/usr/common/jgi/aligners/bwa/0.6.2/bin/bwa index /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/contigs.2k.fasta
/usr/common/jgi/aligners/bwa/0.6.2/bin/bwa aln -t 8 /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/contigs.2k.fasta /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/pct_reads_assembled/ZHYY.8454.1.101266.CGTAC.anqdp.bbqc.norm.fastq_rev > /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/pct_reads_assembled/ZHYY.8454.1.101266.CGTAC.anqdp.bbqc.norm.fastq_rev.sai
/usr/common/jgi/aligners/bwa/0.6.2/bin/bwa sampe -A -P -s /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/contigs.2k.fasta /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/pct_reads_assembled/ZHYY.8454.1.101266.CGTAC.anqdp.bbqc.norm.fastq_fwd.sai /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/pct_reads_assembled/ZHYY.8454.1.101266.CGTAC.anqdp.bbqc.norm.fastq_rev.sai /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/pct_reads_assembled/ZHYY.8454.1.101266.CGTAC.anqdp.bbqc.norm.fastq_fwd /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/pct_reads_assembled/ZHYY.8454.1.101266.CGTAC.anqdp.bbqc.norm.fastq_rev > /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/pct_reads_assembled/out.sam
Running bwa ...

/global/common/genepool/jgi/qaqc/jigsaw/2.4.1-prod_2.4.2-24-gf598c31/bin/pe_bwa.pl -sampe_params "-A -P -s" -t 8 /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/contigs.2k.fasta /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/ZHYY.8454.1.101266.CGTAC.anqdp.bbqc.norm.fastq /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/pct_reads_assembled/out.sam

Gathering stats ...