Using GATK jar /usr/local/bioinfo/src/GATK/gatk-4.4.0.0/gatk-package-4.4.0.0-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xms4000m -Xmx7g -jar /usr/local/bioinfo/src/GATK/gatk-4.4.0.0/gatk-package-4.4.0.0-local.jar MarkDuplicates --INPUT SRR7062654.bam --METRICS_FILE SRR7062654.bam.metrics --TMP_DIR . --ASSUME_SORT_ORDER coordinate --CREATE_INDEX true --OUTPUT SRR7062654.md.bam 11:08:06.806 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/bioinfo/src/GATK/gatk-4.4.0.0/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so [Tue Nov 07 11:08:06 CET 2023] MarkDuplicates --INPUT SRR7062654.bam --OUTPUT SRR7062654.md.bam --METRICS_FILE SRR7062654.bam.metrics --ASSUME_SORT_ORDER coordinate --TMP_DIR . --CREATE_INDEX true --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Tue Nov 07 11:08:06 CET 2023] Executing as formation@n024 on Linux 4.18.0-372.32.1.el8_6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 17.0.6+9-LTS-190; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.4.0.0 INFO 2023-11-07 11:08:06 MarkDuplicates Start of doWork freeMemory: 3984375768; totalMemory: 4054581248; maxMemory: 7265714176 INFO 2023-11-07 11:08:06 MarkDuplicates Reading input file and constructing read end information. INFO 2023-11-07 11:08:06 MarkDuplicates Will retain up to 26325051 data points before spilling to disk. WARNING 2023-11-07 11:08:06 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: SRR7062654.43578889. Cause: String 'SRR7062654.43578889' did not start with a parsable number. INFO 2023-11-07 11:08:12 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 5s. Last read position: 26:1,885,927 INFO 2023-11-07 11:08:12 MarkDuplicates Tracking 81 as yet unmatched pairs. 81 records in RAM. INFO 2023-11-07 11:08:15 MarkDuplicates Read 1988606 records. 0 pairs never matched. INFO 2023-11-07 11:08:16 MarkDuplicates After buildSortedReadEndLists freeMemory: 3581803368; totalMemory: 4054581248; maxMemory: 7265714176 INFO 2023-11-07 11:08:16 MarkDuplicates Will retain up to 227053568 duplicate indices before spilling to disk. INFO 2023-11-07 11:08:16 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2023-11-07 11:08:16 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2023-11-07 11:08:17 MarkDuplicates Sorting list of duplicate records. INFO 2023-11-07 11:08:17 MarkDuplicates After generateDuplicateIndexes freeMemory: 2760140464; totalMemory: 4752711680; maxMemory: 7265714176 INFO 2023-11-07 11:08:17 MarkDuplicates Marking 55438 records as duplicates. INFO 2023-11-07 11:08:17 MarkDuplicates Found 0 optical duplicate clusters. INFO 2023-11-07 11:08:17 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2023-11-07 11:08:30 MarkDuplicates Writing complete. Closing input iterator. INFO 2023-11-07 11:08:30 MarkDuplicates Duplicate Index cleanup. INFO 2023-11-07 11:08:30 MarkDuplicates Getting Memory Stats. INFO 2023-11-07 11:08:30 MarkDuplicates Before output close freeMemory: 4570220976; totalMemory: 4752711680; maxMemory: 7265714176 INFO 2023-11-07 11:08:30 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2023-11-07 11:08:30 MarkDuplicates After output close freeMemory: 4508588648; totalMemory: 4682874880; maxMemory: 7265714176 [Tue Nov 07 11:08:30 CET 2023] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.40 minutes. Runtime.totalMemory()=4682874880