[24/Mar/2015 15:07:14] running: /projectb/sandbox/rqc/prod/pipelines/external_tools/gc_cov/20121130/bin/illToCovGcOnRef.pl -od /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/gc_cov/cov -sl 5000 /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/scaffolds.2k.fasta /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/ZHYY.8454.1.101266.CGTAC.anqdp.bbqc.norm.fastq ...
ok! [nomessage] file=[/global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/scaffolds.2k.fasta]
ok! [nomessage] file=[/global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/ZHYY.8454.1.101266.CGTAC.anqdp.bbqc.norm.fastq]
[24/Mar/2015 15:07:14] creating workdir /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/gc_cov/cov ...
[24/Mar/2015 15:07:14] creating datadir /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/gc_cov/cov/data ...
[24/Mar/2015 15:07:14] scaffToCtg: /global/projectb/sandbox/rqc/prod/pipelines/external_tools/gc_cov/20121130/bin/scaffToContigs.pl  /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/scaffolds.2k.fasta 1 | /global/projectb/sandbox/rqc/prod/pipelines/external_tools/gc_cov/20121130/bin/shredFa.pl -l 5000 -o 0 > /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/gc_cov/cov/data/scaffolds.2k.shreds.fa ...
[24/Mar/2015 15:07:14] running: /global/projectb/sandbox/rqc/prod/pipelines/external_tools/gc_cov/20121130/bin/scaffToContigs.pl /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/scaffolds.2k.fasta 1 ...
[24/Mar/2015 15:07:14] overlap=0 ...
[24/Mar/2015 15:07:14] ratchet=5000 ...
[24/Mar/2015 15:07:14] running: /global/projectb/sandbox/rqc/prod/pipelines/external_tools/gc_cov/20121130/bin/shredFa.pl -l 5000 -o 0 ...
[24/Mar/2015 15:07:14] complete. ...
[24/Mar/2015 15:07:14] complete. exiting ...
ok! [nomessage] file=[/global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/gc_cov/cov/data/scaffolds.2k.shreds.fa]
[24/Mar/2015 15:07:14] calculating GC: /global/projectb/sandbox/rqc/prod/pipelines/external_tools/gc_cov/20121130/bin/gc.pl /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/gc_cov/cov/data/scaffolds.2k.shreds.fa > /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/gc_cov/cov/data/scaffolds.2k.shreds.gc ...
ok! [nomessage] file=[/global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/gc_cov/cov/data/scaffolds.2k.shreds.gc]
ok! [nomessage] file=[/global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/ZHYY.8454.1.101266.CGTAC.anqdp.bbqc.norm.fastq]
[24/Mar/2015 15:07:14] bwa aligning fastq to ref ...
[24/Mar/2015 15:07:14] Creating bwa index: /usr/common/jgi/aligners/bwa/0.6.2/bin/bwa index /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/gc_cov/cov/data/scaffolds.2k.shreds.fa ...
[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/ZHYY/gc_cov/cov/data/scaffolds.2k.shreds.fa
[main] Real time: 0.023 sec; CPU: 0.022 sec
ok! [nomessage] file=[/global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/gc_cov/cov/data/ZHYY.8454.1.101266.CGTAC.anqdp.bbqc.norm.sam]
ok! [nomessage] file=[/global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/gc_cov/cov/data/ZHYY.8454.1.101266.CGTAC.anqdp.bbqc.norm.ale]
ok! [nomessage] file=[/global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/gc_cov/cov/data/scaffolds.2k.fasta.gc_cov.csv]
ok! [nomessage] file=[/global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/gc_cov/cov/scaffolds.2k.gc_cov.legend.png]
ok! [nomessage] file=[/global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/gc_cov/cov/scaffolds.2k.gc_cov.nolegend.png]
ok! [nomessage] file=[/global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/gc_cov/cov/data/ZHYY.8454.1.101266.CGTAC.anqdp.bbqc.norm.cov.gc_vs_cov.multi.csv]
ok! [nomessage] file=[/global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/gc_cov/cov/scaffolds.2k.ZHYY.8454.1.101266.CGTAC.anqdp.bbqc.norm.gc_vs_cov.multi.legend.png]
ok! [nomessage] file=[/global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/gc_cov/cov/scaffolds.2k.ZHYY.8454.1.101266.CGTAC.anqdp.bbqc.norm.gc_vs_cov.multi.nolegend.png]
ok! [nomessage] file=[/global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/gc_cov/cov/scaffolds.2k.gc_vs_cov.multi.legend.png]
ok! [nomessage] file=[/global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/gc_cov/cov/scaffolds.2k.gc_vs_cov.multi.nolegend.png]
ok! [nomessage] file=[/global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/gc_cov/cov/data/scaffolds.2k.fasta.gc_vs_cov.single.csv]
ok! [nomessage] file=[/global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/gc_cov/cov/scaffolds.2k.gc_vs_cov.single.png]
[24/Mar/2015 15:08:40] 
Done.
 ...