BcftoolsStats (FreeBayes - ... [ 0%] 0 of 2 [46/156ff5] process > Vcftools (FreeBayes - FreeB... [ 0%] 0 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (49) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [ac/90fa6d] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [cf/1f7770] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [b8/155e80] process > HaplotypeCaller (SRR7062655... [ 0%] 0 of 4 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [13/9b80df] process > FreebayesSingle (SRR7062654... [100%] 4 of 4 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [56/8fbd8b] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [48/bc0d9d] process > Mpileup (SRR7062655-26_1-53... [100%] 4 of 4 ✔ [a9/333cdc] process > MergeMpileup (SRR7062655) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [9c/91b996] process > BcftoolsStats (FreeBayes - ... [ 0%] 0 of 2 [46/156ff5] process > Vcftools (FreeBayes - FreeB... [ 0%] 0 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (49) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [ac/90fa6d] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [cf/1f7770] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [b8/155e80] process > HaplotypeCaller (SRR7062655... [ 0%] 0 of 4 [- ] process > GenotypeGVCFs - [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [13/9b80df] process > FreebayesSingle (SRR7062654... [100%] 4 of 4 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [56/8fbd8b] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [48/bc0d9d] process > Mpileup (SRR7062655-26_1-53... [100%] 4 of 4 ✔ [a9/333cdc] process > MergeMpileup (SRR7062655) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [9c/91b996] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [46/156ff5] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (49) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [ac/90fa6d] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [cf/1f7770] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [af/efa05e] process > HaplotypeCaller (SRR7062655... [ 25%] 1 of 4 [- ] process > GenotypeGVCFs [ 0%] 0 of 1 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [13/9b80df] process > FreebayesSingle (SRR7062654... [100%] 4 of 4 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [56/8fbd8b] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [48/bc0d9d] process > Mpileup (SRR7062655-26_1-53... [100%] 4 of 4 ✔ [a9/333cdc] process > MergeMpileup (SRR7062655) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [9c/91b996] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [46/156ff5] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (50) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [ac/90fa6d] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [cf/1f7770] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [af/efa05e] process > HaplotypeCaller (SRR7062655... [ 25%] 1 of 4 [3c/0e725d] process > GenotypeGVCFs (SRR7062655-2... [ 0%] 0 of 1 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [13/9b80df] process > FreebayesSingle (SRR7062654... [100%] 4 of 4 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [56/8fbd8b] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [48/bc0d9d] process > Mpileup (SRR7062655-26_1-53... [100%] 4 of 4 ✔ [a9/333cdc] process > MergeMpileup (SRR7062655) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [9c/91b996] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [46/156ff5] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (51) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [ac/90fa6d] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [cf/1f7770] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [01/fb211b] process > HaplotypeCaller (SRR7062654... [ 50%] 2 of 4 [b7/ba2b84] process > GenotypeGVCFs (SRR7062654-2... [ 0%] 0 of 2 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [13/9b80df] process > FreebayesSingle (SRR7062654... [100%] 4 of 4 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [56/8fbd8b] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [48/bc0d9d] process > Mpileup (SRR7062655-26_1-53... [100%] 4 of 4 ✔ [a9/333cdc] process > MergeMpileup (SRR7062655) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [9c/91b996] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [46/156ff5] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (51) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [ac/90fa6d] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [cf/1f7770] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [01/fb211b] process > HaplotypeCaller (SRR7062654... [ 50%] 2 of 4 [b7/ba2b84] process > GenotypeGVCFs (SRR7062654-2... [ 0%] 0 of 2 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [13/9b80df] process > FreebayesSingle (SRR7062654... [100%] 4 of 4 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [56/8fbd8b] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [48/bc0d9d] process > Mpileup (SRR7062655-26_1-53... [100%] 4 of 4 ✔ [a9/333cdc] process > MergeMpileup (SRR7062655) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [9c/91b996] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [46/156ff5] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (51) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [ac/90fa6d] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [cf/1f7770] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [01/fb211b] process > HaplotypeCaller (SRR7062654... [ 50%] 2 of 4 [3c/0e725d] process > GenotypeGVCFs (SRR7062655-2... [ 50%] 1 of 2 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [13/9b80df] process > FreebayesSingle (SRR7062654... [100%] 4 of 4 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [56/8fbd8b] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [48/bc0d9d] process > Mpileup (SRR7062655-26_1-53... [100%] 4 of 4 ✔ [a9/333cdc] process > MergeMpileup (SRR7062655) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [9c/91b996] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [46/156ff5] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (51) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [ac/90fa6d] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [cf/1f7770] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [01/fb211b] process > HaplotypeCaller (SRR7062654... [ 50%] 2 of 4 [b7/ba2b84] process > GenotypeGVCFs (SRR7062654-2... [100%] 2 of 2 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [13/9b80df] process > FreebayesSingle (SRR7062654... [100%] 4 of 4 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [56/8fbd8b] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [48/bc0d9d] process > Mpileup (SRR7062655-26_1-53... [100%] 4 of 4 ✔ [a9/333cdc] process > MergeMpileup (SRR7062655) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [9c/91b996] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [46/156ff5] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (52) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [ac/90fa6d] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [cf/1f7770] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [a5/6d6b32] process > HaplotypeCaller (SRR7062654... [ 75%] 3 of 4 [fb/333a1a] process > GenotypeGVCFs (SRR7062654-2... [ 67%] 2 of 3 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [13/9b80df] process > FreebayesSingle (SRR7062654... [100%] 4 of 4 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [56/8fbd8b] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [48/bc0d9d] process > Mpileup (SRR7062655-26_1-53... [100%] 4 of 4 ✔ [a9/333cdc] process > MergeMpileup (SRR7062655) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [9c/91b996] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [46/156ff5] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (52) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [ac/90fa6d] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [cf/1f7770] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [a5/6d6b32] process > HaplotypeCaller (SRR7062654... [ 75%] 3 of 4 [fb/333a1a] process > GenotypeGVCFs (SRR7062654-2... [ 67%] 2 of 3 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [13/9b80df] process > FreebayesSingle (SRR7062654... [100%] 4 of 4 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [56/8fbd8b] process > ConcatVCF (FreeBayes-SRR706... [100%] 2 of 2 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [48/bc0d9d] process > Mpileup (SRR7062655-26_1-53... [100%] 4 of 4 ✔ [a9/333cdc] process > MergeMpileup (SRR7062655) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [9c/91b996] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [46/156ff5] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (52) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [ac/90fa6d] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [cf/1f7770] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [b8/155e80] process > HaplotypeCaller (SRR7062655... [100%] 4 of 4 ✔ [fb/333a1a] process > GenotypeGVCFs (SRR7062654-2... [ 75%] 3 of 4 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [13/9b80df] process > FreebayesSingle (SRR7062654... [100%] 4 of 4 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [56/8fbd8b] process > ConcatVCF (FreeBayes-SRR706... [ 50%] 2 of 4 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [48/bc0d9d] process > Mpileup (SRR7062655-26_1-53... [100%] 4 of 4 ✔ [a9/333cdc] process > MergeMpileup (SRR7062655) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [9c/91b996] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [46/156ff5] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (55) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [ac/90fa6d] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [cf/1f7770] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [b8/155e80] process > HaplotypeCaller (SRR7062655... [100%] 4 of 4 ✔ [24/75b562] process > GenotypeGVCFs (SRR7062655-2... [ 75%] 3 of 4 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [13/9b80df] process > FreebayesSingle (SRR7062654... [100%] 4 of 4 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e3/11c533] process > ConcatVCF (HaplotypeCallerG... [ 50%] 2 of 4 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [48/bc0d9d] process > Mpileup (SRR7062655-26_1-53... [100%] 4 of 4 ✔ [a9/333cdc] process > MergeMpileup (SRR7062655) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [9c/91b996] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [46/156ff5] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (55) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [ac/90fa6d] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [cf/1f7770] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [b8/155e80] process > HaplotypeCaller (SRR7062655... [100%] 4 of 4 ✔ [24/75b562] process > GenotypeGVCFs (SRR7062655-2... [ 75%] 3 of 4 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [13/9b80df] process > FreebayesSingle (SRR7062654... [100%] 4 of 4 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e3/11c533] process > ConcatVCF (HaplotypeCallerG... [ 50%] 2 of 4 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [48/bc0d9d] process > Mpileup (SRR7062655-26_1-53... [100%] 4 of 4 ✔ [a9/333cdc] process > MergeMpileup (SRR7062655) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [9c/91b996] process > BcftoolsStats (FreeBayes - ... [100%] 2 of 2 [46/156ff5] process > Vcftools (FreeBayes - FreeB... [100%] 2 of 2 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (55) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [ac/90fa6d] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [cf/1f7770] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [b8/155e80] process > HaplotypeCaller (SRR7062655... [100%] 4 of 4 ✔ [24/75b562] process > GenotypeGVCFs (SRR7062655-2... [ 75%] 3 of 4 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [13/9b80df] process > FreebayesSingle (SRR7062654... [100%] 4 of 4 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [dd/611a18] process > ConcatVCF (HaplotypeCallerG... [ 75%] 3 of 4 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [48/bc0d9d] process > Mpileup (SRR7062655-26_1-53... [100%] 4 of 4 ✔ [a9/333cdc] process > MergeMpileup (SRR7062655) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [9c/91b996] process > BcftoolsStats (FreeBayes - ... [ 67%] 2 of 3 [46/156ff5] process > Vcftools (FreeBayes - FreeB... [ 67%] 2 of 3 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (57) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [ac/90fa6d] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [cf/1f7770] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [b8/155e80] process > HaplotypeCaller (SRR7062655... [100%] 4 of 4 ✔ [24/75b562] process > GenotypeGVCFs (SRR7062655-2... [ 75%] 3 of 4 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [13/9b80df] process > FreebayesSingle (SRR7062654... [100%] 4 of 4 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [dd/611a18] process > ConcatVCF (HaplotypeCallerG... [ 75%] 3 of 4 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [48/bc0d9d] process > Mpileup (SRR7062655-26_1-53... [100%] 4 of 4 ✔ [a9/333cdc] process > MergeMpileup (SRR7062655) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [88/ba5bed] process > BcftoolsStats (HaplotypeCal... [ 67%] 2 of 3 [c9/06b57d] process > Vcftools (HaplotypeCallerGV... [ 67%] 2 of 3 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (57) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [ac/90fa6d] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [cf/1f7770] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [b8/155e80] process > HaplotypeCaller (SRR7062655... [100%] 4 of 4 ✔ [24/75b562] process > GenotypeGVCFs (SRR7062655-2... [ 75%] 3 of 4 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [13/9b80df] process > FreebayesSingle (SRR7062654... [100%] 4 of 4 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [dd/611a18] process > ConcatVCF (HaplotypeCallerG... [ 75%] 3 of 4 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [48/bc0d9d] process > Mpileup (SRR7062655-26_1-53... [100%] 4 of 4 ✔ [a9/333cdc] process > MergeMpileup (SRR7062655) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [88/ba5bed] process > BcftoolsStats (HaplotypeCal... [ 67%] 2 of 3 [c9/06b57d] process > Vcftools (HaplotypeCallerGV... [ 50%] 2 of 4 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (59) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [ac/90fa6d] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [cf/1f7770] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [b8/155e80] process > HaplotypeCaller (SRR7062655... [100%] 4 of 4 ✔ [24/75b562] process > GenotypeGVCFs (SRR7062655-2... [ 75%] 3 of 4 [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [13/9b80df] process > FreebayesSingle (SRR7062654... [100%] 4 of 4 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e3/11c533] process > ConcatVCF (HaplotypeCallerG... [100%] 4 of 4 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [48/bc0d9d] process > Mpileup (SRR7062655-26_1-53... [100%] 4 of 4 ✔ [a9/333cdc] process > MergeMpileup (SRR7062655) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [83/4530e4] process > BcftoolsStats (HaplotypeCal... [ 50%] 2 of 4 [5f/3c5402] process > Vcftools (HaplotypeCallerGV... [ 50%] 2 of 4 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (59) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [ac/90fa6d] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [cf/1f7770] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [b8/155e80] process > HaplotypeCaller (SRR7062655... [100%] 4 of 4 ✔ [24/75b562] process > GenotypeGVCFs (SRR7062655-2... [100%] 4 of 4 ✔ [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [13/9b80df] process > FreebayesSingle (SRR7062654... [100%] 4 of 4 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [e3/11c533] process > ConcatVCF (HaplotypeCallerG... [ 80%] 4 of 5 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [48/bc0d9d] process > Mpileup (SRR7062655-26_1-53... [100%] 4 of 4 ✔ [a9/333cdc] process > MergeMpileup (SRR7062655) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [83/4530e4] process > BcftoolsStats (HaplotypeCal... [ 50%] 2 of 4 [5f/3c5402] process > Vcftools (HaplotypeCallerGV... [ 50%] 2 of 4 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (61) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [ac/90fa6d] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [cf/1f7770] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [b8/155e80] process > HaplotypeCaller (SRR7062655... [100%] 4 of 4 ✔ [24/75b562] process > GenotypeGVCFs (SRR7062655-2... [100%] 4 of 4 ✔ [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [13/9b80df] process > FreebayesSingle (SRR7062654... [100%] 4 of 4 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [ba/db2c27] process > ConcatVCF (HaplotypeCaller-... [ 67%] 4 of 6 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [48/bc0d9d] process > Mpileup (SRR7062655-26_1-53... [100%] 4 of 4 ✔ [a9/333cdc] process > MergeMpileup (SRR7062655) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [83/4530e4] process > BcftoolsStats (HaplotypeCal... [ 50%] 2 of 4 [5f/3c5402] process > Vcftools (HaplotypeCallerGV... [ 50%] 2 of 4 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (61) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [ac/90fa6d] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [cf/1f7770] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [b8/155e80] process > HaplotypeCaller (SRR7062655... [100%] 4 of 4 ✔ [24/75b562] process > GenotypeGVCFs (SRR7062655-2... [100%] 4 of 4 ✔ [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [13/9b80df] process > FreebayesSingle (SRR7062654... [100%] 4 of 4 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [ba/db2c27] process > ConcatVCF (HaplotypeCaller-... [ 67%] 4 of 6 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [48/bc0d9d] process > Mpileup (SRR7062655-26_1-53... [100%] 4 of 4 ✔ [a9/333cdc] process > MergeMpileup (SRR7062655) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [83/4530e4] process > BcftoolsStats (HaplotypeCal... [100%] 4 of 4 [5f/3c5402] process > Vcftools (HaplotypeCallerGV... [ 50%] 2 of 4 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (61) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [ac/90fa6d] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [cf/1f7770] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [b8/155e80] process > HaplotypeCaller (SRR7062655... [100%] 4 of 4 ✔ [24/75b562] process > GenotypeGVCFs (SRR7062655-2... [100%] 4 of 4 ✔ [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [13/9b80df] process > FreebayesSingle (SRR7062654... [100%] 4 of 4 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [ba/db2c27] process > ConcatVCF (HaplotypeCaller-... [ 67%] 4 of 6 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [48/bc0d9d] process > Mpileup (SRR7062655-26_1-53... [100%] 4 of 4 ✔ [a9/333cdc] process > MergeMpileup (SRR7062655) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [83/4530e4] process > BcftoolsStats (HaplotypeCal... [100%] 4 of 4 [c9/06b57d] process > Vcftools (HaplotypeCallerGV... [ 75%] 3 of 4 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (61) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [ac/90fa6d] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [cf/1f7770] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [b8/155e80] process > HaplotypeCaller (SRR7062655... [100%] 4 of 4 ✔ [24/75b562] process > GenotypeGVCFs (SRR7062655-2... [100%] 4 of 4 ✔ [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [13/9b80df] process > FreebayesSingle (SRR7062654... [100%] 4 of 4 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [ba/db2c27] process > ConcatVCF (HaplotypeCaller-... [ 67%] 4 of 6 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [48/bc0d9d] process > Mpileup (SRR7062655-26_1-53... [100%] 4 of 4 ✔ [a9/333cdc] process > MergeMpileup (SRR7062655) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [83/4530e4] process > BcftoolsStats (HaplotypeCal... [100%] 4 of 4 [5f/3c5402] process > Vcftools (HaplotypeCallerGV... [100%] 4 of 4 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (61) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [ac/90fa6d] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [cf/1f7770] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [b8/155e80] process > HaplotypeCaller (SRR7062655... [100%] 4 of 4 ✔ [24/75b562] process > GenotypeGVCFs (SRR7062655-2... [100%] 4 of 4 ✔ [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [13/9b80df] process > FreebayesSingle (SRR7062654... [100%] 4 of 4 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [b4/ff97fa] process > ConcatVCF (HaplotypeCaller-... [ 83%] 5 of 6 [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [48/bc0d9d] process > Mpileup (SRR7062655-26_1-53... [100%] 4 of 4 ✔ [a9/333cdc] process > MergeMpileup (SRR7062655) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [83/4530e4] process > BcftoolsStats (HaplotypeCal... [ 80%] 4 of 5 [5f/3c5402] process > Vcftools (HaplotypeCallerGV... [ 80%] 4 of 5 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (65) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [ac/90fa6d] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [cf/1f7770] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [b8/155e80] process > HaplotypeCaller (SRR7062655... [100%] 4 of 4 ✔ [24/75b562] process > GenotypeGVCFs (SRR7062655-2... [100%] 4 of 4 ✔ [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [13/9b80df] process > FreebayesSingle (SRR7062654... [100%] 4 of 4 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [ba/db2c27] process > ConcatVCF (HaplotypeCaller-... [100%] 6 of 6 ✔ [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [48/bc0d9d] process > Mpileup (SRR7062655-26_1-53... [100%] 4 of 4 ✔ [a9/333cdc] process > MergeMpileup (SRR7062655) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f4/bd219b] process > BcftoolsStats (HaplotypeCal... [ 67%] 4 of 6 [da/7e1586] process > Vcftools (HaplotypeCaller -... [ 67%] 4 of 6 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (65) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [ac/90fa6d] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [cf/1f7770] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [b8/155e80] process > HaplotypeCaller (SRR7062655... [100%] 4 of 4 ✔ [24/75b562] process > GenotypeGVCFs (SRR7062655-2... [100%] 4 of 4 ✔ [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [13/9b80df] process > FreebayesSingle (SRR7062654... [100%] 4 of 4 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [ba/db2c27] process > ConcatVCF (HaplotypeCaller-... [100%] 6 of 6 ✔ [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [48/bc0d9d] process > Mpileup (SRR7062655-26_1-53... [100%] 4 of 4 ✔ [a9/333cdc] process > MergeMpileup (SRR7062655) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f4/bd219b] process > BcftoolsStats (HaplotypeCal... [ 67%] 4 of 6 [da/7e1586] process > Vcftools (HaplotypeCaller -... [ 67%] 4 of 6 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (65) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [ac/90fa6d] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [cf/1f7770] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [b8/155e80] process > HaplotypeCaller (SRR7062655... [100%] 4 of 4 ✔ [24/75b562] process > GenotypeGVCFs (SRR7062655-2... [100%] 4 of 4 ✔ [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [13/9b80df] process > FreebayesSingle (SRR7062654... [100%] 4 of 4 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [ba/db2c27] process > ConcatVCF (HaplotypeCaller-... [100%] 6 of 6 ✔ [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [48/bc0d9d] process > Mpileup (SRR7062655-26_1-53... [100%] 4 of 4 ✔ [a9/333cdc] process > MergeMpileup (SRR7062655) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [4b/5534ff] process > BcftoolsStats (HaplotypeCal... [ 83%] 5 of 6 [da/7e1586] process > Vcftools (HaplotypeCaller -... [ 67%] 4 of 6 [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC - [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (65) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [ac/90fa6d] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [cf/1f7770] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [b8/155e80] process > HaplotypeCaller (SRR7062655... [100%] 4 of 4 ✔ [24/75b562] process > GenotypeGVCFs (SRR7062655-2... [100%] 4 of 4 ✔ [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [13/9b80df] process > FreebayesSingle (SRR7062654... [100%] 4 of 4 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [ba/db2c27] process > ConcatVCF (HaplotypeCaller-... [100%] 6 of 6 ✔ [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [48/bc0d9d] process > Mpileup (SRR7062655-26_1-53... [100%] 4 of 4 ✔ [a9/333cdc] process > MergeMpileup (SRR7062655) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f4/bd219b] process > BcftoolsStats (HaplotypeCal... [100%] 6 of 6 ✔ [da/7e1586] process > Vcftools (HaplotypeCaller -... [100%] 6 of 6 ✔ [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [- ] process > MultiQC [ 0%] 0 of 1 [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (66) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [ac/90fa6d] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [cf/1f7770] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [b8/155e80] process > HaplotypeCaller (SRR7062655... [100%] 4 of 4 ✔ [24/75b562] process > GenotypeGVCFs (SRR7062655-2... [100%] 4 of 4 ✔ [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [13/9b80df] process > FreebayesSingle (SRR7062654... [100%] 4 of 4 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [ba/db2c27] process > ConcatVCF (HaplotypeCaller-... [100%] 6 of 6 ✔ [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [48/bc0d9d] process > Mpileup (SRR7062655-26_1-53... [100%] 4 of 4 ✔ [a9/333cdc] process > MergeMpileup (SRR7062655) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f4/bd219b] process > BcftoolsStats (HaplotypeCal... [100%] 6 of 6 ✔ [da/7e1586] process > Vcftools (HaplotypeCaller -... [100%] 6 of 6 ✔ [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [cc/148967] process > MultiQC (1) [ 0%] 0 of 1 [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (66) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [ac/90fa6d] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [cf/1f7770] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [b8/155e80] process > HaplotypeCaller (SRR7062655... [100%] 4 of 4 ✔ [24/75b562] process > GenotypeGVCFs (SRR7062655-2... [100%] 4 of 4 ✔ [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [13/9b80df] process > FreebayesSingle (SRR7062654... [100%] 4 of 4 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [ba/db2c27] process > ConcatVCF (HaplotypeCaller-... [100%] 6 of 6 ✔ [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [48/bc0d9d] process > Mpileup (SRR7062655-26_1-53... [100%] 4 of 4 ✔ [a9/333cdc] process > MergeMpileup (SRR7062655) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f4/bd219b] process > BcftoolsStats (HaplotypeCal... [100%] 6 of 6 ✔ [da/7e1586] process > Vcftools (HaplotypeCaller -... [100%] 6 of 6 ✔ [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [cc/148967] process > MultiQC (1) [ 0%] 0 of 1 [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (66) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [ac/90fa6d] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [cf/1f7770] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [b8/155e80] process > HaplotypeCaller (SRR7062655... [100%] 4 of 4 ✔ [24/75b562] process > GenotypeGVCFs (SRR7062655-2... [100%] 4 of 4 ✔ [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [13/9b80df] process > FreebayesSingle (SRR7062654... [100%] 4 of 4 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [ba/db2c27] process > ConcatVCF (HaplotypeCaller-... [100%] 6 of 6 ✔ [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [48/bc0d9d] process > Mpileup (SRR7062655-26_1-53... [100%] 4 of 4 ✔ [a9/333cdc] process > MergeMpileup (SRR7062655) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f4/bd219b] process > BcftoolsStats (HaplotypeCal... [100%] 6 of 6 ✔ [da/7e1586] process > Vcftools (HaplotypeCaller -... [100%] 6 of 6 ✔ [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [cc/148967] process > MultiQC (1) [100%] 1 of 1 ✔ [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ executor > slurm (66) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [ac/90fa6d] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [cf/1f7770] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [b8/155e80] process > HaplotypeCaller (SRR7062655... [100%] 4 of 4 ✔ [24/75b562] process > GenotypeGVCFs (SRR7062655-2... [100%] 4 of 4 ✔ [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [13/9b80df] process > FreebayesSingle (SRR7062654... [100%] 4 of 4 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [ba/db2c27] process > ConcatVCF (HaplotypeCaller-... [100%] 6 of 6 ✔ [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [48/bc0d9d] process > Mpileup (SRR7062655-26_1-53... [100%] 4 of 4 ✔ [a9/333cdc] process > MergeMpileup (SRR7062655) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f4/bd219b] process > BcftoolsStats (HaplotypeCal... [100%] 6 of 6 ✔ [da/7e1586] process > Vcftools (HaplotypeCaller -... [100%] 6 of 6 ✔ [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [cc/148967] process > MultiQC (1) [100%] 1 of 1 ✔ [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ -[nf-core/sarek] Pipeline completed successfully- executor > slurm (66) [33/5dda4f] process > get_software_versions [100%] 1 of 1 ✔ [- ] process > BuildBWAindexes - [- ] process > BuildDict - [c2/3790da] process > BuildFastaFai (Gallus_gallu... [100%] 1 of 1 ✔ [- ] process > BuildDbsnpIndex - [- ] process > BuildGermlineResourceIndex - [- ] process > BuildKnownIndelsIndex - [- ] process > BuildPonIndex - [e9/6436ea] process > BuildIntervals (Gallus_gall... [100%] 1 of 1 ✔ [46/84aaf5] process > CreateIntervalBeds (Gallus_... [100%] 1 of 1 ✔ [88/6971dd] process > FastQCFQ (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > FastQCBAM - [- ] process > TrimGalore - [- ] process > UMIFastqToBAM - [- ] process > UMIMapBamFile - [- ] process > GroupReadsByUmi - [- ] process > CallMolecularConsensusReads - [e4/0bcdf0] process > MapReads (F_Aln-SNP-1) [100%] 2 of 2 ✔ [- ] process > Sentieon_MapReads - [- ] process > MergeBamMapped - [- ] process > IndexBamMergedForSentieon - [- ] process > IndexBamFile - [05/7bf9f8] process > MarkDuplicates (F_Aln-SNP-S... [100%] 2 of 2 ✔ [- ] process > Sentieon_Dedup - [2c/0d5cd0] process > BaseRecalibrator (F_Aln-SNP... [100%] 4 of 4 ✔ [97/cf337e] process > GatherBQSRReports (F_Aln-SN... [100%] 2 of 2 ✔ [7d/33e6a2] process > ApplyBQSR (F_Aln-SNP-SRR706... [100%] 4 of 4 ✔ [- ] process > Sentieon_BQSR - [20/351169] process > MergeBamRecal (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [- ] process > IndexBamRecal - [ac/90fa6d] process > SamtoolsStats (F_Aln-SNP-SR... [100%] 2 of 2 ✔ [cf/1f7770] process > BamQC (F_Aln-SNP-SRR7062655) [100%] 4 of 4 ✔ [b8/155e80] process > HaplotypeCaller (SRR7062655... [100%] 4 of 4 ✔ [24/75b562] process > GenotypeGVCFs (SRR7062655-2... [100%] 4 of 4 ✔ [- ] process > Sentieon_DNAseq - [- ] process > Sentieon_DNAscope - [- ] process > StrelkaSingle - [- ] process > MantaSingle - [- ] process > TIDDIT - [13/9b80df] process > FreebayesSingle (SRR7062654... [100%] 4 of 4 ✔ [- ] process > FreeBayes - [- ] process > Mutect2 - [- ] process > Mutect2Single - [- ] process > MergeMutect2Stats - [ba/db2c27] process > ConcatVCF (HaplotypeCaller-... [100%] 6 of 6 ✔ [- ] process > ConcatVCF_Mutect2 - [- ] process > PileupSummariesForMutect2 - [- ] process > MergePileupSummaries - [- ] process > CalculateContamination - [- ] process > FilterMutect2Calls - [- ] process > Sentieon_TNscope - [- ] process > CompressSentieonVCF - [- ] process > Strelka - [- ] process > Manta - [- ] process > StrelkaBP - [- ] process > CNVkit - [- ] process > MSIsensor_scan - [- ] process > MSIsensor_msi - [- ] process > MSIsensor_msiSingle - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [48/bc0d9d] process > Mpileup (SRR7062655-26_1-53... [100%] 4 of 4 ✔ [a9/333cdc] process > MergeMpileup (SRR7062655) [100%] 2 of 2 ✔ [- ] process > ControlFREEC - [- ] process > ControlFREECSingle - [- ] process > ControlFreecViz - [- ] process > ControlFreecVizSingle - [f4/bd219b] process > BcftoolsStats (HaplotypeCal... [100%] 6 of 6 ✔ [da/7e1586] process > Vcftools (HaplotypeCaller -... [100%] 6 of 6 ✔ [- ] process > Snpeff - [- ] process > CompressVCFsnpEff - [- ] process > VEP - [- ] process > VEPmerge - [- ] process > CompressVCFvep - [cc/148967] process > MultiQC (1) [100%] 1 of 1 ✔ [e4/aa7c4c] process > Output_documentation [100%] 1 of 1 ✔ -[nf-core/sarek] Pipeline completed successfully- Completed at: 25-oct.-2021 14:29:27 Duration : 23m 28s CPU hours : 2.3 Succeeded : 66