[bwa_index] Pack FASTA... 0.00 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 0.00 seconds elapse.
[bwa_index] Update BWT... 0.00 sec
[bwa_index] Pack forward-only FASTA... 0.00 sec
[bwa_index] Construct SA from BWT and Occ... 0.01 sec
[main] Version: 0.6.2-r126
[main] CMD: /usr/common/jgi/aligners/bwa/0.6.2/bin/bwa index /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/AAUAN/spades/contigs.2k.fasta
[main] Real time: 0.016 sec; CPU: 0.020 sec
[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] 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... [bwa_aln_core] calculate SA coordinate... 1.98 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 50043 sequences have been processed.
[main] Version: 0.6.2-r126
[main] CMD: /usr/common/jgi/aligners/bwa/0.6.2/bin/bwa aln -t 8 /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/AAUAN/spades/contigs.2k.fasta /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/AAUAN/pct_reads_assembled/AAUAN.15M.bbqc.fq.gz.fastq_fwd
[main] Real time: 0.432 sec; CPU: 2.118 sec
2.26 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 50043 sequences have been processed.
[main] Version: 0.6.2-r126
[main] CMD: /usr/common/jgi/aligners/bwa/0.6.2/bin/bwa aln -t 8 /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/AAUAN/spades/contigs.2k.fasta /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/AAUAN/pct_reads_assembled/AAUAN.15M.bbqc.fq.gz.fastq_rev
[main] Real time: 0.512 sec; CPU: 2.398 sec
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (222, 260, 307)
[infer_isize] low and high boundaries: 150 and 477 for estimating avg and std
[infer_isize] inferred external isize from 46030 pairs: 268.027 +/- 61.076
[infer_isize] skewness: 0.618; kurtosis: 0.036; ap_prior: 4.74e-05
[infer_isize] inferred maximum insert size: 583 (5.16 sigma)
[bwa_cal_pac_pos_pe] discard insert size estimate as user's request.
[bwa_sai2sam_pe_core] time elapses: 0.31 sec
[bwa_sai2sam_pe_core] changing coordinates of 0 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_sai2sam_pe_core] time elapses: 0.00 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.40 sec
[bwa_sai2sam_pe_core] print alignments... 0.33 sec
[bwa_sai2sam_pe_core] 50043 sequences have been processed.
[main] Version: 0.6.2-r126
[main] CMD: /usr/common/jgi/aligners/bwa/0.6.2/bin/bwa sampe -A -P -s /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/AAUAN/spades/contigs.2k.fasta /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/AAUAN/pct_reads_assembled/AAUAN.15M.bbqc.fq.gz.fastq_fwd.sai /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/AAUAN/pct_reads_assembled/AAUAN.15M.bbqc.fq.gz.fastq_rev.sai /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/AAUAN/pct_reads_assembled/AAUAN.15M.bbqc.fq.gz.fastq_fwd /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/AAUAN/pct_reads_assembled/AAUAN.15M.bbqc.fq.gz.fastq_rev
[main] Real time: 1.388 sec; CPU: 1.314 sec