[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 178.97 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 141.35 sec
[bwa_aln_core] write to the disk... [bwa_aln_core] convert to sequence coordinate... 8.14 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... [samopen] SAM header is present: 79926 sequences.
2.43 sec
[bwa_aln_core] 262144 sequences have been processed.
0.06 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 159.32 sec
[bwa_aln_core] write to the disk... [bwa_aln_core] convert to sequence coordinate... 8.75 sec
[bwa_aln_core] refine gapped alignments... 0.48 sec
[bwa_aln_core] print alignments... 2.65 sec
[bwa_aln_core] 524288 sequences have been processed.
0.04 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 183.04 sec
[bwa_aln_core] write to the disk... [bwa_aln_core] convert to sequence coordinate... 7.76 sec
[bwa_aln_core] refine gapped alignments... 0.65 sec
[bwa_aln_core] print alignments... 2.40 sec
[bwa_aln_core] 786432 sequences have been processed.
0.03 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 113.69 sec
[bwa_aln_core] write to the disk... [bwa_aln_core] convert to sequence coordinate... 7.27 sec
[bwa_aln_core] refine gapped alignments... 0.50 sec
[bwa_aln_core] print alignments... 2.35 sec
[bwa_aln_core] 1048576 sequences have been processed.
0.04 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 171.27 sec
[bwa_aln_core] write to the disk... [bwa_aln_core] convert to sequence coordinate... 8.08 sec
[bwa_aln_core] refine gapped alignments... 0.49 sec
[bwa_aln_core] print alignments... 2.83 sec
[bwa_aln_core] 1310720 sequences have been processed.
0.03 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 183.95 sec
[bwa_aln_core] write to the disk... [bwa_aln_core] convert to sequence coordinate... 7.18 sec
[bwa_aln_core] refine gapped alignments... 0.58 sec
[bwa_aln_core] print alignments... 2.41 sec
[bwa_aln_core] 1572864 sequences have been processed.
0.03 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 132.59 sec
[bwa_aln_core] write to the disk... [bwa_aln_core] convert to sequence coordinate... 7.38 sec
[bwa_aln_core] refine gapped alignments... 0.53 sec
[bwa_aln_core] print alignments... 2.57 sec
[bwa_aln_core] 1835008 sequences have been processed.
0.04 sec
[bwa_aln_core] 2097152 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 72.82 sec
[bwa_aln_core] write to the disk... [bwa_aln_core] convert to sequence coordinate... 7.77 sec
[bwa_aln_core] refine gapped alignments... 0.52 sec
[bwa_aln_core] print alignments... 2.62 sec
[bwa_aln_core] 2097152 sequences have been processed.
0.03 sec
[bwa_aln_core] 2258316 sequences have been processed.
[bwa_aln_core] convert to sequence coordinate... 6.50 sec
[bwa_aln_core] refine gapped alignments... 0.44 sec
[bwa_aln_core] print alignments... 2.11 sec
[bwa_aln_core] 2258316 sequences have been processed.
[bam_sort_core] merging from 2 files...