Hello everyone,
I get the following error when I try to run Single variant analysis using EPACTS tool. the output files seems to be alright (not 100% sure though as I am very new to this tool) but the plotting isn't working. It is generating plots but they are empty. I was just wondering if anyone here have encountered such an error and can assist me in fixing it. the following is the running process with errors. as th space was quite limited here so I had to remove most parts of the run. the trace back was quite similar to the error here ( https://groups.google.com/forum/#!topic/epacts/OiiaJmU1qwQ )
*Command used: perl epacts-single --vcf /home/ijlal/Burden_test_EPACTS/Test/filtered.vcf.gz --ped /home/ijlal/Burden_test_EPACTS/Test/phenotype.ped --min-maf 0.001 --pheno PHENO --test b.glrt --anno --out /home/ijlal/Burden_test_EPACTS/With_filter_b.glrt/Single_SNP_Analysis_COmplete --run 2*
Running Process:
Detected phenotypes with 2 unique values - 1 and 2 - considering them as binary phenotypes... re-encoding them into 1 and 2 Successfully written phenotypes and 0 covariates across 18125 individuals Processing chromosome 1... Processing chromosome 2... Processing chromosome 3... Processing chromosome 4... Processing chromosome 5... Processing chromosome 6... Processing chromosome 7... Processing chromosome 8... Processing chromosome 9... Processing chromosome 10... Processing chromosome 11... Processing chromosome 12... Processing chromosome 13... Processing chromosome 14... Processing chromosome 15... Processing chromosome 16... Processing chromosome 17... Processing chromosome 18... Processing chromosome 19... Processing chromosome 20... Processing chromosome 21... Processing chromosome 22... Processing chromosome X... Processing chromosome Y... Processing chromosome MT... Finished generating EPACTS Makefile Running 2 parallel jobs of EPACTS forkExecWait(): make -f /home/ijlal/Burden_test_EPACTS/With_filter_b.glrt/Single_SNP_Analysis_COmplete.Makefile -j 2 /opt/epacts-20170222/bin/pEmmax GLRT --vcf /home/ijlal/Burden_test_EPACTS/Test/filtered.vcf.gz --phenof /home/ijlal/Burden_test_EPACTS/With_filter_b.glrt/Single_SNP_Analysis_COmplete.phe --indf /home/ijlal/Burden_test_EPACTS/With_filter_b.glrt/Single_SNP_Analysis_COmplete.ind --region 1:1-10000000 --out /home/ijlal/Burden_test_EPACTS/With_filter_b.glrt/Single_SNP_Analysis_COmplete.1.1.10000000.epacts --field PL --minMAF 0.001 --maxMAF 1 --maxMAC 1000000000 --ignoreFilter /opt/epacts-20170222/bin/pEmmax GLRT --vcf /home/ijlal/Burden_test_EPACTS/Test/filtered.vcf.gz --phenof /home/ijlal/Burden_test_EPACTS/With_filter_b.glrt/Single_SNP_Analysis_COmplete.phe --indf /home/ijlal/Burden_test_EPACTS/With_filter_b.glrt/Single_SNP_Analysis_COmplete.ind --region 1:10000001-20000000 --out /home/ijlal/Burden_test_EPACTS/With_filter_b.glrt/Single_SNP_Analysis_COmplete.1.10000001.20000000.epacts --field PL --minMAF 0.001 --maxMAF 1 --maxMAC 1000000000 --ignoreFilter
The following parameters are available. Ones with "[]" are in effect:
The following parameters are available. Ones with "[]" are in effect:
Available Options VCF Input Options : Available Options VCF Input Options : --vcf [/home/ijlal/Burden_test_EPACTS/Test/filtered.vcf.gz], --vcf [/home/ijlal/Burden_test_EPACTS/Test/filtered.vcf.gz] --region [1:1-10000000], --region [1:10000001-20000000], --unit [10000], --unit [10000], , --indf [/home/ijlal/Burden_test_EPACTS/With_filter_b.glrt/Single_SNP_Analysis_COmplete.ind] --indf [/home/ijlal/Burden_test_EPACTS/With_filter_b.glrt/Single_SNP_Analysis_COmplete.ind], , --field [PL] --field [PL], --rule [], --rule [], --minMAF [1.0e-03], --minMAF [1.0e-03], , --maxMAF [1.00] --maxMAF [1.00], --minMAC [1], --minMAC [1], --maxMAC [1000000000], --maxMAC [1000000000], , --minCallRate [1.0e-06] --minCallRate [1.0e-06], --ignoreFilter [ON], --ignoreFilter [ON] Other Input Options : Other Input Options : --phenof [/home/ijlal/Burden_test_EPACTS/With_filter_b.glrt/Single_SNP_Analysis_COmplete.phe] --phenof [/home/ijlal/Burden_test_EPACTS/With_filter_b.glrt/Single_SNP_Analysis_COmplete.phe], , --indf [/home/ijlal/Burden_test_EPACTS/With_filter_b.glrt/Single_SNP_Analysis_COmplete.ind] --indf [/home/ijlal/Burden_test_EPACTS/With_filter_b.glrt/Single_SNP_Analysis_COmplete.ind] Output Options : Output Options : --out [/home/ijlal/Burden_test_EPACTS/With_filter_b.glrt/Single_SNP_Analysis_COmplete.1.1.10000000.epacts] --out [/home/ijlal/Burden_test_EPACTS/With_filter_b.glrt/Single_SNP_Analysis_COmplete.1.10000001.20000000.epacts], , --verbose --verbose
NOTICE - Finished loading phenotypes across 18125 individuals with 1 covariates (including interception) NOTICE - Finished loading phenotypes across 18125 individuals with 1 covariates (including interception)
Available Options Required Parameters : -i [/home/ijlal/Burden_test_EPACTS/With_filter_b.glrt/Single_SNP_Analysis_COmplete.1.1.10000000.epacts] -o [/home/ijlal/Burden_test_EPACTS/With_filter_b.glrt/Single_SNP_Analysis_COmplete.1.1.10000000.epacts.tmp] Gene Annotation Parameters : -g [/opt/epacts-20170222/share/EPACTS/hg19_gencodeV14.txt.gz] -r [/opt/epacts-20170222/share/EPACTS/human_g1k_v37.fasta] --inputFormat [epacts], --checkReference, -f [refGene] -p [/opt/epacts-20170222/share/EPACTS/priority.txt] -c [/opt/epacts-20170222/share/EPACTS/codon.txt] -u [], -d [], --se [], --si [], --outputFormat [] Other Annotation Tools : --genomeScore [], --bed [], --tabix [] Load reference genome /opt/epacts-20170222/share/EPACTS/human_g1k_v37.fasta... DONE: 84 chromosomes and 3101804739 bases are loaded. Load codon file /opt/epacts-20170222/share/EPACTS/codon.txt... DONE: codon file loaded. Load priority file /opt/epacts-20170222/share/EPACTS/priority.txt... DONE: 24 priority annotation types loaded. Load gene file /opt/epacts-20170222/share/EPACTS/hg19_gencodeV14.txt.gz... Processing 51 markers across 18125 individuals...4 markers included /opt/epacts-20170222/bin/epacts-anno --in /home/ijlal/Burden_test_EPACTS/With_filter_b.glrt/Single_SNP_Analysis_COmplete.1.10000001.20000000.epacts --ref /opt/epacts-20170222/share/EPACTS/human_g1k_v37.fasta /opt/epacts-20170222/bin/anno -i /home/ijlal/Burden_test_EPACTS/With_filter_b.glrt/Single_SNP_Analysis_COmplete.1.10000001.20000000.epacts -r /opt/epacts-20170222/share/EPACTS/human_g1k_v37.fasta -f refGene -g /opt/epacts-20170222/share/EPACTS/hg19_gencodeV14.txt.gz -c /opt/epacts-20170222/share/EPACTS/codon.txt -o /home/ijlal/Burden_test_EPACTS/With_filter_b.glrt/Single_SNP_Analysis_COmplete.1.10000001.20000000.epacts.tmp --inputFormat epacts -p /opt/epacts-20170222/share/EPACTS/priority.txt
WARNING - Cannot parse region Y:30000001-40000000.. Returning empty /opt/epacts-20170222/bin/epacts-anno --in /home/ijlal/Burden_test_EPACTS/With_filter_b.glrt/Single_SNP_Analysis_COmplete.Y.30000001.40000000.epacts --ref /opt/epacts-20170222/share/EPACTS/human_g1k_v37.fasta /opt/epacts-20170222/bin/anno -i /home/ijlal/Burden_test_EPACTS/With_filter_b.glrt/Single_SNP_Analysis_COmplete.Y.30000001.40000000.epacts -r /opt/epacts-20170222/share/EPACTS/human_g1k_v37.fasta -f refGene -g /opt/epacts-20170222/share/EPACTS/hg19_gencodeV14.txt.gz -c /opt/epacts-20170222/share/EPACTS/codon.txt -o /home/ijlal/Burden_test_EPACTS/With_filter_b.glrt/Single_SNP_Analysis_COmplete.Y.30000001.40000000.epacts.tmp --inputFormat epacts -p /opt/epacts-20170222/share/EPACTS/priority.txt The following parameters are available. Ones with "[]" are in effect:
export GDFONTPATH=/opt/epacts-20170222/share/EPACTS; export GNUPLOT_FONTPATH=/opt/epacts-20170222/share/EPACTS; export GNUPLOT_PS_DIR=/opt/epacts-20170222/share/EPACTS; export PATH=$PATH:/opt/epacts-20170222/bin/; export GNUPLOT_PFBTOPFA="pfbtops %s"; gnuplot /home/ijlal/Burden_test_EPACTS/With_filter_b.glrt/Single_SNP_Analysis_COmplete.epacts.cmd export GDFONTPATH=/opt/epacts-20170222/share/EPACTS; export GNUPLOT_FONTPATH=/opt/epacts-20170222/share/EPACTS; export GNUPLOT_PS_DIR=/opt/epacts-20170222/share/EPACTS; export PATH=$PATH:/opt/epacts-20170222/bin/; export GNUPLOT_PFBTOPFA="pfbtops %s"; /opt/epacts-20170222/bin/epstopdf /home/ijlal/Burden_test_EPACTS/With_filter_b.glrt/Single_SNP_Analysis_COmplete.epacts.qq.eps GPL Ghostscript 9.26: Unrecoverable error, exit code 1 Error: /undefined in LTB Operand stack:
Execution stack: %interp_exit .runexec2 --nostringval-- --nostringval-- --nostringval-- 2 %stopped_push --nostringval-- --nostringval-- --nostringval-- false 1 %stopped_push 2045 1 3 %oparray_pop 2044 1 3 %oparray_pop --nostringval-- 2025 1 3 %oparray_pop 1884 1 3 %oparray_pop --nostringval-- %errorexec_pop .runexec2 --nostringval-- --nostringval-- --nostringval-- 2 %stopped_push --nostringval-- Dictionary stack: --dict:974/1684(ro)(G)-- --dict:0/20(G)-- --dict:87/200(L)-- --dict:205/256(L)-- Current allocation mode is local export GDFONTPATH=/opt/epacts-20170222/share/EPACTS; export GNUPLOT_FONTPATH=/opt/epacts-20170222/share/EPACTS; export GNUPLOT_PS_DIR=/opt/epacts-20170222/share/EPACTS; export PATH=$PATH:/opt/epacts-20170222/bin/; export GNUPLOT_PFBTOPFA="pfbtops %s"; gnuplot /home/ijlal/Burden_test_EPACTS/With_filter_b.glrt/Single_SNP_Analysis_COmplete.epacts.cmd export GDFONTPATH=/opt/epacts-20170222/share/EPACTS; export GNUPLOT_FONTPATH=/opt/epacts-20170222/share/EPACTS; export GNUPLOT_PS_DIR=/opt/epacts-20170222/share/EPACTS; export PATH=$PATH:/opt/epacts-20170222/bin/; export GNUPLOT_PFBTOPFA="pfbtops %s"; /opt/epacts-20170222/bin/epstopdf /home/ijlal/Burden_test_EPACTS/With_filter_b.glrt/Single_SNP_Analysis_COmplete.epacts.mh.eps GPL Ghostscript 9.26: Unrecoverable error, exit code 1 Error: /undefined in LTB Operand stack:
Execution stack: %interp_exit .runexec2 --nostringval-- --nostringval-- --nostringval-- 2 %stopped_push --nostringval-- --nostringval-- --nostringval-- false 1 %stopped_push 2045 1 3 %oparray_pop 2044 1 3 %oparray_pop --nostringval-- 2025 1 3 %oparray_pop 1884 1 3 %oparray_pop --nostringval-- %errorexec_pop .runexec2 --nostringval-- --nostringval-- --nostringval-- 2 %stopped_push --nostringval-- Dictionary stack: --dict:974/1684(ro)(G)-- --dict:0/20(G)-- --dict:87/200(L)-- --dict:205/256(L)-- Current allocation mode is local rm /home/ijlal/Burden_test_EPACTS/With_filter_b.glrt/Single_SNP_Analysis_COmplete.epacts.cmd /home/ijlal/Burden_test_EPACTS/With_filter_b.glrt/Single_SNP_Analysis_COmplete.epacts.qq.eps /home/ijlal/Burden_test_EPACTS/With_filter_b.glrt/Single_SNP_Analysis_COmplete.epacts.mh.eps /home/ijlal/Burden_test_EPACTS/With_filter_b.glrt/Single_SNP_Analysis_COmplete.epacts.*.dat zcat /home/ijlal/Burden_test_EPACTS/With_filter_b.glrt/Single_SNP_Analysis_COmplete.epacts.gz | awk '$8 != "NA" { print $0 }' | sort -g -k 8 | head -n 5000 > /home/ijlal/Burden_test_EPACTS/With_filter_b.glrt/Single_SNP_Analysis_COmplete.epacts.top5000 touch /home/ijlal/Burden_test_EPACTS/With_filter_b.glrt/Single_SNP_Analysis_COmplete.epacts.OK
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