Concatenating/uncompressing fastq file(s) ...
/global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/concatFastqFiles.pl.sh > /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/concatFastqFiles.pl.sh.log 2> /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/concatFastqFiles.pl.sh.err.log

Created /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/spades/spades.sh > /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/spades.sh.log 2> /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/spades.sh.err.log

Created /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/contigs.fasta.

Created /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/contigs.2k.fasta.

Created /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/scaffolds.2k.fasta.

Creating spades agp file ...

/global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/agp.pl.sh > /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/agp.pl.sh.log 2> /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/agp.pl.sh.err.log

Created /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/submission.agp.

Running qc analysis tools ...

Creating GC vs coverage plot file ...

/global/common/genepool/jgi/qaqc/jigsaw/2.4.1-prod_2.4.2-24-gf598c31/bin/assemblyQc.pl -config /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/jigsaw.config -od /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY -aligner last /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/spades/contigs.2k.fasta

/global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/gc_cov/gcCovTaxPlotWrap.py.sh > /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/gc_cov/gcCovTaxPlotWrap.py.sh.log 2> /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/gc_cov/gcCovTaxPlotWrap.py.sh.err.log

/global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/ncbi_screen/ncbiPreScreen.pl.sh > /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/ncbi_screen/ncbiPreScreen.pl.sh.log 2> /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/ncbi_screen/ncbiPreScreen.pl.sh.err.log

/global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/pct_reads_assembled/calcPctReadsAssembled.py.sh > /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/pct_reads_assembled/calcPctReadsAssembled.py.sh.log 2> /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/pct_reads_assembled/calcPctReadsAssembled.py.sh.err.log

Created /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/megan/contigs_Kingdom.png.
Created /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/megan/contigs_Phylum.png.
Created /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/megan/contigs_Class.png.
Created /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/megan/contigs_Order.png.
Created /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/megan/contigs_Family.png.
Created /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/megan/contigs_Genus.png.
Created /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/megan/contigs_Species.png.
Created /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/megan/contigs_nototal_Kingdom.png.
Created /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/megan/contigs_nototal_Phylum.png.
Created /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/megan/contigs_nototal_Class.png.
Created /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/megan/contigs_nototal_Order.png.
Created /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/megan/contigs_nototal_Family.png.
Created /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/megan/contigs_nototal_Genus.png.
Created /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/megan/contigs_nototal_Species.png.

Created /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/gc_cov/gc_cov_Kingdom.png.
Created /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/gc_cov/gc_cov_Phylum.png.
Created /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/gc_cov/gc_cov_Class.png.
Created /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/gc_cov/gc_cov_Order.png.
Created /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/gc_cov/gc_cov_Family.png.
Created /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/gc_cov/gc_cov_Genus.png.
Created /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/gc_cov/gc_cov_Species.png.
Created /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/gc_cov/gc_cov_Kingdom_nolegend.png.
Created /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/gc_cov/gc_cov_Phylum_nolegend.png.
Created /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/gc_cov/gc_cov_Class_nolegend.png.
Created /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/gc_cov/gc_cov_Order_nolegend.png.
Created /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/gc_cov/gc_cov_Family_nolegend.png.
Created /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/gc_cov/gc_cov_Genus_nolegend.png.
Created /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/gc_cov/gc_cov_Species_nolegend.png.

Gathering assembly and qc metrics ...

cat spades/scaffolds.2k.fasta | /global/common/genepool/jgi/qaqc/jigsaw/2.4.1-prod_2.4.2-24-gf598c31/bin/gc.pl -v | grep -v 'G+C' | /global/common/genepool/jgi/qaqc/jigsaw/2.4.1-prod_2.4.2-24-gf598c31/bin/drawHistogram.pl -c 5 |  grep '# Mean' |  awk '{ print "Avg GC Content: "$4" +/- "$6"%"}'

/global/common/genepool/jgi/qaqc/jigsaw/2.4.1-prod_2.4.2-24-gf598c31/bin/fastalen.pl -max spades/scaffolds.2k.fasta | awk '$0 ~ /[0-9]+/ {print $2}'

/global/common/genepool/jgi/qaqc/jigsaw/2.4.1-prod_2.4.2-24-gf598c31/bin/fasta_stats2.linux -n 1 spades/scaffolds.2k.fasta

Created /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/jigsaw_stats.yaml.

Creating jigsaw report ...

/global/common/genepool/jgi/qaqc/jigsaw/2.4.1-prod_2.4.2-24-gf598c31/bin/jigsaw_pdf.pl -d /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY -od /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY -of /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/jigsaw_report.pdf /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/pdf_desc.yaml /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/jigsaw_stats.yaml > /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/pdf_report.log 2>&1

Created /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/jigsaw_report.pdf.

Creating QD report ...

/global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/jigsaw_qd_reporter.pl.sh > /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/jigsaw_qd_reporter.pl.sh.log 2> /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/jigsaw_qd_reporter.pl.sh.err.log

Created /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/final/QD.finalReport.txt.

Creating pipeline output file list ...

/global/common/genepool/jgi/qaqc/jigsaw/2.4.1-prod_2.4.2-24-gf598c31/bin/jigsaw_file_lister.pl /global/common/genepool/jgi/qaqc/jigsaw/2.4.1-prod_2.4.2-24-gf598c31/bin/../config/rqc_output_fof.txt /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/rqc.txt.tmp > /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/jigsaw_file_lister.pl.log.out 2> /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/jigsaw_file_lister.pl.log.err

Created /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/rqc.txt.tmp.

Created /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/rqc.txt.

Removing /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY/rqc.txt.tmp ...

Cleaning files ...

Creating final symlinks ...

Done.