From 013d2a5dc24d79942d79fd4d963fbc5bd8ade0e1 Mon Sep 17 00:00:00 2001 From: RoanKanninga Date: Tue, 16 Jun 2015 07:45:13 +0200 Subject: [PATCH 1/2] increase walltime for SpikePhiX protocol --- compute5/NGS_DNA-2.1.1/protocols/SpikePhiX.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/compute5/NGS_DNA-2.1.1/protocols/SpikePhiX.sh b/compute5/NGS_DNA-2.1.1/protocols/SpikePhiX.sh index bed0eb64..41fe090f 100644 --- a/compute5/NGS_DNA-2.1.1/protocols/SpikePhiX.sh +++ b/compute5/NGS_DNA-2.1.1/protocols/SpikePhiX.sh @@ -1,4 +1,4 @@ -#MOLGENIS nodes=1 ppn=1 mem=1gb walltime=02:30:00 +#MOLGENIS nodes=1 ppn=1 mem=1gb walltime=12:30:00 #Parameter mapping #string seqType From 8ec4df35871771629777d5811cd6c085de238967 Mon Sep 17 00:00:00 2001 From: RoanKanninga Date: Mon, 22 Jun 2015 19:41:35 +0200 Subject: [PATCH 2/2] changed the SpikePhiX number of cores on which it will run --- compute5/NGS_DNA-2.1.1/protocols/SpikePhiX.sh | 8 +++++--- compute5/NGS_DNA-2.1.1/workflow.csv | 2 +- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/compute5/NGS_DNA-2.1.1/protocols/SpikePhiX.sh b/compute5/NGS_DNA-2.1.1/protocols/SpikePhiX.sh index 41fe090f..ac8a2870 100644 --- a/compute5/NGS_DNA-2.1.1/protocols/SpikePhiX.sh +++ b/compute5/NGS_DNA-2.1.1/protocols/SpikePhiX.sh @@ -1,4 +1,4 @@ -#MOLGENIS nodes=1 ppn=1 mem=1gb walltime=12:30:00 +#MOLGENIS nodes=1 ppn=8 mem=1gb walltime=12:30:00 #Parameter mapping #string seqType @@ -17,6 +17,8 @@ echo "srBarcodeFqGz: ${srBarcodeFqGz}" sleep 10 +module load pigz/2.3.3 + # Spike phiX only once samp=`tail -10 ${peEnd1BarcodeFqGz}` phiX=`tail -10 ${phiXEnd1Gz}` @@ -33,8 +35,8 @@ else elif [ $seqType == "PE" ] then echo "Append phiX reads" - zcat ${peEnd1BarcodeFqGz} ${phiXEnd1Gz} | gzip -c - > ${peEnd1BarcodeFqGz}.tmp - zcat ${peEnd2BarcodeFqGz} ${phiXEnd2Gz} | gzip -c - > ${peEnd2BarcodeFqGz}.tmp + zcat ${peEnd1BarcodeFqGz} ${phiXEnd1Gz} | ${PIGZ_HOME}/pigz > ${peEnd1BarcodeFqGz}.tmp + zcat ${peEnd2BarcodeFqGz} ${phiXEnd2Gz} | ${PIGZ_HOME}/pigz > ${peEnd2BarcodeFqGz}.tmp mv ${peEnd1BarcodeFqGz}.tmp ${peEnd1BarcodeFqGz} mv ${peEnd2BarcodeFqGz}.tmp ${peEnd2BarcodeFqGz} fi diff --git a/compute5/NGS_DNA-2.1.1/workflow.csv b/compute5/NGS_DNA-2.1.1/workflow.csv index 152c3f7e..7b34406b 100755 --- a/compute5/NGS_DNA-2.1.1/workflow.csv +++ b/compute5/NGS_DNA-2.1.1/workflow.csv @@ -24,7 +24,7 @@ s21b_IndelFiltration,protocols/IndelFiltration.sh,s20_SplitIndelsAndSNPs s22_dbNSFPAnnotation,protocols/dbNSFPAnnotation.sh,s21a_SnpFiltration s23_MergeIndelsAndSnps,protocols/MergeIndelsAndSnps.sh,s21b_IndelFiltration;s22_dbNSFPAnnotation s24_VcfToTable,protocols/VcfToTable.sh,s23_MergeIndelsAndSnps -s25_InSilicoConcordance,protocols/InSilicoConcordance.sh,s16_VariantCalling;s24_VcfToTable +s25_InSilicoConcordance,protocols/InSilicoConcordance.sh,s24_VcfToTable s26_QCReport,protocols/QCReport.sh,s12_SequenomConcordanceCheck;s25_InSilicoConcordance s27_CountAllFinishedFiles,protocols/CountAllFinishedFiles.sh,s26_QCReport s28_CopyToResultsDir,protocols/CopyToResultsDir.sh,s27_CountAllFinishedFiles