Performing EPACTS Binary Single Variant Score Test.. Finished generating EPACTS Makefile Running 5 parallel jobs of EPACTS forkExecWait(): make -f /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.Makefile -j 5 Rscript /tmp2/EPACTS-3.2.6/share/EPACTS/epactsSingle.R --vanilla /tmp2/EPACTS-3.2.6 /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.phe /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.cov /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.ind /tmp2/EPACTS-3.2.6/bin/../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz 20:1-10000000 /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.1.10000000.epacts GT 0.001 1 3 1000000000 0.5 0 FALSE single.b.score Rscript /tmp2/EPACTS-3.2.6/share/EPACTS/epactsSingle.R --vanilla /tmp2/EPACTS-3.2.6 /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.phe /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.cov /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.ind /tmp2/EPACTS-3.2.6/bin/../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz 20:10000001-20000000 /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.10000001.20000000.epacts GT 0.001 1 3 1000000000 0.5 0 FALSE single.b.score Rscript /tmp2/EPACTS-3.2.6/share/EPACTS/epactsSingle.R --vanilla /tmp2/EPACTS-3.2.6 /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.phe /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.cov /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.ind /tmp2/EPACTS-3.2.6/bin/../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz 20:20000001-30000000 /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.20000001.30000000.epacts GT 0.001 1 3 1000000000 0.5 0 FALSE single.b.score Rscript /tmp2/EPACTS-3.2.6/share/EPACTS/epactsSingle.R --vanilla /tmp2/EPACTS-3.2.6 /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.phe /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.cov /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.ind /tmp2/EPACTS-3.2.6/bin/../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz 20:30000001-40000000 /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.30000001.40000000.epacts GT 0.001 1 3 1000000000 0.5 0 FALSE single.b.score Rscript /tmp2/EPACTS-3.2.6/share/EPACTS/epactsSingle.R --vanilla /tmp2/EPACTS-3.2.6 /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.phe /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.cov /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.ind /tmp2/EPACTS-3.2.6/bin/../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz 20:40000001-50000000 /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.40000001.50000000.epacts GT 0.001 1 3 1000000000 0.5 0 FALSE single.b.score NULL NULL NULL /tmp2/EPACTS-3.2.6/bin/epacts-anno --in /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.10000001.20000000.epacts --ref /tmp2/EPACTS-3.2.6/share/EPACTS/human_g1k_v37.fasta NULL /tmp2/EPACTS-3.2.6/bin/epacts-anno --in /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.20000001.30000000.epacts --ref /tmp2/EPACTS-3.2.6/share/EPACTS/human_g1k_v37.fasta /tmp2/EPACTS-3.2.6/bin/anno -i /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.10000001.20000000.epacts -r /tmp2/EPACTS-3.2.6/share/EPACTS/human_g1k_v37.fasta -f refGene -g /tmp2/EPACTS-3.2.6/share/EPACTS/hg19_gencodeV14.txt.gz -c /tmp2/EPACTS-3.2.6/share/EPACTS/codon.txt -o /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.10000001.20000000.epacts.tmp --inputFormat epacts -p /tmp2/EPACTS-3.2.6/share/EPACTS/priority.txt /tmp2/EPACTS-3.2.6/bin/anno -i /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.20000001.30000000.epacts -r /tmp2/EPACTS-3.2.6/share/EPACTS/human_g1k_v37.fasta -f refGene -g /tmp2/EPACTS-3.2.6/share/EPACTS/hg19_gencodeV14.txt.gz -c /tmp2/EPACTS-3.2.6/share/EPACTS/codon.txt -o /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.20000001.30000000.epacts.tmp --inputFormat epacts -p /tmp2/EPACTS-3.2.6/share/EPACTS/priority.txt NULL NULL NULL NULL /tmp2/EPACTS-3.2.6/bin/epacts-anno --in /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.40000001.50000000.epacts --ref /tmp2/EPACTS-3.2.6/share/EPACTS/human_g1k_v37.fasta /tmp2/EPACTS-3.2.6/bin/epacts-anno --in /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.1.10000000.epacts --ref /tmp2/EPACTS-3.2.6/share/EPACTS/human_g1k_v37.fasta /tmp2/EPACTS-3.2.6/bin/anno -i /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.40000001.50000000.epacts -r /tmp2/EPACTS-3.2.6/share/EPACTS/human_g1k_v37.fasta -f refGene -g /tmp2/EPACTS-3.2.6/share/EPACTS/hg19_gencodeV14.txt.gz -c /tmp2/EPACTS-3.2.6/share/EPACTS/codon.txt -o /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.40000001.50000000.epacts.tmp --inputFormat epacts -p /tmp2/EPACTS-3.2.6/share/EPACTS/priority.txt /tmp2/EPACTS-3.2.6/bin/anno -i /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.1.10000000.epacts -r /tmp2/EPACTS-3.2.6/share/EPACTS/human_g1k_v37.fasta -f refGene -g /tmp2/EPACTS-3.2.6/share/EPACTS/hg19_gencodeV14.txt.gz -c /tmp2/EPACTS-3.2.6/share/EPACTS/codon.txt -o /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.1.10000000.epacts.tmp --inputFormat epacts -p /tmp2/EPACTS-3.2.6/share/EPACTS/priority.txt NULL NULL /tmp2/EPACTS-3.2.6/bin/epacts-anno --in /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.30000001.40000000.epacts --ref /tmp2/EPACTS-3.2.6/share/EPACTS/human_g1k_v37.fasta /tmp2/EPACTS-3.2.6/bin/anno -i /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.30000001.40000000.epacts -r /tmp2/EPACTS-3.2.6/share/EPACTS/human_g1k_v37.fasta -f refGene -g /tmp2/EPACTS-3.2.6/share/EPACTS/hg19_gencodeV14.txt.gz -c /tmp2/EPACTS-3.2.6/share/EPACTS/codon.txt -o /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.30000001.40000000.epacts.tmp --inputFormat epacts -p /tmp2/EPACTS-3.2.6/share/EPACTS/priority.txt .............................................. ... Anno(tation) ... ... Xiaowei Zhan, Goncalo Abecasis ... ... Speical Thanks: ... ... Hyun Ming Kang, Yanming Li ... ... zhanxw@umich.edu ... ... Sep 2011 ... ................................................ DONE: 1248 varaints are annotated. DONE: Generated annotation output in [ /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.10000001.20000000.epacts.tmp ]. Annotation succeed! mv /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.10000001.20000000.epacts.tmp /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.10000001.20000000.epacts rm /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.10000001.20000000.epacts.tmp.log /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.10000001.20000000.epacts.tmp.top.anno.frq /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.10000001.20000000.epacts.tmp.anno.frq /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.10000001.20000000.epacts.tmp.base.frq /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.10000001.20000000.epacts.tmp.codon.frq /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.10000001.20000000.epacts.tmp.indel.frq Rscript /tmp2/EPACTS-3.2.6/share/EPACTS/epactsSingle.R --vanilla /tmp2/EPACTS-3.2.6 /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.phe /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.cov /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.ind /tmp2/EPACTS-3.2.6/bin/../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz 20:50000001-60000000 /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.50000001.60000000.epacts GT 0.001 1 3 1000000000 0.5 0 FALSE single.b.score .............................................. ... Anno(tation) ... ... Xiaowei Zhan, Goncalo Abecasis ... ... Speical Thanks: ... ... Hyun Ming Kang, Yanming Li ... ... zhanxw@umich.edu ... ... Sep 2011 ... ................................................ DONE: 1466 varaints are annotated. DONE: Generated annotation output in [ /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.20000001.30000000.epacts.tmp ]. Annotation succeed! mv /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.20000001.30000000.epacts.tmp /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.20000001.30000000.epacts rm /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.20000001.30000000.epacts.tmp.log /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.20000001.30000000.epacts.tmp.top.anno.frq /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.20000001.30000000.epacts.tmp.anno.frq /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.20000001.30000000.epacts.tmp.base.frq /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.20000001.30000000.epacts.tmp.codon.frq /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.20000001.30000000.epacts.tmp.indel.frq Rscript /tmp2/EPACTS-3.2.6/share/EPACTS/epactsSingle.R --vanilla /tmp2/EPACTS-3.2.6 /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.phe /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.cov /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.ind /tmp2/EPACTS-3.2.6/bin/../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz 20:60000001-63025520 /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.60000001.63025520.epacts GT 0.001 1 3 1000000000 0.5 0 FALSE single.b.score .............................................. ... Anno(tation) ... ... Xiaowei Zhan, Goncalo Abecasis ... ... Speical Thanks: ... ... Hyun Ming Kang, Yanming Li ... ... zhanxw@umich.edu ... ... Sep 2011 ... ................................................ DONE: 3367 varaints are annotated. DONE: Generated annotation output in [ /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.1.10000000.epacts.tmp ]. Annotation succeed! mv /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.1.10000000.epacts.tmp /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.1.10000000.epacts rm /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.1.10000000.epacts.tmp.log /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.1.10000000.epacts.tmp.top.anno.frq /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.1.10000000.epacts.tmp.anno.frq /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.1.10000000.epacts.tmp.base.frq /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.1.10000000.epacts.tmp.codon.frq /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.1.10000000.epacts.tmp.indel.frq NULL NULL /tmp2/EPACTS-3.2.6/bin/epacts-anno --in /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.50000001.60000000.epacts --ref /tmp2/EPACTS-3.2.6/share/EPACTS/human_g1k_v37.fasta /tmp2/EPACTS-3.2.6/bin/anno -i /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.50000001.60000000.epacts -r /tmp2/EPACTS-3.2.6/share/EPACTS/human_g1k_v37.fasta -f refGene -g /tmp2/EPACTS-3.2.6/share/EPACTS/hg19_gencodeV14.txt.gz -c /tmp2/EPACTS-3.2.6/share/EPACTS/codon.txt -o /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.50000001.60000000.epacts.tmp --inputFormat epacts -p /tmp2/EPACTS-3.2.6/share/EPACTS/priority.txt NULL NULL /tmp2/EPACTS-3.2.6/bin/epacts-anno --in /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.60000001.63025520.epacts --ref /tmp2/EPACTS-3.2.6/share/EPACTS/human_g1k_v37.fasta .............................................. ... Anno(tation) ... ... Xiaowei Zhan, Goncalo Abecasis ... ... Speical Thanks: ... ... Hyun Ming Kang, Yanming Li ... ... zhanxw@umich.edu ... ... Sep 2011 ... ................................................ DONE: 3662 varaints are annotated. DONE: Generated annotation output in [ /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.40000001.50000000.epacts.tmp ]. Annotation succeed! mv /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.40000001.50000000.epacts.tmp /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.40000001.50000000.epacts rm /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.40000001.50000000.epacts.tmp.log /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.40000001.50000000.epacts.tmp.top.anno.frq /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.40000001.50000000.epacts.tmp.anno.frq /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.40000001.50000000.epacts.tmp.base.frq /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.40000001.50000000.epacts.tmp.codon.frq /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.40000001.50000000.epacts.tmp.indel.frq /tmp2/EPACTS-3.2.6/bin/anno -i /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.60000001.63025520.epacts -r /tmp2/EPACTS-3.2.6/share/EPACTS/human_g1k_v37.fasta -f refGene -g /tmp2/EPACTS-3.2.6/share/EPACTS/hg19_gencodeV14.txt.gz -c /tmp2/EPACTS-3.2.6/share/EPACTS/codon.txt -o /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.60000001.63025520.epacts.tmp --inputFormat epacts -p /tmp2/EPACTS-3.2.6/share/EPACTS/priority.txt .............................................. ... Anno(tation) ... ... Xiaowei Zhan, Goncalo Abecasis ... ... Speical Thanks: ... ... Hyun Ming Kang, Yanming Li ... ... zhanxw@umich.edu ... ... Sep 2011 ... ................................................ DONE: 4170 varaints are annotated. DONE: Generated annotation output in [ /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.30000001.40000000.epacts.tmp ]. Annotation succeed! mv /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.30000001.40000000.epacts.tmp /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.30000001.40000000.epacts rm /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.30000001.40000000.epacts.tmp.log /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.30000001.40000000.epacts.tmp.top.anno.frq /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.30000001.40000000.epacts.tmp.anno.frq /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.30000001.40000000.epacts.tmp.base.frq /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.30000001.40000000.epacts.tmp.codon.frq /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.30000001.40000000.epacts.tmp.indel.frq .............................................. ... Anno(tation) ... ... Xiaowei Zhan, Goncalo Abecasis ... ... Speical Thanks: ... ... Hyun Ming Kang, Yanming Li ... ... zhanxw@umich.edu ... ... Sep 2011 ... ................................................ DONE: 1763 varaints are annotated. DONE: Generated annotation output in [ /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.50000001.60000000.epacts.tmp ]. Annotation succeed! mv /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.50000001.60000000.epacts.tmp /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.50000001.60000000.epacts rm /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.50000001.60000000.epacts.tmp.log /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.50000001.60000000.epacts.tmp.top.anno.frq /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.50000001.60000000.epacts.tmp.anno.frq /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.50000001.60000000.epacts.tmp.base.frq /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.50000001.60000000.epacts.tmp.codon.frq /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.50000001.60000000.epacts.tmp.indel.frq .............................................. ... Anno(tation) ... ... Xiaowei Zhan, Goncalo Abecasis ... ... Speical Thanks: ... ... Hyun Ming Kang, Yanming Li ... ... zhanxw@umich.edu ... ... Sep 2011 ... ................................................ DONE: 3425 varaints are annotated. DONE: Generated annotation output in [ /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.60000001.63025520.epacts.tmp ]. Annotation succeed! mv /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.60000001.63025520.epacts.tmp /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.60000001.63025520.epacts rm /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.60000001.63025520.epacts.tmp.log /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.60000001.63025520.epacts.tmp.top.anno.frq /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.60000001.63025520.epacts.tmp.anno.frq /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.60000001.63025520.epacts.tmp.base.frq /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.60000001.63025520.epacts.tmp.codon.frq /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.60000001.63025520.epacts.tmp.indel.frq /tmp2/EPACTS-3.2.6/bin/epacts-cat /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.1.10000000.epacts /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.10000001.20000000.epacts /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.20000001.30000000.epacts /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.30000001.40000000.epacts /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.40000001.50000000.epacts /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.50000001.60000000.epacts /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.60000001.63025520.epacts | /tmp2/EPACTS-3.2.6/bin/bgzip -c > /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.epacts.gz /tmp2/EPACTS-3.2.6/bin/tabix -f -pbed /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.epacts.gz rm -f /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.1.10000000.epacts /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.10000001.20000000.epacts /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.20000001.30000000.epacts /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.30000001.40000000.epacts /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.40000001.50000000.epacts /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.50000001.60000000.epacts /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.20.60000001.63025520.epacts /tmp2/EPACTS-3.2.6/bin/epacts-plot --in /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.epacts.gz --region 20:0 Rscript /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.epacts.R --vanilla export GDFONTPATH=/tmp2/EPACTS-3.2.6/share/EPACTS; export GNUPLOT_FONTPATH=/tmp2/EPACTS-3.2.6/share/EPACTS; export GNUPLOT_PS_DIR=/tmp2/EPACTS-3.2.6/share/EPACTS; export PATH=$PATH:/tmp2/EPACTS-3.2.6/bin/; export GNUPLOT_PFBTOPFA="pfbtops %s"; gnuplot /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.epacts.cmd export GDFONTPATH=/tmp2/EPACTS-3.2.6/share/EPACTS; export GNUPLOT_FONTPATH=/tmp2/EPACTS-3.2.6/share/EPACTS; export GNUPLOT_PS_DIR=/tmp2/EPACTS-3.2.6/share/EPACTS; export PATH=$PATH:/tmp2/EPACTS-3.2.6/bin/; export GNUPLOT_PFBTOPFA="pfbtops %s"; /tmp2/EPACTS-3.2.6/bin/epstopdf /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.epacts.qq.eps export GDFONTPATH=/tmp2/EPACTS-3.2.6/share/EPACTS; export GNUPLOT_FONTPATH=/tmp2/EPACTS-3.2.6/share/EPACTS; export GNUPLOT_PS_DIR=/tmp2/EPACTS-3.2.6/share/EPACTS; export PATH=$PATH:/tmp2/EPACTS-3.2.6/bin/; export GNUPLOT_PFBTOPFA="pfbtops %s"; gnuplot /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.epacts.cmd export GDFONTPATH=/tmp2/EPACTS-3.2.6/share/EPACTS; export GNUPLOT_FONTPATH=/tmp2/EPACTS-3.2.6/share/EPACTS; export GNUPLOT_PS_DIR=/tmp2/EPACTS-3.2.6/share/EPACTS; export PATH=$PATH:/tmp2/EPACTS-3.2.6/bin/; export GNUPLOT_PFBTOPFA="pfbtops %s"; /tmp2/EPACTS-3.2.6/bin/epstopdf /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.epacts.mh.eps rm /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.epacts.cmd /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.epacts.qq.eps /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.epacts.mh.eps /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.epacts.*.dat zcat /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.epacts.gz | awk '$9 != "NA" { print $0 }' | sort -g -k 9 | head -n 5000 > /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.epacts.top5000 /tmp2/EPACTS-3.2.6/bin/epacts-zoom --vcf /tmp2/EPACTS-3.2.6/bin/../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz --prefix /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score --top 1 touch /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.b.score.epacts.OK Creating Empirical Kinship matrix... Finished generating EPACTS Makefile Running 5 parallel jobs of EPACTS make -f out/test.single.q.emmax.kinf.Makefile -j 5 /tmp2/EPACTS-3.2.6/bin/pEmmax gen-kin --vcf /tmp2/EPACTS-3.2.6/bin/../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz --indf out/test.single.q.emmax.kinf.ind --region 20:1-10000000 --field GT --minMAF 0.01 --minCallRate 0.95 --out-kinf out/test.single.q.emmax.kinf.20.1.10000000.kin --raw --ignoreFilter /tmp2/EPACTS-3.2.6/bin/pEmmax gen-kin --vcf /tmp2/EPACTS-3.2.6/bin/../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz --indf out/test.single.q.emmax.kinf.ind --region 20:10000001-20000000 --field GT --minMAF 0.01 --minCallRate 0.95 --out-kinf out/test.single.q.emmax.kinf.20.10000001.20000000.kin --raw --ignoreFilter /tmp2/EPACTS-3.2.6/bin/pEmmax gen-kin --vcf /tmp2/EPACTS-3.2.6/bin/../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz --indf out/test.single.q.emmax.kinf.ind --region 20:20000001-30000000 --field GT --minMAF 0.01 --minCallRate 0.95 --out-kinf out/test.single.q.emmax.kinf.20.20000001.30000000.kin --raw --ignoreFilter /tmp2/EPACTS-3.2.6/bin/pEmmax gen-kin --vcf /tmp2/EPACTS-3.2.6/bin/../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz --indf out/test.single.q.emmax.kinf.ind --region 20:30000001-40000000 --field GT --minMAF 0.01 --minCallRate 0.95 --out-kinf out/test.single.q.emmax.kinf.20.30000001.40000000.kin --raw --ignoreFilter /tmp2/EPACTS-3.2.6/bin/pEmmax gen-kin --vcf /tmp2/EPACTS-3.2.6/bin/../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz --indf out/test.single.q.emmax.kinf.ind --region 20:40000001-50000000 --field GT --minMAF 0.01 --minCallRate 0.95 --out-kinf out/test.single.q.emmax.kinf.20.40000001.50000000.kin --raw --ignoreFilter /tmp2/EPACTS-3.2.6/bin/pEmmax gen-kin --vcf /tmp2/EPACTS-3.2.6/bin/../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz --indf out/test.single.q.emmax.kinf.ind --region 20:50000001-60000000 --field GT --minMAF 0.01 --minCallRate 0.95 --out-kinf out/test.single.q.emmax.kinf.20.50000001.60000000.kin --raw --ignoreFilter /tmp2/EPACTS-3.2.6/bin/pEmmax gen-kin --vcf /tmp2/EPACTS-3.2.6/bin/../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz --indf out/test.single.q.emmax.kinf.ind --region 20:60000001-63025520 --field GT --minMAF 0.01 --minCallRate 0.95 --out-kinf out/test.single.q.emmax.kinf.20.60000001.63025520.kin --raw --ignoreFilter /tmp2/EPACTS-3.2.6/bin/pEmmax merge-kin --out-kinf out/test.single.q.emmax.kinf out/test.single.q.emmax.kinf.20.1.10000000.kin out/test.single.q.emmax.kinf.20.10000001.20000000.kin out/test.single.q.emmax.kinf.20.20000001.30000000.kin out/test.single.q.emmax.kinf.20.30000001.40000000.kin out/test.single.q.emmax.kinf.20.40000001.50000000.kin out/test.single.q.emmax.kinf.20.50000001.60000000.kin out/test.single.q.emmax.kinf.20.60000001.63025520.kin out/test.single.q.emmax.kinf.20.1.10000000.kin out/test.single.q.emmax.kinf.20.10000001.20000000.kin out/test.single.q.emmax.kinf.20.20000001.30000000.kin out/test.single.q.emmax.kinf.20.30000001.40000000.kin out/test.single.q.emmax.kinf.20.40000001.50000000.kin out/test.single.q.emmax.kinf.20.50000001.60000000.kin out/test.single.q.emmax.kinf.20.60000001.63025520.kin rm -f out/test.single.q.emmax.kinf.20.1.10000000.kin out/test.single.q.emmax.kinf.20.10000001.20000000.kin out/test.single.q.emmax.kinf.20.20000001.30000000.kin out/test.single.q.emmax.kinf.20.30000001.40000000.kin out/test.single.q.emmax.kinf.20.40000001.50000000.kin out/test.single.q.emmax.kinf.20.50000001.60000000.kin out/test.single.q.emmax.kinf.20.60000001.63025520.kin Running EMMAX single variant test... Finished generating EPACTS Makefile Running 5 parallel jobs of EPACTS forkExecWait(): make -f /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.Makefile -j 5 /tmp2/EPACTS-3.2.6/bin/pEmmax reml --phenof /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.phe --covf /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.cov --kinf /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.kinf --indf /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.ind --out-eigf /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.eigR --out-remlf /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.reml /tmp2/EPACTS-3.2.6/bin/pEmmax assoc --vcf /tmp2/EPACTS-3.2.6/bin/../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz --region 20:1-10000000 --phenof /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.phe --field GT --indf /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.ind --eigf /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.eigR --remlf /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.reml --out-assocf /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.1.10000000.epacts --minMAF 0.001 --maxMAF 1 --maxMAC 1000000000 --minRSQ 0 --minCallRate 0.5 --minMAC 3 /tmp2/EPACTS-3.2.6/bin/pEmmax assoc --vcf /tmp2/EPACTS-3.2.6/bin/../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz --region 20:10000001-20000000 --phenof /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.phe --field GT --indf /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.ind --eigf /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.eigR --remlf /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.reml --out-assocf /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.10000001.20000000.epacts --minMAF 0.001 --maxMAF 1 --maxMAC 1000000000 --minRSQ 0 --minCallRate 0.5 --minMAC 3 /tmp2/EPACTS-3.2.6/bin/pEmmax assoc --vcf /tmp2/EPACTS-3.2.6/bin/../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz --region 20:20000001-30000000 --phenof /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.phe --field GT --indf /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.ind --eigf /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.eigR --remlf /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.reml --out-assocf /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.20000001.30000000.epacts --minMAF 0.001 --maxMAF 1 --maxMAC 1000000000 --minRSQ 0 --minCallRate 0.5 --minMAC 3 /tmp2/EPACTS-3.2.6/bin/pEmmax assoc --vcf /tmp2/EPACTS-3.2.6/bin/../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz --region 20:30000001-40000000 --phenof /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.phe --field GT --indf /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.ind --eigf /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.eigR --remlf /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.reml --out-assocf /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.30000001.40000000.epacts --minMAF 0.001 --maxMAF 1 --maxMAC 1000000000 --minRSQ 0 --minCallRate 0.5 --minMAC 3 /tmp2/EPACTS-3.2.6/bin/pEmmax assoc --vcf /tmp2/EPACTS-3.2.6/bin/../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz --region 20:40000001-50000000 --phenof /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.phe --field GT --indf /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.ind --eigf /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.eigR --remlf /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.reml --out-assocf /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.40000001.50000000.epacts --minMAF 0.001 --maxMAF 1 --maxMAC 1000000000 --minRSQ 0 --minCallRate 0.5 --minMAC 3 /tmp2/EPACTS-3.2.6/bin/epacts-anno --in /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.10000001.20000000.epacts --ref /tmp2/EPACTS-3.2.6/share/EPACTS/human_g1k_v37.fasta /tmp2/EPACTS-3.2.6/bin/anno -i /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.10000001.20000000.epacts -r /tmp2/EPACTS-3.2.6/share/EPACTS/human_g1k_v37.fasta -f refGene -g /tmp2/EPACTS-3.2.6/share/EPACTS/hg19_gencodeV14.txt.gz -c /tmp2/EPACTS-3.2.6/share/EPACTS/codon.txt -o /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.10000001.20000000.epacts.tmp --inputFormat epacts -p /tmp2/EPACTS-3.2.6/share/EPACTS/priority.txt /tmp2/EPACTS-3.2.6/bin/epacts-anno --in /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.20000001.30000000.epacts --ref /tmp2/EPACTS-3.2.6/share/EPACTS/human_g1k_v37.fasta /tmp2/EPACTS-3.2.6/bin/epacts-anno --in /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.1.10000000.epacts --ref /tmp2/EPACTS-3.2.6/share/EPACTS/human_g1k_v37.fasta /tmp2/EPACTS-3.2.6/bin/anno -i /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.20000001.30000000.epacts -r /tmp2/EPACTS-3.2.6/share/EPACTS/human_g1k_v37.fasta -f refGene -g /tmp2/EPACTS-3.2.6/share/EPACTS/hg19_gencodeV14.txt.gz -c /tmp2/EPACTS-3.2.6/share/EPACTS/codon.txt -o /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.20000001.30000000.epacts.tmp --inputFormat epacts -p /tmp2/EPACTS-3.2.6/share/EPACTS/priority.txt /tmp2/EPACTS-3.2.6/bin/anno -i /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.1.10000000.epacts -r /tmp2/EPACTS-3.2.6/share/EPACTS/human_g1k_v37.fasta -f refGene -g /tmp2/EPACTS-3.2.6/share/EPACTS/hg19_gencodeV14.txt.gz -c /tmp2/EPACTS-3.2.6/share/EPACTS/codon.txt -o /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.1.10000000.epacts.tmp --inputFormat epacts -p /tmp2/EPACTS-3.2.6/share/EPACTS/priority.txt /tmp2/EPACTS-3.2.6/bin/epacts-anno --in /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.40000001.50000000.epacts --ref /tmp2/EPACTS-3.2.6/share/EPACTS/human_g1k_v37.fasta /tmp2/EPACTS-3.2.6/bin/epacts-anno --in /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.30000001.40000000.epacts --ref /tmp2/EPACTS-3.2.6/share/EPACTS/human_g1k_v37.fasta /tmp2/EPACTS-3.2.6/bin/anno -i /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.40000001.50000000.epacts -r /tmp2/EPACTS-3.2.6/share/EPACTS/human_g1k_v37.fasta -f refGene -g /tmp2/EPACTS-3.2.6/share/EPACTS/hg19_gencodeV14.txt.gz -c /tmp2/EPACTS-3.2.6/share/EPACTS/codon.txt -o /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.40000001.50000000.epacts.tmp --inputFormat epacts -p /tmp2/EPACTS-3.2.6/share/EPACTS/priority.txt /tmp2/EPACTS-3.2.6/bin/anno -i /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.30000001.40000000.epacts -r /tmp2/EPACTS-3.2.6/share/EPACTS/human_g1k_v37.fasta -f refGene -g /tmp2/EPACTS-3.2.6/share/EPACTS/hg19_gencodeV14.txt.gz -c /tmp2/EPACTS-3.2.6/share/EPACTS/codon.txt -o /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.30000001.40000000.epacts.tmp --inputFormat epacts -p /tmp2/EPACTS-3.2.6/share/EPACTS/priority.txt .............................................. ... Anno(tation) ... ... Xiaowei Zhan, Goncalo Abecasis ... ... Speical Thanks: ... ... Hyun Ming Kang, Yanming Li ... ... zhanxw@umich.edu ... ... Sep 2011 ... ................................................ DONE: 1225 varaints are annotated. DONE: Generated annotation output in [ /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.10000001.20000000.epacts.tmp ]. Annotation succeed! mv /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.10000001.20000000.epacts.tmp /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.10000001.20000000.epacts rm /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.10000001.20000000.epacts.tmp.log /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.10000001.20000000.epacts.tmp.top.anno.frq /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.10000001.20000000.epacts.tmp.anno.frq /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.10000001.20000000.epacts.tmp.base.frq /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.10000001.20000000.epacts.tmp.codon.frq /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.10000001.20000000.epacts.tmp.indel.frq /tmp2/EPACTS-3.2.6/bin/pEmmax assoc --vcf /tmp2/EPACTS-3.2.6/bin/../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz --region 20:50000001-60000000 --phenof /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.phe --field GT --indf /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.ind --eigf /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.eigR --remlf /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.reml --out-assocf /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.50000001.60000000.epacts --minMAF 0.001 --maxMAF 1 --maxMAC 1000000000 --minRSQ 0 --minCallRate 0.5 --minMAC 3 .............................................. ... Anno(tation) ... ... Xiaowei Zhan, Goncalo Abecasis ... ... Speical Thanks: ... ... Hyun Ming Kang, Yanming Li ... ... zhanxw@umich.edu ... ... Sep 2011 ... ................................................ DONE: 3245 varaints are annotated. DONE: Generated annotation output in [ /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.1.10000000.epacts.tmp ]. Annotation succeed! mv /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.1.10000000.epacts.tmp /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.1.10000000.epacts rm /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.1.10000000.epacts.tmp.log /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.1.10000000.epacts.tmp.top.anno.frq /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.1.10000000.epacts.tmp.anno.frq /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.1.10000000.epacts.tmp.base.frq /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.1.10000000.epacts.tmp.codon.frq /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.1.10000000.epacts.tmp.indel.frq /tmp2/EPACTS-3.2.6/bin/pEmmax assoc --vcf /tmp2/EPACTS-3.2.6/bin/../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz --region 20:60000001-63025520 --phenof /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.phe --field GT --indf /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.ind --eigf /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.eigR --remlf /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.reml --out-assocf /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.60000001.63025520.epacts --minMAF 0.001 --maxMAF 1 --maxMAC 1000000000 --minRSQ 0 --minCallRate 0.5 --minMAC 3 /tmp2/EPACTS-3.2.6/bin/epacts-anno --in /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.50000001.60000000.epacts --ref /tmp2/EPACTS-3.2.6/share/EPACTS/human_g1k_v37.fasta /tmp2/EPACTS-3.2.6/bin/anno -i /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.50000001.60000000.epacts -r /tmp2/EPACTS-3.2.6/share/EPACTS/human_g1k_v37.fasta -f refGene -g /tmp2/EPACTS-3.2.6/share/EPACTS/hg19_gencodeV14.txt.gz -c /tmp2/EPACTS-3.2.6/share/EPACTS/codon.txt -o /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.50000001.60000000.epacts.tmp --inputFormat epacts -p /tmp2/EPACTS-3.2.6/share/EPACTS/priority.txt /tmp2/EPACTS-3.2.6/bin/epacts-anno --in /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.60000001.63025520.epacts --ref /tmp2/EPACTS-3.2.6/share/EPACTS/human_g1k_v37.fasta .............................................. ... Anno(tation) ... ... Xiaowei Zhan, Goncalo Abecasis ... ... Speical Thanks: ... ... Hyun Ming Kang, Yanming Li ... ... zhanxw@umich.edu ... ... Sep 2011 ... ................................................ DONE: 1423 varaints are annotated. DONE: Generated annotation output in [ /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.20000001.30000000.epacts.tmp ]. Annotation succeed! mv /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.20000001.30000000.epacts.tmp /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.20000001.30000000.epacts .............................................. ... Anno(tation) ... ... Xiaowei Zhan, Goncalo Abecasis ... ... Speical Thanks: ... ... Hyun Ming Kang, Yanming Li ... ... zhanxw@umich.edu ... ... Sep 2011 ... ................................................ DONE: 4061 varaints are annotated. DONE: Generated annotation output in [ /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.30000001.40000000.epacts.tmp ]. Annotation succeed! mv /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.30000001.40000000.epacts.tmp /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.30000001.40000000.epacts rm /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.20000001.30000000.epacts.tmp.log /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.20000001.30000000.epacts.tmp.top.anno.frq /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.20000001.30000000.epacts.tmp.anno.frq /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.20000001.30000000.epacts.tmp.base.frq /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.20000001.30000000.epacts.tmp.codon.frq /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.20000001.30000000.epacts.tmp.indel.frq rm /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.30000001.40000000.epacts.tmp.log /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.30000001.40000000.epacts.tmp.top.anno.frq /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.30000001.40000000.epacts.tmp.anno.frq /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.30000001.40000000.epacts.tmp.base.frq /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.30000001.40000000.epacts.tmp.codon.frq /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.30000001.40000000.epacts.tmp.indel.frq /tmp2/EPACTS-3.2.6/bin/anno -i /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.60000001.63025520.epacts -r /tmp2/EPACTS-3.2.6/share/EPACTS/human_g1k_v37.fasta -f refGene -g /tmp2/EPACTS-3.2.6/share/EPACTS/hg19_gencodeV14.txt.gz -c /tmp2/EPACTS-3.2.6/share/EPACTS/codon.txt -o /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.60000001.63025520.epacts.tmp --inputFormat epacts -p /tmp2/EPACTS-3.2.6/share/EPACTS/priority.txt .............................................. ... Anno(tation) ... ... Xiaowei Zhan, Goncalo Abecasis ... ... Speical Thanks: ... ... Hyun Ming Kang, Yanming Li ... ... zhanxw@umich.edu ... ... Sep 2011 ... ................................................ DONE: 3578 varaints are annotated. DONE: Generated annotation output in [ /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.40000001.50000000.epacts.tmp ]. Annotation succeed! mv /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.40000001.50000000.epacts.tmp /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.40000001.50000000.epacts rm /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.40000001.50000000.epacts.tmp.log /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.40000001.50000000.epacts.tmp.top.anno.frq /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.40000001.50000000.epacts.tmp.anno.frq /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.40000001.50000000.epacts.tmp.base.frq /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.40000001.50000000.epacts.tmp.codon.frq /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.40000001.50000000.epacts.tmp.indel.frq .............................................. ... Anno(tation) ... ... Xiaowei Zhan, Goncalo Abecasis ... ... Speical Thanks: ... ... Hyun Ming Kang, Yanming Li ... ... zhanxw@umich.edu ... ... Sep 2011 ... ................................................ DONE: 1732 varaints are annotated. DONE: Generated annotation output in [ /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.50000001.60000000.epacts.tmp ]. Annotation succeed! mv /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.50000001.60000000.epacts.tmp /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.50000001.60000000.epacts rm /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.50000001.60000000.epacts.tmp.log /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.50000001.60000000.epacts.tmp.top.anno.frq /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.50000001.60000000.epacts.tmp.anno.frq /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.50000001.60000000.epacts.tmp.base.frq /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.50000001.60000000.epacts.tmp.codon.frq /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.50000001.60000000.epacts.tmp.indel.frq .............................................. ... Anno(tation) ... ... Xiaowei Zhan, Goncalo Abecasis ... ... Speical Thanks: ... ... Hyun Ming Kang, Yanming Li ... ... zhanxw@umich.edu ... ... Sep 2011 ... ................................................ DONE: 3292 varaints are annotated. DONE: Generated annotation output in [ /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.60000001.63025520.epacts.tmp ]. Annotation succeed! mv /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.60000001.63025520.epacts.tmp /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.60000001.63025520.epacts rm /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.60000001.63025520.epacts.tmp.log /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.60000001.63025520.epacts.tmp.top.anno.frq /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.60000001.63025520.epacts.tmp.anno.frq /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.60000001.63025520.epacts.tmp.base.frq /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.60000001.63025520.epacts.tmp.codon.frq /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.60000001.63025520.epacts.tmp.indel.frq /tmp2/EPACTS-3.2.6/bin/epacts-cat /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.1.10000000.epacts /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.10000001.20000000.epacts /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.20000001.30000000.epacts /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.30000001.40000000.epacts /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.40000001.50000000.epacts /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.50000001.60000000.epacts /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.60000001.63025520.epacts | /tmp2/EPACTS-3.2.6/bin/bgzip -c > /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.epacts.gz /tmp2/EPACTS-3.2.6/bin/tabix -f -pbed /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.epacts.gz rm -f /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.1.10000000.epacts /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.10000001.20000000.epacts /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.20000001.30000000.epacts /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.30000001.40000000.epacts /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.40000001.50000000.epacts /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.50000001.60000000.epacts /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.20.60000001.63025520.epacts /tmp2/EPACTS-3.2.6/bin/epacts-plot --in /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.epacts.gz --region 20:0 Rscript /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.epacts.R --vanilla export GDFONTPATH=/tmp2/EPACTS-3.2.6/share/EPACTS; export GNUPLOT_FONTPATH=/tmp2/EPACTS-3.2.6/share/EPACTS; export GNUPLOT_PS_DIR=/tmp2/EPACTS-3.2.6/share/EPACTS; export PATH=$PATH:/tmp2/EPACTS-3.2.6/bin/; export GNUPLOT_PFBTOPFA="pfbtops %s"; gnuplot /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.epacts.cmd export GDFONTPATH=/tmp2/EPACTS-3.2.6/share/EPACTS; export GNUPLOT_FONTPATH=/tmp2/EPACTS-3.2.6/share/EPACTS; export GNUPLOT_PS_DIR=/tmp2/EPACTS-3.2.6/share/EPACTS; export PATH=$PATH:/tmp2/EPACTS-3.2.6/bin/; export GNUPLOT_PFBTOPFA="pfbtops %s"; /tmp2/EPACTS-3.2.6/bin/epstopdf /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.epacts.qq.eps export GDFONTPATH=/tmp2/EPACTS-3.2.6/share/EPACTS; export GNUPLOT_FONTPATH=/tmp2/EPACTS-3.2.6/share/EPACTS; export GNUPLOT_PS_DIR=/tmp2/EPACTS-3.2.6/share/EPACTS; export PATH=$PATH:/tmp2/EPACTS-3.2.6/bin/; export GNUPLOT_PFBTOPFA="pfbtops %s"; gnuplot /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.epacts.cmd export GDFONTPATH=/tmp2/EPACTS-3.2.6/share/EPACTS; export GNUPLOT_FONTPATH=/tmp2/EPACTS-3.2.6/share/EPACTS; export GNUPLOT_PS_DIR=/tmp2/EPACTS-3.2.6/share/EPACTS; export PATH=$PATH:/tmp2/EPACTS-3.2.6/bin/; export GNUPLOT_PFBTOPFA="pfbtops %s"; /tmp2/EPACTS-3.2.6/bin/epstopdf /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.epacts.mh.eps rm /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.epacts.cmd /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.epacts.qq.eps /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.epacts.mh.eps /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.epacts.*.dat zcat /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.epacts.gz | awk '$11 != "NA" { print $0 }' | sort -g -k 11 | head -n 5000 > /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.epacts.top5000 touch /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.single.q.emmax.epacts.OK Taking the site list from the VCF file Annotate the VCF file /tmp2/EPACTS-3.2.6/bin/anno -i out/1000G_exome_chr20_example_softFiltered.calls.sites.vcf.gz -r /tmp2/EPACTS-3.2.6/share/EPACTS/human_g1k_v37.fasta -f refGene -g /tmp2/EPACTS-3.2.6/share/EPACTS/hg19_gencodeV14.txt.gz -c /tmp2/EPACTS-3.2.6/share/EPACTS/codon.txt -o out/1000G_exome_chr20_example_softFiltered.calls.sites.anno.vcf.gz --inputFormat vcf -p /tmp2/EPACTS-3.2.6/share/EPACTS/priority.txt .............................................. ... Anno(tation) ... ... Xiaowei Zhan, Goncalo Abecasis ... ... Speical Thanks: ... ... Hyun Ming Kang, Yanming Li ... ... zhanxw@umich.edu ... ... Sep 2011 ... ................................................ DONE: 19101 varaints are annotated. DONE: Generated annotation output in [ out/1000G_exome_chr20_example_softFiltered.calls.sites.anno.vcf.gz ]. Annotation succeed! mv out/1000G_exome_chr20_example_softFiltered.calls.sites.anno.vcf.gz out/1000G_exome_chr20_example_softFiltered.calls.sites.vcf.gz.tmp /tmp2/EPACTS-3.2.6/bin/bgzip -c out/1000G_exome_chr20_example_softFiltered.calls.sites.vcf.gz.tmp > out/1000G_exome_chr20_example_softFiltered.calls.sites.anno.vcf.gz /tmp2/EPACTS-3.2.6/bin/tabix -pvcf -f out/1000G_exome_chr20_example_softFiltered.calls.sites.anno.vcf.gz rm out/1000G_exome_chr20_example_softFiltered.calls.sites.vcf.gz.tmp rm out/1000G_exome_chr20_example_softFiltered.calls.sites.anno.vcf.gz.log out/1000G_exome_chr20_example_softFiltered.calls.sites.anno.vcf.gz.top.anno.frq out/1000G_exome_chr20_example_softFiltered.calls.sites.anno.vcf.gz.anno.frq out/1000G_exome_chr20_example_softFiltered.calls.sites.anno.vcf.gz.base.frq out/1000G_exome_chr20_example_softFiltered.calls.sites.anno.vcf.gz.codon.frq out/1000G_exome_chr20_example_softFiltered.calls.sites.anno.vcf.gz.indel.frq Create the input group file for burden test Succesfully create group information for 508 genes Performing SKAT-O test Finished generating EPACTS Makefile Running 5 parallel jobs of EPACTS forkExecWait(): make -f /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.gene.skat.Makefile -j 5 Rscript /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.gene.skat.0.R --vanilla Rscript /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.gene.skat.1.R --vanilla Rscript /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.gene.skat.2.R --vanilla Rscript /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.gene.skat.3.R --vanilla Rscript /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.gene.skat.4.R --vanilla NULL Rscript /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.gene.skat.5.R --vanilla NULL NULL NULL NULL NULL (head -1 /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.gene.skat.0.epacts; cat /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.gene.skat.0.epacts /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.gene.skat.1.epacts /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.gene.skat.2.epacts /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.gene.skat.3.epacts /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.gene.skat.4.epacts /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.gene.skat.5.epacts | grep -v ^#;) > /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.gene.skat.epacts rm /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.gene.skat.0.epacts /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.gene.skat.1.epacts /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.gene.skat.2.epacts /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.gene.skat.3.epacts /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.gene.skat.4.epacts /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.gene.skat.5.epacts /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.gene.skat.0.R /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.gene.skat.1.R /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.gene.skat.2.R /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.gene.skat.3.R /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.gene.skat.4.R /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.gene.skat.5.R /tmp2/EPACTS-3.2.6/bin/epacts-plot --in /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.gene.skat.epacts Rscript /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.gene.skat.epacts.R --vanilla export GDFONTPATH=/tmp2/EPACTS-3.2.6/share/EPACTS; export GNUPLOT_FONTPATH=/tmp2/EPACTS-3.2.6/share/EPACTS; export GNUPLOT_PS_DIR=/tmp2/EPACTS-3.2.6/share/EPACTS; export PATH=$PATH:/tmp2/EPACTS-3.2.6/bin/; export GNUPLOT_PFBTOPFA="pfbtops %s"; gnuplot /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.gene.skat.epacts.cmd export GDFONTPATH=/tmp2/EPACTS-3.2.6/share/EPACTS; export GNUPLOT_FONTPATH=/tmp2/EPACTS-3.2.6/share/EPACTS; export GNUPLOT_PS_DIR=/tmp2/EPACTS-3.2.6/share/EPACTS; export PATH=$PATH:/tmp2/EPACTS-3.2.6/bin/; export GNUPLOT_PFBTOPFA="pfbtops %s"; /tmp2/EPACTS-3.2.6/bin/epstopdf /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.gene.skat.epacts.qq.eps export GDFONTPATH=/tmp2/EPACTS-3.2.6/share/EPACTS; export GNUPLOT_FONTPATH=/tmp2/EPACTS-3.2.6/share/EPACTS; export GNUPLOT_PS_DIR=/tmp2/EPACTS-3.2.6/share/EPACTS; export PATH=$PATH:/tmp2/EPACTS-3.2.6/bin/; export GNUPLOT_PFBTOPFA="pfbtops %s"; gnuplot /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.gene.skat.epacts.cmd export GDFONTPATH=/tmp2/EPACTS-3.2.6/share/EPACTS; export GNUPLOT_FONTPATH=/tmp2/EPACTS-3.2.6/share/EPACTS; export GNUPLOT_PS_DIR=/tmp2/EPACTS-3.2.6/share/EPACTS; export PATH=$PATH:/tmp2/EPACTS-3.2.6/bin/; export GNUPLOT_PFBTOPFA="pfbtops %s"; /tmp2/EPACTS-3.2.6/bin/epstopdf /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.gene.skat.epacts.mh.eps rm /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.gene.skat.epacts.cmd /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.gene.skat.epacts.qq.eps /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.gene.skat.epacts.mh.eps /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.gene.skat.epacts.*.dat cat /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.gene.skat.epacts | awk '$10 != "NA" { print $0 }' | sort -g -k 10 | head -n 5000 > /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.gene.skat.epacts.top5000 touch /cromwell-executions/w/54df75c4-79dc-44d3-9e86-a27d45d99667/call-test_epacts/execution/out/test.gene.skat.epacts.OK