Commit e706cf5c authored by Andreas Kusalananda Kähäri's avatar Andreas Kusalananda Kähäri
Browse files

Also write error reports.

parent 9888a01d
......@@ -38,7 +38,7 @@ then
outdir=$PWD
fi
echo "\nOutput dir is '${outdir}'\n"
print "Output dir is '${outdir}'"
# Make sure this is a core database.
if [[ -n ${dbname##*_core_*} ]]; then
......@@ -49,7 +49,9 @@ fi
print "Submitting percent GC calculation to queue 'normal'"
print "\tThe output from this job goes to the file"
print "\t'${dbname}_gc.out'"
bsub -q normal -J gc_calc -oo ${outdir}/${dbname}_gc.out \
bsub -q normal -J gc_calc \
-oo ${outdir}/${dbname}_gc.out \
-eo ${outdir}/${dbname}_gc.err \
perl ./percent_gc_calc.pl \
-host ${host} \
-port ${port} \
......@@ -60,7 +62,9 @@ bsub -q normal -J gc_calc -oo ${outdir}/${dbname}_gc.out \
print "Submitting gene density calculation to queue 'normal'"
print "\tThe output from this job goes to the file"
print "\t'${dbname}_gene.out'"
bsub -q normal -J gene_density -oo ${outdir}/${dbname}_gene.out \
bsub -q normal -J gene_density \
-oo ${outdir}/${dbname}_gene.out \
-eo ${outdir}/${dbname}_gene.err \
perl ./gene_density_calc.pl \
-host ${host} \
-port ${port} \
......@@ -71,7 +75,9 @@ bsub -q normal -J gene_density -oo ${outdir}/${dbname}_gene.out \
print "Submitting repeat coverage calculation to queue 'long'"
print "\tThe output from this job goes to the file"
print "\t'${dbname}_repeat.out'"
bsub -q long -J repeat_cov -oo ${outdir}/${dbname}_repeat.out \
bsub -q long -J repeat_cov \
-oo ${outdir}/${dbname}_repeat.out \
-eo ${outdir}/${dbname}_repeat.err \
perl ./repeat_coverage_calc.pl \
-host ${host} \
-port ${port} \
......@@ -82,7 +88,9 @@ bsub -q long -J repeat_cov -oo ${outdir}/${dbname}_repeat.out \
print "Submitting variation density calculation to queue 'normal'"
print "\tThe output from this job goes to the file"
print "\t'${dbname}_var.out'"
bsub -q normal -J var_density -oo ${outdir}/${dbname}_var.out \
bsub -q normal -J var_density \
-oo ${outdir}/${dbname}_var.out \
-eo ${outdir}/${dbname}_var.err \
perl ./variation_density.pl \
-host ${host} \
-port ${port} \
......@@ -93,7 +101,9 @@ bsub -q normal -J var_density -oo ${outdir}/${dbname}_var.out \
print "Submitting seq region stats calculation to queue 'normal'"
print "\tThe output from this job goes to the file"
print "\t'${dbname}_seqreg.out'"
bsub -q normal -J seqreg_stats -oo ${outdir}/${dbname}_seqreg.out \
bsub -q normal -J seqreg_stats \
-oo ${outdir}/${dbname}_seqreg.out \
-eo ${outdir}/${dbname}_seqreg.err \
perl ./seq_region_stats.pl \
-host ${host} \
-port ${port} \
......@@ -104,7 +114,9 @@ bsub -q normal -J seqreg_stats -oo ${outdir}/${dbname}_seqreg.out \
print "Submitting gene_gc content calculation to queue 'normal'"
print "\tThe output from this job goes to the file"
print "\t'${dbname}_genegc.out'"
bsub -q normal -J genegc_stats -oo ${outdir}/${dbname}_genegc.out \
bsub -q normal -J genegc_stats \
-oo ${outdir}/${dbname}_genegc.out \
-eo ${outdir}/${dbname}_genegc.err \
perl ../gene_gc.pl \
-host ${host} \
-port ${port} \
......
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