[bwa_index] Pack FASTA... 0.00 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 0.01 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... 0.00 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/AAUAO/spades/contigs.2k.fasta
[main] Real time: 0.022 sec; CPU: 0.025 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... 1.23 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 33383 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/AAUAO/spades/contigs.2k.fasta /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/AAUAO/pct_reads_assembled/AAUAO.10M.bbqc.fq.gz.fastq_rev
[main] Real time: 0.261 sec; CPU: 1.320 sec
1.30 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 33383 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/AAUAO/spades/contigs.2k.fasta /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/AAUAO/pct_reads_assembled/AAUAO.10M.bbqc.fq.gz.fastq_fwd
[main] Real time: 0.287 sec; CPU: 1.382 sec
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (224, 265, 315)
[infer_isize] low and high boundaries: 150 and 497 for estimating avg and std
[infer_isize] inferred external isize from 31054 pairs: 273.182 +/- 64.359
[infer_isize] skewness: 0.595; kurtosis: -0.031; ap_prior: 4.61e-05
[infer_isize] inferred maximum insert size: 608 (5.21 sigma)
[bwa_cal_pac_pos_pe] discard insert size estimate as user's request.
[bwa_sai2sam_pe_core] time elapses: 0.22 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... 0.13 sec
[bwa_sai2sam_pe_core] print alignments... 0.23 sec
[bwa_sai2sam_pe_core] 33383 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/AAUAO/spades/contigs.2k.fasta /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/AAUAO/pct_reads_assembled/AAUAO.10M.bbqc.fq.gz.fastq_fwd.sai /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/AAUAO/pct_reads_assembled/AAUAO.10M.bbqc.fq.gz.fastq_rev.sai /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/AAUAO/pct_reads_assembled/AAUAO.10M.bbqc.fq.gz.fastq_fwd /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/AAUAO/pct_reads_assembled/AAUAO.10M.bbqc.fq.gz.fastq_rev
[main] Real time: 0.777 sec; CPU: 0.768 sec