GPL Ghostscript 9.26: Unrecoverable error, exit code 1 Error: /undefined in LTB
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huang...@gmail.com
Dec 5, 2018, 1:22:52 PM12/5/18
to EPACTS
Dear All,
I get the following error when run test files of EPACTS. It seems output files are fine except the PDF files, which are empty without pictures or dots or figures.
The error message is "GPL Ghostscript 9.26: Unrecoverable error, exit code 1 Error: /undefined in LTB" .
The following is running process with the error message maked by red.
Thanks,
Bo
~/local/EPACTS/bin$ ./test_run_epacts.sh
Performing EPACTS Binary Single Variant Score Test..
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 2 covariates across 266 individuals
Processing chromosome 20...
Finished generating EPACTS Makefile
Running 5 parallel jobs of EPACTS
forkExecWait(): make -f /home/bohuang/local/EPACTS/bin/out/test.single.b.score.Makefile -j 5
Rscript /home/bohuang/local/EPACTS/share/EPACTS/epactsSingle.R --vanilla /home/bohuang/local/EPACTS /home/bohuang/local/EPACTS/bin/out/test.single.b.score.phe /home/bohuang/local/EPACTS/bin/out/test.single.b.score.cov /home/bohuang/local/EPACTS/bin/out/test.single.b.score.ind /home/bohuang/local/EPACTS/bin/./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz 20:1-10000000 /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.1.10000000.epacts GT 0.001 1 3 1000000000 0.5 0 FALSE single.b.score
Rscript /home/bohuang/local/EPACTS/share/EPACTS/epactsSingle.R --vanilla /home/bohuang/local/EPACTS /home/bohuang/local/EPACTS/bin/out/test.single.b.score.phe /home/bohuang/local/EPACTS/bin/out/test.single.b.score.cov /home/bohuang/local/EPACTS/bin/out/test.single.b.score.ind /home/bohuang/local/EPACTS/bin/./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz 20:10000001-20000000 /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.10000001.20000000.epacts GT 0.001 1 3 1000000000 0.5 0 FALSE single.b.score
Rscript /home/bohuang/local/EPACTS/share/EPACTS/epactsSingle.R --vanilla /home/bohuang/local/EPACTS /home/bohuang/local/EPACTS/bin/out/test.single.b.score.phe /home/bohuang/local/EPACTS/bin/out/test.single.b.score.cov /home/bohuang/local/EPACTS/bin/out/test.single.b.score.ind /home/bohuang/local/EPACTS/bin/./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz 20:20000001-30000000 /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.20000001.30000000.epacts GT 0.001 1 3 1000000000 0.5 0 FALSE single.b.score
Rscript /home/bohuang/local/EPACTS/share/EPACTS/epactsSingle.R --vanilla /home/bohuang/local/EPACTS /home/bohuang/local/EPACTS/bin/out/test.single.b.score.phe /home/bohuang/local/EPACTS/bin/out/test.single.b.score.cov /home/bohuang/local/EPACTS/bin/out/test.single.b.score.ind /home/bohuang/local/EPACTS/bin/./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz 20:30000001-40000000 /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.30000001.40000000.epacts GT 0.001 1 3 1000000000 0.5 0 FALSE single.b.score
Rscript /home/bohuang/local/EPACTS/share/EPACTS/epactsSingle.R --vanilla /home/bohuang/local/EPACTS /home/bohuang/local/EPACTS/bin/out/test.single.b.score.phe /home/bohuang/local/EPACTS/bin/out/test.single.b.score.cov /home/bohuang/local/EPACTS/bin/out/test.single.b.score.ind /home/bohuang/local/EPACTS/bin/./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz 20:40000001-50000000 /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.40000001.50000000.epacts GT 0.001 1 3 1000000000 0.5 0 FALSE single.b.score
Loading required package: epactsR
Loading required package: epactsR
Loading required package: epactsR
Loading required package: epactsR
Loading required package: epactsR
NULL
Sucessfully wrote ( 1248 * 10 ) matrix
NULL
NULL
Sucessfully wrote ( 1466 * 10 ) matrix
NULL
NULL
Sucessfully wrote ( 3367 * 10 ) matrix
NULL
/home/bohuang/local/EPACTS/bin/epacts-anno --in /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.10000001.20000000.epacts --ref /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta
/home/bohuang/local/EPACTS/bin/epacts-anno --in /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.20000001.30000000.epacts --ref /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta
/home/bohuang/local/EPACTS/bin/epacts-anno --in /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.1.10000000.epacts --ref /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta
NULL
Sucessfully wrote ( 4170 * 10 ) matrix
NULL
/home/bohuang/local/EPACTS/bin/epacts-anno --in /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.30000001.40000000.epacts --ref /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta
NULL
Sucessfully wrote ( 3662 * 10 ) matrix
NULL
/home/bohuang/local/EPACTS/bin/epacts-anno --in /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.40000001.50000000.epacts --ref /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta
/home/bohuang/local/EPACTS/bin/anno -i /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.30000001.40000000.epacts -r /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta -f refGene -g /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz -c /home/bohuang/local/EPACTS/share/EPACTS/codon.txt -o /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.30000001.40000000.epacts.tmp --inputFormat epacts -p /home/bohuang/local/EPACTS/share/EPACTS/priority.txt
/home/bohuang/local/EPACTS/bin/anno -i /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.20000001.30000000.epacts -r /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta -f refGene -g /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz -c /home/bohuang/local/EPACTS/share/EPACTS/codon.txt -o /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.20000001.30000000.epacts.tmp --inputFormat epacts -p /home/bohuang/local/EPACTS/share/EPACTS/priority.txt
The following parameters are available. Ones with "[]" are in effect:
Available Options
Required Parameters :
-i [/home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.30000001.40000000.epacts]
-o [/home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.30000001.40000000.epacts.tmp]
Gene Annotation
Parameters : -g [/home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz]
-r [/home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta]
--inputFormat [epacts], --checkReference, -f [refGene]
-p [/home/bohuang/local/EPACTS/share/EPACTS/priority.txt]
-c [/home/bohuang/local/EPACTS/share/EPACTS/codon.txt]
-u [], -d [], --se [], --si [], --outputFormat []
Other Annotation Tools : --genomeScore [], --bed [], --tabix []
/home/bohuang/local/EPACTS/bin/anno -i /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.10000001.20000000.epacts -r /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta -f refGene -g /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz -c /home/bohuang/local/EPACTS/share/EPACTS/codon.txt -o /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.10000001.20000000.epacts.tmp --inputFormat epacts -p /home/bohuang/local/EPACTS/share/EPACTS/priority.txt
Load reference genome /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta...
DONE: 84 chromosomes and 3101804739 bases are loaded.
Load codon file /home/bohuang/local/EPACTS/share/EPACTS/codon.txt...
The following parameters are available. Ones with "[]" are in effect:
DONE: codon file loaded.
Load priority file /home/bohuang/local/EPACTS/share/EPACTS/priority.txt...
Available Options
Required Parameters :
-i [/home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.20000001.30000000.epacts]
-o [/home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.20000001.30000000.epacts.tmp]
Gene Annotation
Parameters : -g [/home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz]
-r [/home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta]
--inputFormat [epacts], --checkReference, -f [refGene]
-p [/home/bohuang/local/EPACTS/share/EPACTS/priority.txt]
-c [/home/bohuang/local/EPACTS/share/EPACTS/codon.txt]
-u [], -d [], --se [], --si [], --outputFormat []
Other Annotation Tools : --genomeScore [], --bed [], --tabix []
Load reference genome /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta...
DONE: 84 chromosomes and 3101804739 bases are loaded.
Load codon file /home/bohuang/local/EPACTS/share/EPACTS/codon.txt...
DONE: codon file loaded.
Load priority file /home/bohuang/local/EPACTS/share/EPACTS/priority.txt...
DONE: 24 priority annotation types loaded.
DONE: 24 priority annotation types loaded.
Load gene file /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz...
Load gene file /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz...
The following parameters are available. Ones with "[]" are in effect:
Available Options
Required Parameters :
-i [/home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.10000001.20000000.epacts]
-o [/home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.10000001.20000000.epacts.tmp]
Gene Annotation
Parameters : -g [/home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz]
-r [/home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta]
--inputFormat [epacts], --checkReference, -f [refGene]
-p [/home/bohuang/local/EPACTS/share/EPACTS/priority.txt]
-c [/home/bohuang/local/EPACTS/share/EPACTS/codon.txt]
-u [], -d [], --se [], --si [], --outputFormat []
Other Annotation Tools : --genomeScore [], --bed [], --tabix []
Load reference genome /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta...
DONE: 84 chromosomes and 3101804739 bases are loaded.
Load codon file /home/bohuang/local/EPACTS/share/EPACTS/codon.txt...
DONE: codon file loaded.
Load priority file /home/bohuang/local/EPACTS/share/EPACTS/priority.txt...
DONE: 24 priority annotation types loaded.
Load gene file /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz...
/home/bohuang/local/EPACTS/bin/anno -i /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.1.10000000.epacts -r /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta -f refGene -g /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz -c /home/bohuang/local/EPACTS/share/EPACTS/codon.txt -o /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.1.10000000.epacts.tmp --inputFormat epacts -p /home/bohuang/local/EPACTS/share/EPACTS/priority.txt
The following parameters are available. Ones with "[]" are in effect:
Available Options
Required Parameters :
-i [/home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.1.10000000.epacts]
-o [/home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.1.10000000.epacts.tmp]
Gene Annotation
Parameters : -g [/home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz]
-r [/home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta]
--inputFormat [epacts], --checkReference, -f [refGene]
-p [/home/bohuang/local/EPACTS/share/EPACTS/priority.txt]
-c [/home/bohuang/local/EPACTS/share/EPACTS/codon.txt]
-u [], -d [], --se [], --si [], --outputFormat []
Other Annotation Tools : --genomeScore [], --bed [], --tabix []
Load reference genome /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta...
DONE: 84 chromosomes and 3101804739 bases are loaded.
Load codon file /home/bohuang/local/EPACTS/share/EPACTS/codon.txt...
DONE: codon file loaded.
Load priority file /home/bohuang/local/EPACTS/share/EPACTS/priority.txt...
DONE: 24 priority annotation types loaded.
Load gene file /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz...
/home/bohuang/local/EPACTS/bin/anno -i /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.40000001.50000000.epacts -r /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta -f refGene -g /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz -c /home/bohuang/local/EPACTS/share/EPACTS/codon.txt -o /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.40000001.50000000.epacts.tmp --inputFormat epacts -p /home/bohuang/local/EPACTS/share/EPACTS/priority.txt
The following parameters are available. Ones with "[]" are in effect:
Available Options
Required Parameters :
-i [/home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.40000001.50000000.epacts]
-o [/home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.40000001.50000000.epacts.tmp]
Gene Annotation
Parameters : -g [/home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz]
-r [/home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta]
--inputFormat [epacts], --checkReference, -f [refGene]
-p [/home/bohuang/local/EPACTS/share/EPACTS/priority.txt]
-c [/home/bohuang/local/EPACTS/share/EPACTS/codon.txt]
-u [], -d [], --se [], --si [], --outputFormat []
Other Annotation Tools : --genomeScore [], --bed [], --tabix []
Load reference genome /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta...
DONE: 84 chromosomes and 3101804739 bases are loaded.
Load codon file /home/bohuang/local/EPACTS/share/EPACTS/codon.txt...
DONE: codon file loaded.
Load priority file /home/bohuang/local/EPACTS/share/EPACTS/priority.txt...
DONE: 24 priority annotation types loaded.
Load gene file /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz...
DONE: 92627 gene loaded.
DONE: Generated frequency of each annotype type in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.10000001.20000000.epacts.tmp.anno.frq ].
DONE: Generated frequency of each highest priority annotation type in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.10000001.20000000.epacts.tmp.top.anno.frq ].
Ts/Tv ratio: 2.87578
Ts observed: 926 times; Tv observed: 322 times.
DONE: Generated frequency of each base change in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.10000001.20000000.epacts.tmp.base.frq ].
DONE: Generated frequency of each codon change in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.10000001.20000000.epacts.tmp.codon.frq ].
DONE: Generated frequency of indel length in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.10000001.20000000.epacts.tmp.indel.frq ].
..............................................
... Anno(tation) ...
... Xiaowei Zhan, Goncalo Abecasis ...
... Speical Thanks: ...
... Hyun Ming Kang, Yanming Li ...
... zha...@umich.edu ...
... Sep 2011 ...
................................................
DONE: 1248 varaints are annotated.
DONE: Generated annotation output in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.10000001.20000000.epacts.tmp ].
Annotation succeed!
mv /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.10000001.20000000.epacts.tmp /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.10000001.20000000.epacts
rm /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.10000001.20000000.epacts.tmp.log /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.10000001.20000000.epacts.tmp.top.anno.frq /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.10000001.20000000.epacts.tmp.anno.frq /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.10000001.20000000.epacts.tmp.base.frq /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.10000001.20000000.epacts.tmp.codon.frq /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.10000001.20000000.epacts.tmp.indel.frq
DONE: 92627 gene loaded.
Rscript /home/bohuang/local/EPACTS/share/EPACTS/epactsSingle.R --vanilla /home/bohuang/local/EPACTS /home/bohuang/local/EPACTS/bin/out/test.single.b.score.phe /home/bohuang/local/EPACTS/bin/out/test.single.b.score.cov /home/bohuang/local/EPACTS/bin/out/test.single.b.score.ind /home/bohuang/local/EPACTS/bin/./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz 20:50000001-60000000 /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.50000001.60000000.epacts GT 0.001 1 3 1000000000 0.5 0 FALSE single.b.score
DONE: 92627 gene loaded.
DONE: 92627 gene loaded.
DONE: 92627 gene loaded.
DONE: Generated frequency of each annotype type in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.40000001.50000000.epacts.tmp.anno.frq ].
DONE: Generated frequency of each highest priority annotation type in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.40000001.50000000.epacts.tmp.top.anno.frq ].
Ts/Tv ratio: 2.69153
Ts observed: 2670 times; Tv observed: 992 times.
DONE: Generated frequency of each base change in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.40000001.50000000.epacts.tmp.base.frq ].
DONE: Generated frequency of each codon change in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.40000001.50000000.epacts.tmp.codon.frq ].
DONE: Generated frequency of indel length in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.40000001.50000000.epacts.tmp.indel.frq ].
..............................................
... Anno(tation) ...
... Xiaowei Zhan, Goncalo Abecasis ...
... Speical Thanks: ...
... Hyun Ming Kang, Yanming Li ...
... zha...@umich.edu ...
... Sep 2011 ...
................................................
DONE: 3662 varaints are annotated.
DONE: Generated annotation output in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.40000001.50000000.epacts.tmp ].
Annotation succeed!
mv /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.40000001.50000000.epacts.tmp /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.40000001.50000000.epacts
rm /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.40000001.50000000.epacts.tmp.log /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.40000001.50000000.epacts.tmp.top.anno.frq /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.40000001.50000000.epacts.tmp.anno.frq /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.40000001.50000000.epacts.tmp.base.frq /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.40000001.50000000.epacts.tmp.codon.frq /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.40000001.50000000.epacts.tmp.indel.frq
Rscript /home/bohuang/local/EPACTS/share/EPACTS/epactsSingle.R --vanilla /home/bohuang/local/EPACTS /home/bohuang/local/EPACTS/bin/out/test.single.b.score.phe /home/bohuang/local/EPACTS/bin/out/test.single.b.score.cov /home/bohuang/local/EPACTS/bin/out/test.single.b.score.ind /home/bohuang/local/EPACTS/bin/./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz 20:60000001-63025520 /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.60000001.63025520.epacts GT 0.001 1 3 1000000000 0.5 0 FALSE single.b.score
DONE: Generated frequency of each annotype type in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.1.10000000.epacts.tmp.anno.frq ].
DONE: Generated frequency of each highest priority annotation type in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.1.10000000.epacts.tmp.top.anno.frq ].
Ts/Tv ratio: 2.8524
Ts observed: 2493 times; Tv observed: 874 times.
DONE: Generated frequency of each base change in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.1.10000000.epacts.tmp.base.frq ].
DONE: Generated frequency of each codon change in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.1.10000000.epacts.tmp.codon.frq ].
DONE: Generated frequency of indel length in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.1.10000000.epacts.tmp.indel.frq ].
..............................................
... Anno(tation) ...
... Xiaowei Zhan, Goncalo Abecasis ...
... Speical Thanks: ...
... Hyun Ming Kang, Yanming Li ...
... zha...@umich.edu ...
... Sep 2011 ...
................................................
DONE: 3367 varaints are annotated.
DONE: Generated annotation output in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.1.10000000.epacts.tmp ].
Annotation succeed!
mv /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.1.10000000.epacts.tmp /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.1.10000000.epacts
rm /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.1.10000000.epacts.tmp.log /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.1.10000000.epacts.tmp.top.anno.frq /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.1.10000000.epacts.tmp.anno.frq /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.1.10000000.epacts.tmp.base.frq /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.1.10000000.epacts.tmp.codon.frq /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.1.10000000.epacts.tmp.indel.frq
DONE: Generated frequency of each annotype type in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.20000001.30000000.epacts.tmp.anno.frq ].
DONE: Generated frequency of each highest priority annotation type in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.20000001.30000000.epacts.tmp.top.anno.frq ].
Ts/Tv ratio: 2.59314
Ts observed: 1058 times; Tv observed: 408 times.
DONE: Generated frequency of each base change in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.20000001.30000000.epacts.tmp.base.frq ].
DONE: Generated frequency of each codon change in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.20000001.30000000.epacts.tmp.codon.frq ].
DONE: Generated frequency of indel length in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.20000001.30000000.epacts.tmp.indel.frq ].
..............................................
... Anno(tation) ...
... Xiaowei Zhan, Goncalo Abecasis ...
... Speical Thanks: ...
... Hyun Ming Kang, Yanming Li ...
... zha...@umich.edu ...
... Sep 2011 ...
................................................
DONE: 1466 varaints are annotated.
DONE: Generated annotation output in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.20000001.30000000.epacts.tmp ].
Annotation succeed!
mv /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.20000001.30000000.epacts.tmp /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.20000001.30000000.epacts
rm /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.20000001.30000000.epacts.tmp.log /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.20000001.30000000.epacts.tmp.top.anno.frq /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.20000001.30000000.epacts.tmp.anno.frq /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.20000001.30000000.epacts.tmp.base.frq /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.20000001.30000000.epacts.tmp.codon.frq /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.20000001.30000000.epacts.tmp.indel.frq
Loading required package: epactsR
Loading required package: epactsR
DONE: Generated frequency of each annotype type in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.30000001.40000000.epacts.tmp.anno.frq ].
DONE: Generated frequency of each highest priority annotation type in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.30000001.40000000.epacts.tmp.top.anno.frq ].
Ts/Tv ratio: 2.90815
Ts observed: 3103 times; Tv observed: 1067 times.
DONE: Generated frequency of each base change in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.30000001.40000000.epacts.tmp.base.frq ].
DONE: Generated frequency of each codon change in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.30000001.40000000.epacts.tmp.codon.frq ].
DONE: Generated frequency of indel length in [ /home/bohuang/local/EPACTS/bin/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 ...
... zha...@umich.edu ...
... Sep 2011 ...
................................................
DONE: 4170 varaints are annotated.
DONE: Generated annotation output in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.30000001.40000000.epacts.tmp ].
Annotation succeed!
mv /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.30000001.40000000.epacts.tmp /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.30000001.40000000.epacts
rm /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.30000001.40000000.epacts.tmp.log /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.30000001.40000000.epacts.tmp.top.anno.frq /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.30000001.40000000.epacts.tmp.anno.frq /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.30000001.40000000.epacts.tmp.base.frq /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.30000001.40000000.epacts.tmp.codon.frq /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.30000001.40000000.epacts.tmp.indel.frq
NULL
Sucessfully wrote ( 1763 * 10 ) matrix
NULL
/home/bohuang/local/EPACTS/bin/epacts-anno --in /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.50000001.60000000.epacts --ref /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta
/home/bohuang/local/EPACTS/bin/anno -i /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.50000001.60000000.epacts -r /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta -f refGene -g /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz -c /home/bohuang/local/EPACTS/share/EPACTS/codon.txt -o /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.50000001.60000000.epacts.tmp --inputFormat epacts -p /home/bohuang/local/EPACTS/share/EPACTS/priority.txt
The following parameters are available. Ones with "[]" are in effect:
Available Options
Required Parameters :
-i [/home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.50000001.60000000.epacts]
-o [/home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.50000001.60000000.epacts.tmp]
Gene Annotation
Parameters : -g [/home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz]
-r [/home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta]
--inputFormat [epacts], --checkReference, -f [refGene]
-p [/home/bohuang/local/EPACTS/share/EPACTS/priority.txt]
-c [/home/bohuang/local/EPACTS/share/EPACTS/codon.txt]
-u [], -d [], --se [], --si [], --outputFormat []
Other Annotation Tools : --genomeScore [], --bed [], --tabix []
Load reference genome /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta...
DONE: 84 chromosomes and 3101804739 bases are loaded.
Load codon file /home/bohuang/local/EPACTS/share/EPACTS/codon.txt...
DONE: codon file loaded.
Load priority file /home/bohuang/local/EPACTS/share/EPACTS/priority.txt...
DONE: 24 priority annotation types loaded.
Load gene file /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz...
NULL
Sucessfully wrote ( 3425 * 10 ) matrix
NULL
/home/bohuang/local/EPACTS/bin/epacts-anno --in /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.60000001.63025520.epacts --ref /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta
/home/bohuang/local/EPACTS/bin/anno -i /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.60000001.63025520.epacts -r /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta -f refGene -g /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz -c /home/bohuang/local/EPACTS/share/EPACTS/codon.txt -o /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.60000001.63025520.epacts.tmp --inputFormat epacts -p /home/bohuang/local/EPACTS/share/EPACTS/priority.txt
The following parameters are available. Ones with "[]" are in effect:
Available Options
Required Parameters :
-i [/home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.60000001.63025520.epacts]
-o [/home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.60000001.63025520.epacts.tmp]
Gene Annotation
Parameters : -g [/home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz]
-r [/home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta]
--inputFormat [epacts], --checkReference, -f [refGene]
-p [/home/bohuang/local/EPACTS/share/EPACTS/priority.txt]
-c [/home/bohuang/local/EPACTS/share/EPACTS/codon.txt]
-u [], -d [], --se [], --si [], --outputFormat []
Other Annotation Tools : --genomeScore [], --bed [], --tabix []
Load reference genome /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta...
DONE: 84 chromosomes and 3101804739 bases are loaded.
Load codon file /home/bohuang/local/EPACTS/share/EPACTS/codon.txt...
DONE: codon file loaded.
Load priority file /home/bohuang/local/EPACTS/share/EPACTS/priority.txt...
DONE: 24 priority annotation types loaded.
Load gene file /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz...
DONE: 92627 gene loaded.
DONE: Generated frequency of each annotype type in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.50000001.60000000.epacts.tmp.anno.frq ].
DONE: Generated frequency of each highest priority annotation type in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.50000001.60000000.epacts.tmp.top.anno.frq ].
Ts/Tv ratio: 2.66528
Ts observed: 1282 times; Tv observed: 481 times.
DONE: Generated frequency of each base change in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.50000001.60000000.epacts.tmp.base.frq ].
DONE: Generated frequency of each codon change in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.50000001.60000000.epacts.tmp.codon.frq ].
DONE: Generated frequency of indel length in [ /home/bohuang/local/EPACTS/bin/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 ...
... zha...@umich.edu ...
... Sep 2011 ...
................................................
DONE: 1763 varaints are annotated.
DONE: Generated annotation output in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.50000001.60000000.epacts.tmp ].
Annotation succeed!
mv /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.50000001.60000000.epacts.tmp /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.50000001.60000000.epacts
rm /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.50000001.60000000.epacts.tmp.log /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.50000001.60000000.epacts.tmp.top.anno.frq /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.50000001.60000000.epacts.tmp.anno.frq /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.50000001.60000000.epacts.tmp.base.frq /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.50000001.60000000.epacts.tmp.codon.frq /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.50000001.60000000.epacts.tmp.indel.frq
DONE: 92627 gene loaded.
DONE: Generated frequency of each annotype type in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.60000001.63025520.epacts.tmp.anno.frq ].
DONE: Generated frequency of each highest priority annotation type in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.60000001.63025520.epacts.tmp.top.anno.frq ].
Ts/Tv ratio: 3.97097
Ts observed: 2736 times; Tv observed: 689 times.
DONE: Generated frequency of each base change in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.60000001.63025520.epacts.tmp.base.frq ].
DONE: Generated frequency of each codon change in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.60000001.63025520.epacts.tmp.codon.frq ].
DONE: Generated frequency of indel length in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.60000001.63025520.epacts.tmp.indel.frq ].
..............................................
... Anno(tation) ...
... Xiaowei Zhan, Goncalo Abecasis ...
... Speical Thanks: ...
... Hyun Ming Kang, Yanming Li ...
... zha...@umich.edu ...
... Sep 2011 ...
................................................
DONE: 3425 varaints are annotated.
DONE: Generated annotation output in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.60000001.63025520.epacts.tmp ].
Annotation succeed!
mv /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.60000001.63025520.epacts.tmp /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.60000001.63025520.epacts
rm /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.60000001.63025520.epacts.tmp.log /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.60000001.63025520.epacts.tmp.top.anno.frq /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.60000001.63025520.epacts.tmp.anno.frq /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.60000001.63025520.epacts.tmp.base.frq /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.60000001.63025520.epacts.tmp.codon.frq /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.60000001.63025520.epacts.tmp.indel.frq
/home/bohuang/local/EPACTS/bin/epacts-cat /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.1.10000000.epacts /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.10000001.20000000.epacts /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.20000001.30000000.epacts /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.30000001.40000000.epacts /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.40000001.50000000.epacts /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.50000001.60000000.epacts /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.60000001.63025520.epacts | /home/bohuang/local/EPACTS/bin/bgzip -c > /home/bohuang/local/EPACTS/bin/out/test.single.b.score.epacts.gz
/home/bohuang/local/EPACTS/bin/tabix -f -pbed /home/bohuang/local/EPACTS/bin/out/test.single.b.score.epacts.gz
rm -f /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.1.10000000.epacts /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.10000001.20000000.epacts /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.20000001.30000000.epacts /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.30000001.40000000.epacts /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.40000001.50000000.epacts /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.50000001.60000000.epacts /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.60000001.63025520.epacts
/home/bohuang/local/EPACTS/bin/epacts-plot --in /home/bohuang/local/EPACTS/bin/out/test.single.b.score.epacts.gz --region 20:0
nsnps = 3331
Rscript /home/bohuang/local/EPACTS/bin/out/test.single.b.score.epacts.R --vanilla
export GDFONTPATH=/home/bohuang/local/EPACTS/share/EPACTS; export GNUPLOT_FONTPATH=/home/bohuang/local/EPACTS/share/EPACTS; export GNUPLOT_PS_DIR=/home/bohuang/local/EPACTS/share/EPACTS; export PATH=$PATH:/home/bohuang/local/EPACTS/bin/; export GNUPLOT_PFBTOPFA="pfbtops %s"; gnuplot /home/bohuang/local/EPACTS/bin/out/test.single.b.score.epacts.cmd
export GDFONTPATH=/home/bohuang/local/EPACTS/share/EPACTS; export GNUPLOT_FONTPATH=/home/bohuang/local/EPACTS/share/EPACTS; export GNUPLOT_PS_DIR=/home/bohuang/local/EPACTS/share/EPACTS; export PATH=$PATH:/home/bohuang/local/EPACTS/bin/; export GNUPLOT_PFBTOPFA="pfbtops %s"; /home/bohuang/local/EPACTS/bin/epstopdf /home/bohuang/local/EPACTS/bin/out/test.single.b.score.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=/home/bohuang/local/EPACTS/share/EPACTS; export GNUPLOT_FONTPATH=/home/bohuang/local/EPACTS/share/EPACTS; export GNUPLOT_PS_DIR=/home/bohuang/local/EPACTS/share/EPACTS; export PATH=$PATH:/home/bohuang/local/EPACTS/bin/; export GNUPLOT_PFBTOPFA="pfbtops %s"; gnuplot /home/bohuang/local/EPACTS/bin/out/test.single.b.score.epacts.cmd
export GDFONTPATH=/home/bohuang/local/EPACTS/share/EPACTS; export GNUPLOT_FONTPATH=/home/bohuang/local/EPACTS/share/EPACTS; export GNUPLOT_PS_DIR=/home/bohuang/local/EPACTS/share/EPACTS; export PATH=$PATH:/home/bohuang/local/EPACTS/bin/; export GNUPLOT_PFBTOPFA="pfbtops %s"; /home/bohuang/local/EPACTS/bin/epstopdf /home/bohuang/local/EPACTS/bin/out/test.single.b.score.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/bohuang/local/EPACTS/bin/out/test.single.b.score.epacts.cmd /home/bohuang/local/EPACTS/bin/out/test.single.b.score.epacts.qq.eps /home/bohuang/local/EPACTS/bin/out/test.single.b.score.epacts.mh.eps /home/bohuang/local/EPACTS/bin/out/test.single.b.score.epacts.*.dat
zcat /home/bohuang/local/EPACTS/bin/out/test.single.b.score.epacts.gz | awk '$9 != "NA" { print $0 }' | sort -g -k 9 | head -n 5000 > /home/bohuang/local/EPACTS/bin/out/test.single.b.score.epacts.top5000
/home/bohuang/local/EPACTS/bin/epacts-zoom --vcf /home/bohuang/local/EPACTS/bin/./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz --prefix /home/bohuang/local/EPACTS/bin/out/test.single.b.score --top 1
SNP ID : 20:1610894
Examining +-300000 bp window
Examining genomic region 20:1310894-1910894
Index SNP's cM position is 5.854019
Unextended interval is 20:1610894-1610894 (0 bps)
Extending the intervals by .02 cM
export GDFONTPATH=/home/bohuang/local/EPACTS/share/EPACTS; export GNUPLOT_FONTPATH=/home/bohuang/local/EPACTS/share/EPACTS; export GNUPLOT_PS_DIR=/home/bohuang/local/EPACTS/share/EPACTS; export PATH=$PATH:/home/bohuang/local/EPACTS/bin/; export GNUPLOT_PFBTOPFA="pfbtops %s"; gnuplot /home/bohuang/local/EPACTS/bin/out/test.single.b.score.zoom.20.1610894.cmd
export GDFONTPATH=/home/bohuang/local/EPACTS/share/EPACTS; export GNUPLOT_FONTPATH=/home/bohuang/local/EPACTS/share/EPACTS; export GNUPLOT_PS_DIR=/home/bohuang/local/EPACTS/share/EPACTS; export PATH=$PATH:/home/bohuang/local/EPACTS/bin/; export GNUPLOT_PFBTOPFA="pfbtops %s"; /home/bohuang/local/EPACTS/bin/epstopdf /home/bohuang/local/EPACTS/bin/out/test.single.b.score.zoom.20.1610894.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
touch /home/bohuang/local/EPACTS/bin/out/test.single.b.score.epacts.OK
Creating Empirical Kinship matrix...
Kinship : Processing chromosome 20...
Finished generating EPACTS Makefile
Running 5 parallel jobs of EPACTS
make -f out/test.single.q.emmax.kinf.Makefile -j 5
The following parameters are available. Ones with "[]" are in effect:
Available Options
Input Options : --vcf [./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz],
--indf [out/test.single.q.emmax.kinf.ind],
The following parameters are available. Ones with "[]" are in effect:
Available Options
Input Options : --vcf [./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz],
--indf [out/test.single.q.emmax.kinf.ind],
--region [20:10000001-20000000], --unit [10000],
--field [GT], --rule [], --ignoreFilter [ON]
Filtering Options : --weight [], --minMAF [0.01],
--minCallRate [0.95], --minRSQ [0.00]
Empircial Kinship Method : --BN [ON], --IBS
Output Options : --out-kinf [out/test.single.q.emmax.kinf.20.10000001.20000000.kin],
--raw [ON], --adj-diag, --cov, --verbose
The following parameters are available. Ones with "[]" are in effect:
Available Options
Input Options : --vcf [./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz],
--indf [out/test.single.q.emmax.kinf.ind],
The following parameters are available. Ones with "[]" are in effect:
--region [20:20000001-30000000]
Available Options
Input Options : --vcf [./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz],
--region [20:30000001-40000000]NOTICE - nInds = 266 : HG00096 ..., --unit [10000]
,
--field [GT], --rule [], --ignoreFilter [ON]
Filtering Options : --weight [], --minMAF [0.01],
--minCallRate [0.95], --minRSQ [0.00]
Empircial Kinship Method : --BN [ON], --IBS
Output Options : --out-kinf [out/test.single.q.emmax.kinf.20.30000001.40000000.kin],
--raw [ON], --adj-diag, --cov, --verbose
The following parameters are available. Ones with "[]" are in effect:
Available Options
, --unit [10000],
--indf [out/test.single.q.emmax.kinf.ind],
--region [20:1-10000000], --unit [10000],
--field [GT], --rule [], --ignoreFilter [ON]
Filtering Options :
--weight [], --minMAF [0.01],
--minCallRate [0.95], --minRSQ [0.00]
Empircial Kinship Method :
--BN [ON], --IBS
Output Options : --out-kinf [out/test.single.q.emmax.kinf.20.1.10000000.kin],
--raw [ON], --adj-diag, --cov, --verbose
NOTICE - NOTICE - nInds = 266 : HG00096 ...nInds = 266 : HG00096 ...
Input Options : --vcf [./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz],
--indf [out/test.single.q.emmax.kinf.ind],
--region [20:40000001-50000000], --unit [10000],
--field [GT], --rule [], --ignoreFilter [ON]
Filtering Options : --weight [], --minMAF [0.01],
--minCallRate [0.95], --minRSQ [0.00]
Empircial Kinship Method : --BN [ON], --IBS
Output Options : --out-kinf [out/test.single.q.emmax.kinf.20.40000001.50000000.kin],
--raw [ON], --adj-diag, --cov, --verbose
NOTICE - nInds = 266 : HG00096 ...
--field [GT], --rule [], --ignoreFilter [ON]
Filtering Options : --weight [], --minMAF [0.01],
--minCallRate [0.95], --minRSQ [0.00]
Empircial Kinship Method : --BN [ON], --IBS
Output Options : --out-kinf [out/test.single.q.emmax.kinf.20.20000001.30000000.kin],
--raw [ON], --adj-diag, --cov, --verbose
NOTICE - nInds = 266 : HG00096 ...
NOTICE - Processing 1466 markers across 266 individuals...
192 markers included
NOTICE - Processing 3662 markers across 266 individuals...
493 markers included
NOTICE - Started writing kinship matrix into out/test.single.q.emmax.kinf.20.20000001.30000000.kin
NOTICE - Allocating a memory of size 284112
NOTICE - Finished writing kinship matrix into out/test.single.q.emmax.kinf.20.20000001.30000000.kin
The following parameters are available. Ones with "[]" are in effect:
Available Options
Input Options : --vcf [./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz],
--indf [out/test.single.q.emmax.kinf.ind],
--region [20:50000001-60000000], --unit [10000],
--field [GT], --rule [], --ignoreFilter [ON]
Filtering Options : --weight [], --minMAF [0.01],
--minCallRate [0.95], --minRSQ [0.00]NOTICE -
Empircial Kinship Method : --BN [ON], --IBS
Output Options : --out-kinf [out/test.single.q.emmax.kinf.20.50000001.60000000.kin],
--raw [ON], --adj-diag, --cov, --verbose
Started writing kinship matrix into out/test.single.q.emmax.kinf.20.40000001.50000000.kin
NOTICE - Allocating a memory of size 284112
NOTICE - Finished writing kinship matrix into out/test.single.q.emmax.kinf.20.40000001.50000000.kin
NOTICE - nInds = 266 : HG00096 ...
The following parameters are available. Ones with "[]" are in effect:
Available Options
Input Options : --vcf [./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz],
--indf [out/test.single.q.emmax.kinf.ind],
--region [20:60000001-63025520], --unit [10000],
--field [GT], --rule [], --ignoreFilter [ON]
Filtering Options : --weight [], --minMAF [0.01],
--minCallRate [0.95], --minRSQ [0.00]
Empircial Kinship Method : --BN [ON], --IBS
Output Options : --out-kinf [out/test.single.q.emmax.kinf.20.60000001.63025520.kin],
--raw [ON], --adj-diag, --cov, --verbose
NOTICE - nInds = 266 : HG00096 ...
NOTICE - Processing 3367 markers across 266 individuals...
582 markers included
NOTICE - Started writing kinship matrix into out/test.single.q.emmax.kinf.20.1.10000000.kin
NOTICE - Allocating a memory of size 284112
NOTICE - Finished writing kinship matrix into out/test.single.q.emmax.kinf.20.1.10000000.kin
NOTICE - Processing 1763 markers across 266 individuals...
256 markers included
NOTICE - Started writing kinship matrix into out/test.single.q.emmax.kinf.20.50000001.60000000.kin
NOTICE - Allocating a memory of size 284112
NOTICE - Finished writing kinship matrix into out/test.single.q.emmax.kinf.20.50000001.60000000.kin
NOTICE - Processing 1248 markers across 266 individuals...
191 markers included
NOTICE - Started writing kinship matrix into out/test.single.q.emmax.kinf.20.10000001.20000000.kin
NOTICE - Allocating a memory of size 284112
NOTICE - Finished writing kinship matrix into out/test.single.q.emmax.kinf.20.10000001.20000000.kin
NOTICE - Processing 3425 markers across 266 individuals...
557 markers included
NOTICE - Started writing kinship matrix into out/test.single.q.emmax.kinf.20.60000001.63025520.kin
NOTICE - Allocating a memory of size 284112
NOTICE - Finished writing kinship matrix into out/test.single.q.emmax.kinf.20.60000001.63025520.kin
NOTICE - Processing 4170 markers across 266 individuals...
442 markers included
NOTICE - Started writing kinship matrix into out/test.single.q.emmax.kinf.20.30000001.40000000.kin
NOTICE - Allocating a memory of size 284112
NOTICE - Finished writing kinship matrix into out/test.single.q.emmax.kinf.20.30000001.40000000.kin
The following parameters are available. Ones with "[]" are in effect:
Available Options
Input Options : --raw, --cov
Empircial Kinship Method : --BN [ON], --IBS, --YV
Output Options : --out-kinf [out/test.single.q.emmax.kinf],
--verbose
NOTICE - Merging the following kinship matrices
NOTICE - Allocating size 284088 bytes..
NOTICE - Allocating size 284088 bytes..
NOTICE - Allocating size 284088 bytes..
NOTICE - Allocating size 284088 bytes..
NOTICE - Allocating size 284088 bytes..
NOTICE - Allocating size 284088 bytes..
NOTICE - Allocating size 284088 bytes..
NOTICE - Allocating a memory of size 284112
/home/bohuang/local/EPACTS/bin/pEmmax gen-kin --vcf ./../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
/home/bohuang/local/EPACTS/bin/pEmmax gen-kin --vcf ./../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
/home/bohuang/local/EPACTS/bin/pEmmax gen-kin --vcf ./../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
/home/bohuang/local/EPACTS/bin/pEmmax gen-kin --vcf ./../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
/home/bohuang/local/EPACTS/bin/pEmmax gen-kin --vcf ./../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
/home/bohuang/local/EPACTS/bin/pEmmax gen-kin --vcf ./../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
/home/bohuang/local/EPACTS/bin/pEmmax gen-kin --vcf ./../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
/home/bohuang/local/EPACTS/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...
Detected phenotypes with more than 3 unique values -- considering as quantitative phenotypes.
Successfully written phenotypes and 2 covariates across 266 individuals
Processing chromosome 20...
Finished generating EPACTS Makefile
Running 5 parallel jobs of EPACTS
forkExecWait(): make -f /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.Makefile -j 5
/home/bohuang/local/EPACTS/bin/pEmmax assoc --vcf /home/bohuang/local/EPACTS/bin/./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz --region 20:1-10000000 --phenof /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.phe --field GT --indf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.ind --eigf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.eigR --remlf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.reml --out-assocf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.1.10000000.epacts --minMAF 0.001 --maxMAF 1 --maxMAC 1000000000 --minRSQ 0 --minCallRate 0.5 --minMAC 3
/home/bohuang/local/EPACTS/bin/pEmmax assoc --vcf /home/bohuang/local/EPACTS/bin/./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz --region 20:10000001-20000000 --phenof /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.phe --field GT --indf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.ind --eigf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.eigR --remlf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.reml --out-assocf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.10000001.20000000.epacts --minMAF 0.001 --maxMAF 1 --maxMAC 1000000000 --minRSQ 0 --minCallRate 0.5 --minMAC 3
/home/bohuang/local/EPACTS/bin/pEmmax assoc --vcf /home/bohuang/local/EPACTS/bin/./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz --region 20:20000001-30000000 --phenof /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.phe --field GT --indf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.ind --eigf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.eigR --remlf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.reml --out-assocf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.20000001.30000000.epacts --minMAF 0.001 --maxMAF 1 --maxMAC 1000000000 --minRSQ 0 --minCallRate 0.5 --minMAC 3
/home/bohuang/local/EPACTS/bin/pEmmax assoc --vcf /home/bohuang/local/EPACTS/bin/./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz --region 20:30000001-40000000 --phenof /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.phe --field GT --indf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.ind --eigf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.eigR --remlf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.reml --out-assocf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.30000001.40000000.epacts --minMAF 0.001 --maxMAF 1 --maxMAC 1000000000 --minRSQ 0 --minCallRate 0.5 --minMAC 3
/home/bohuang/local/EPACTS/bin/pEmmax assoc --vcf /home/bohuang/local/EPACTS/bin/./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz --region 20:40000001-50000000 --phenof /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.phe --field GT --indf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.ind --eigf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.eigR --remlf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.reml --out-assocf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.40000001.50000000.epacts --minMAF 0.001 --maxMAF 1 --maxMAC 1000000000 --minRSQ 0 --minCallRate 0.5 --minMAC 3
The following parameters are available. Ones with "[]" are in effect:
Available Options
VCF Input Options : --vcf [/home/bohuang/local/EPACTS/bin/./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz],
--region [20:1-10000000], --unit [10000],
--indf [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.ind],
--field [GT], --rule []
The following parameters are available. Ones with "[]" are in effect:
Available Options
VCF Input Options : --vcf [/home/bohuang/local/EPACTS/bin/./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz], --minMAF [1.0e-03],
--maxMAF [1.00], --minMAC [3], --maxMAC [1000000000],
--minCallRate [0.50], --minRSQ [0.00], --ignoreFilter
Other Input Options : --phenof [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.phe],
,
--region [20:30000001-40000000], --unit [10000],
--indf [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.ind],
--field [GT], --rule [], --minMAF [1.0e-03],
--maxMAF [1.00], --minMAC [3], --maxMAC [1000000000],
--minCallRate [0.50]
The following parameters are available. Ones with "[]" are in effect:
--eigf [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.eigR],
--remlf [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.reml], --minRSQ [0.00]
Output Options : --out-assocf [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.1.10000000.epacts], --ignoreFilter,
--verbose
Other Input Options : --phenof [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.phe],
--eigf [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.eigR],
--remlf [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.reml]
Output Options : --out-assocf [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.30000001.40000000.epacts],
--verbose
NOTICE -
Reading eigenvectors
Available Options
VCF Input Options : --vcf [/home/bohuang/local/EPACTS/bin/./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz],
--region [20:20000001-30000000], --unit [10000],
--indf [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.ind],
--field [GT], --rule [], --minMAF [1.0e-03],
--maxMAF [1.00], --minMAC [3], --maxMAC [1000000000],
--minCallRate [0.50], --minRSQ [0.00], --ignoreFilter
Other Input Options : --phenof [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.phe],
--eigf [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.eigR],
--remlf [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.reml]
Output Options : --out-assocf [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.20000001.30000000.epacts],
--verbose
The following parameters are available. Ones with "[]" are in effect:
NOTICE - Reading eigenvectors
Available Options
VCF Input Options : --vcf [/home/bohuang/local/EPACTS/bin/./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz],
--region [20:10000001-20000000], --unit [10000],
--indf [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.ind],
--field [GT], --rule [], --minMAF [1.0e-03],
--maxMAF [1.00], --minMAC [3], --maxMAC [1000000000],
--minCallRate [0.50], --minRSQ [0.00], --ignoreFilter
Other Input Options : --phenof [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.phe],
--eigf [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.eigR],
--remlf [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.reml]
Output Options : --out-assocf [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.10000001.20000000.epacts],
--verbose
NOTICE - Reading eigenvectors
NOTICE - NOTICE - Allocating a size 70221 bytes
NOTICE - Allocating a size 70221 bytes
The following parameters are available. Ones with "[]" are in effect:
Available Options
VCF Input Options : --vcf [/home/bohuang/local/EPACTS/bin/./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz],
--region [20:40000001-50000000], --unit [10000],
--indf [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.ind],
--field [GT], --rule [], --minMAF [1.0e-03],
--maxMAF [1.00], --minMAC [3], --maxMAC [1000000000],
--minCallRate [0.50], --minRSQ [0.00], --ignoreFilter
Other Input Options : --phenof [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.phe],
--eigf [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.eigR],
--remlf [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.reml]
Output Options : --out-assocf [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.40000001.50000000.epacts],
--verbose
NOTICE - Reading eigenvectors
NOTICE - Allocating a size 70221 bytes
Reading eigenvectors
NOTICE - Allocating a size 70221 bytes
NOTICE - Finished loading phenotypes across 266 individuals with 1 covariates (including interception)
NOTICE - NOTICE - Finished loading phenotypes across 266 individuals with 1 covariates (including interception)
NOTICE - NOTICE - Finished loading phenotypes across 266 individuals with 1 covariates (including interception)
Finished loading phenotypes across 266 individuals with 1 covariates (including interception)
NOTICE - Reading delta = 50.118679
NOTICE - Reading delta = 50.118679
NOTICE - Reading delta = 50.118679
Allocating a size 70221 bytes
NOTICE - Finished loading phenotypes across 266 individuals with 1 covariates (including interception)
NOTICE - Reading delta = 50.118679
NOTICE - Reading delta = 50.118679
NOTICE - Processing 1225 markers across 266 individuals...
243 markers included
/home/bohuang/local/EPACTS/bin/epacts-anno --in /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.10000001.20000000.epacts --ref /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta
/home/bohuang/local/EPACTS/bin/anno -i /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.10000001.20000000.epacts -r /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta -f refGene -g /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz -c /home/bohuang/local/EPACTS/share/EPACTS/codon.txt -o /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.10000001.20000000.epacts.tmp --inputFormat epacts -p /home/bohuang/local/EPACTS/share/EPACTS/priority.txt
The following parameters are available. Ones with "[]" are in effect:
Available Options
Required Parameters :
-i [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.10000001.20000000.epacts]
-o [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.10000001.20000000.epacts.tmp]
Gene Annotation
Parameters : -g [/home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz]
-r [/home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta]
--inputFormat [epacts], --checkReference, -f [refGene]
-p [/home/bohuang/local/EPACTS/share/EPACTS/priority.txt]
-c [/home/bohuang/local/EPACTS/share/EPACTS/codon.txt]
-u [], -d [], --se [], --si [], --outputFormat []
Other Annotation Tools : --genomeScore [], --bed [], --tabix []
Load reference genome /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta...
DONE: 84 chromosomes and 3101804739 bases are loaded.
Load codon file /home/bohuang/local/EPACTS/share/EPACTS/codon.txt...
DONE: codon file loaded.
Load priority file /home/bohuang/local/EPACTS/share/EPACTS/priority.txt...
DONE: 24 priority annotation types loaded.
Load gene file /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz...
NOTICE - Processing 1423 markers across 266 individuals...
231 markers included
/home/bohuang/local/EPACTS/bin/epacts-anno --in /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.20000001.30000000.epacts --ref /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta
/home/bohuang/local/EPACTS/bin/anno -i /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.20000001.30000000.epacts -r /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta -f refGene -g /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz -c /home/bohuang/local/EPACTS/share/EPACTS/codon.txt -o /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.20000001.30000000.epacts.tmp --inputFormat epacts -p /home/bohuang/local/EPACTS/share/EPACTS/priority.txt
The following parameters are available. Ones with "[]" are in effect:
Available Options
Required Parameters :
-i [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.20000001.30000000.epacts]
-o [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.20000001.30000000.epacts.tmp]
Gene Annotation
Parameters : -g [/home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz]
-r [/home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta]
--inputFormat [epacts], --checkReference, -f [refGene]
-p [/home/bohuang/local/EPACTS/share/EPACTS/priority.txt]
-c [/home/bohuang/local/EPACTS/share/EPACTS/codon.txt]
-u [], -d [], --se [], --si [], --outputFormat []
Other Annotation Tools : --genomeScore [], --bed [], --tabix []
Load reference genome /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta...
DONE: 84 chromosomes and 3101804739 bases are loaded.
Load codon file /home/bohuang/local/EPACTS/share/EPACTS/codon.txt...
DONE: codon file loaded.
Load priority file /home/bohuang/local/EPACTS/share/EPACTS/priority.txt...
DONE: 24 priority annotation types loaded.
Load gene file /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz...
NOTICE - Processing 4061 markers across 266 individuals...
NOTICE - Processing 3578 markers across 266 individuals...
NOTICE - Processing 3245 markers across 266 individuals...
550 markers included
/home/bohuang/local/EPACTS/bin/epacts-anno --in /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.30000001.40000000.epacts --ref /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta
634 markers included
/home/bohuang/local/EPACTS/bin/epacts-anno --in /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.1.10000000.epacts --ref /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta
612 markers included
/home/bohuang/local/EPACTS/bin/epacts-anno --in /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.40000001.50000000.epacts --ref /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta
/home/bohuang/local/EPACTS/bin/anno -i /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.1.10000000.epacts -r /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta -f refGene -g /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz -c /home/bohuang/local/EPACTS/share/EPACTS/codon.txt -o /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.1.10000000.epacts.tmp --inputFormat epacts -p /home/bohuang/local/EPACTS/share/EPACTS/priority.txt
/home/bohuang/local/EPACTS/bin/anno -i /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.30000001.40000000.epacts -r /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta -f refGene -g /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz -c /home/bohuang/local/EPACTS/share/EPACTS/codon.txt -o /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.30000001.40000000.epacts.tmp --inputFormat epacts -p /home/bohuang/local/EPACTS/share/EPACTS/priority.txt
The following parameters are available. Ones with "[]" are in effect:
Available Options
Required Parameters :
-i [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.30000001.40000000.epacts]
-o [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.30000001.40000000.epacts.tmp]
Gene Annotation
Parameters : -g [/home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz]
-r [/home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta]
--inputFormat [epacts], --checkReference, -f [refGene]
-p [/home/bohuang/local/EPACTS/share/EPACTS/priority.txt]
-c [/home/bohuang/local/EPACTS/share/EPACTS/codon.txt]
-u [], -d [], --se [], --si [], --outputFormat []
Other Annotation Tools : --genomeScore [], --bed [], --tabix []
Load reference genome /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta...
DONE: 84 chromosomes and 3101804739 bases are loaded.
Load codon file /home/bohuang/local/EPACTS/share/EPACTS/codon.txt...
DONE: codon file loaded.
Load priority file /home/bohuang/local/EPACTS/share/EPACTS/priority.txt...
DONE: 24 priority annotation types loaded.
Load gene file /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz...
The following parameters are available. Ones with "[]" are in effect:
Available Options
Required Parameters :
-i [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.1.10000000.epacts]
-o [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.1.10000000.epacts.tmp]
Gene Annotation
Parameters : -g [/home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz]
-r [/home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta]
--inputFormat [epacts], --checkReference, -f [refGene]
-p [/home/bohuang/local/EPACTS/share/EPACTS/priority.txt]
-c [/home/bohuang/local/EPACTS/share/EPACTS/codon.txt]
-u [], -d [], --se [], --si [], --outputFormat []
Other Annotation Tools : --genomeScore [], --bed [], --tabix []
Load reference genome /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta...
DONE: 84 chromosomes and 3101804739 bases are loaded.
Load codon file /home/bohuang/local/EPACTS/share/EPACTS/codon.txt...
DONE: codon file loaded.
Load priority file /home/bohuang/local/EPACTS/share/EPACTS/priority.txt...
DONE: 24 priority annotation types loaded.
Load gene file /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz...
/home/bohuang/local/EPACTS/bin/anno -i /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.40000001.50000000.epacts -r /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta -f refGene -g /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz -c /home/bohuang/local/EPACTS/share/EPACTS/codon.txt -o /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.40000001.50000000.epacts.tmp --inputFormat epacts -p /home/bohuang/local/EPACTS/share/EPACTS/priority.txt
The following parameters are available. Ones with "[]" are in effect:
Available Options
Required Parameters :
-i [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.40000001.50000000.epacts]
-o [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.40000001.50000000.epacts.tmp]
Gene Annotation
Parameters : -g [/home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz]
-r [/home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta]
--inputFormat [epacts], --checkReference, -f [refGene]
-p [/home/bohuang/local/EPACTS/share/EPACTS/priority.txt]
-c [/home/bohuang/local/EPACTS/share/EPACTS/codon.txt]
-u [], -d [], --se [], --si [], --outputFormat []
Other Annotation Tools : --genomeScore [], --bed [], --tabix []
Load reference genome /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta...
DONE: 84 chromosomes and 3101804739 bases are loaded.
Load codon file /home/bohuang/local/EPACTS/share/EPACTS/codon.txt...
DONE: codon file loaded.
Load priority file /home/bohuang/local/EPACTS/share/EPACTS/priority.txt...
DONE: 24 priority annotation types loaded.
Load gene file /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz...
DONE: 92627 gene loaded.
DONE: Generated frequency of each annotype type in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.20000001.30000000.epacts.tmp.anno.frq ].
DONE: Generated frequency of each highest priority annotation type in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.20000001.30000000.epacts.tmp.top.anno.frq ].
Ts/Tv ratio: 2.6581
Ts observed: 1034 times; Tv observed: 389 times.
DONE: Generated frequency of each base change in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.20000001.30000000.epacts.tmp.base.frq ].
DONE: Generated frequency of each codon change in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.20000001.30000000.epacts.tmp.codon.frq ].
DONE: Generated frequency of indel length in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.20000001.30000000.epacts.tmp.indel.frq ].
..............................................
... Anno(tation) ...
... Xiaowei Zhan, Goncalo Abecasis ...
... Speical Thanks: ...
... Hyun Ming Kang, Yanming Li ...
... zha...@umich.edu ...
... Sep 2011 ...
................................................
DONE: 1423 varaints are annotated.
DONE: Generated annotation output in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.20000001.30000000.epacts.tmp ].
Annotation succeed!
mv /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.20000001.30000000.epacts.tmp /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.20000001.30000000.epacts
rm /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.20000001.30000000.epacts.tmp.log /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.20000001.30000000.epacts.tmp.top.anno.frq /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.20000001.30000000.epacts.tmp.anno.frq /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.20000001.30000000.epacts.tmp.base.frq /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.20000001.30000000.epacts.tmp.codon.frq /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.20000001.30000000.epacts.tmp.indel.frq
/home/bohuang/local/EPACTS/bin/pEmmax assoc --vcf /home/bohuang/local/EPACTS/bin/./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz --region 20:50000001-60000000 --phenof /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.phe --field GT --indf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.ind --eigf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.eigR --remlf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.reml --out-assocf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.50000001.60000000.epacts --minMAF 0.001 --maxMAF 1 --maxMAC 1000000000 --minRSQ 0 --minCallRate 0.5 --minMAC 3
The following parameters are available. Ones with "[]" are in effect:
Available Options
VCF Input Options : --vcf [/home/bohuang/local/EPACTS/bin/./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz],
--region [20:50000001-60000000], --unit [10000],
--indf [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.ind],
--field [GT], --rule [], --minMAF [1.0e-03],
--maxMAF [1.00], --minMAC [3], --maxMAC [1000000000],
--minCallRate [0.50], --minRSQ [0.00], --ignoreFilter
Other Input Options : --phenof [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.phe],
--eigf [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.eigR],
--remlf [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.reml]
Output Options : --out-assocf [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.50000001.60000000.epacts],
--verbose
NOTICE - Reading eigenvectors
NOTICE - Allocating a size 70221 bytes
NOTICE - Finished loading phenotypes across 266 individuals with 1 covariates (including interception)
NOTICE - Reading delta = 50.118679
DONE: 92627 gene loaded.
DONE: 92627 gene loaded.
NOTICE - Processing 1732 markers across 266 individuals...
309 markers included
/home/bohuang/local/EPACTS/bin/epacts-anno --in /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.50000001.60000000.epacts --ref /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta
DONE: Generated frequency of each annotype type in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.40000001.50000000.epacts.tmp.anno.frq ].
DONE: Generated frequency of each highest priority annotation type in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.40000001.50000000.epacts.tmp.top.anno.frq ].
Ts/Tv ratio: 2.73486
Ts observed: 2620 times; Tv observed: 958 times.
DONE: Generated frequency of each base change in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.40000001.50000000.epacts.tmp.base.frq ].
DONE: Generated frequency of each codon change in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.40000001.50000000.epacts.tmp.codon.frq ].
DONE: Generated frequency of indel length in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.40000001.50000000.epacts.tmp.indel.frq ].
/home/bohuang/local/EPACTS/bin/anno -i /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.50000001.60000000.epacts -r /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta -f refGene -g /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz -c /home/bohuang/local/EPACTS/share/EPACTS/codon.txt -o /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.50000001.60000000.epacts.tmp --inputFormat epacts -p /home/bohuang/local/EPACTS/share/EPACTS/priority.txt
..............................................
... Anno(tation) ...
... Xiaowei Zhan, Goncalo Abecasis ...
... Speical Thanks: ...
... Hyun Ming Kang, Yanming Li ...
... zha...@umich.edu ...
... Sep 2011 ...
................................................
DONE: 3578 varaints are annotated.
DONE: Generated annotation output in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.40000001.50000000.epacts.tmp ].
Annotation succeed!
mv /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.40000001.50000000.epacts.tmp /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.40000001.50000000.epacts
The following parameters are available. Ones with "[]" are in effect:
Available Options
Required Parameters :
-i [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.50000001.60000000.epacts]
-o [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.50000001.60000000.epacts.tmp]
Gene Annotation
Parameters : -g [/home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz]
-r [/home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta]
--inputFormat [epacts], --checkReference, -f [refGene]
-p [/home/bohuang/local/EPACTS/share/EPACTS/priority.txt]
-c [/home/bohuang/local/EPACTS/share/EPACTS/codon.txt]
-u [], -d [], --se [], --si [], --outputFormat []
Other Annotation Tools : --genomeScore [], --bed [], --tabix []
rm /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.40000001.50000000.epacts.tmp.log /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.40000001.50000000.epacts.tmp.top.anno.frq /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.40000001.50000000.epacts.tmp.anno.frq /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.40000001.50000000.epacts.tmp.base.frq /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.40000001.50000000.epacts.tmp.codon.frq /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.40000001.50000000.epacts.tmp.indel.frq
Load reference genome /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta...
DONE: 84 chromosomes and 3101804739 bases are loaded.
Load codon file /home/bohuang/local/EPACTS/share/EPACTS/codon.txt...
DONE: codon file loaded.
Load priority file /home/bohuang/local/EPACTS/share/EPACTS/priority.txt...
DONE: 24 priority annotation types loaded.
Load gene file /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz...
/home/bohuang/local/EPACTS/bin/pEmmax assoc --vcf /home/bohuang/local/EPACTS/bin/./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz --region 20:60000001-63025520 --phenof /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.phe --field GT --indf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.ind --eigf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.eigR --remlf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.reml --out-assocf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.60000001.63025520.epacts --minMAF 0.001 --maxMAF 1 --maxMAC 1000000000 --minRSQ 0 --minCallRate 0.5 --minMAC 3
The following parameters are available. Ones with "[]" are in effect:
Available Options
VCF Input Options : --vcf [/home/bohuang/local/EPACTS/bin/./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz],
--region [20:60000001-63025520], --unit [10000],
--indf [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.ind],
--field [GT], --rule [], --minMAF [1.0e-03],
--maxMAF [1.00], --minMAC [3], --maxMAC [1000000000],
--minCallRate [0.50], --minRSQ [0.00], --ignoreFilter
Other Input Options : --phenof [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.phe],
--eigf [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.eigR],
--remlf [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.reml]
Output Options : --out-assocf [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.60000001.63025520.epacts],
--verbose
NOTICE - Reading eigenvectors
NOTICE - Allocating a size 70221 bytes
DONE: 92627 gene loaded.
NOTICE - Finished loading phenotypes across 266 individuals with 1 covariates (including interception)
NOTICE - Reading delta = 50.118679
DONE: Generated frequency of each annotype type in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.1.10000000.epacts.tmp.anno.frq ].
DONE: Generated frequency of each highest priority annotation type in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.1.10000000.epacts.tmp.top.anno.frq ].
Ts/Tv ratio: 2.96215
Ts observed: 2426 times; Tv observed: 819 times.
DONE: Generated frequency of each base change in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.1.10000000.epacts.tmp.base.frq ].
DONE: Generated frequency of each codon change in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.1.10000000.epacts.tmp.codon.frq ].
DONE: Generated frequency of indel length in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.1.10000000.epacts.tmp.indel.frq ].
DONE: Generated frequency of each annotype type in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.10000001.20000000.epacts.tmp.anno.frq ].
DONE: Generated frequency of each highest priority annotation type in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.10000001.20000000.epacts.tmp.top.anno.frq ].
Ts/Tv ratio: 2.91374
Ts observed: 912 times; Tv observed: 313 times.
DONE: Generated frequency of each base change in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.10000001.20000000.epacts.tmp.base.frq ].
DONE: Generated frequency of each codon change in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.10000001.20000000.epacts.tmp.codon.frq ].
DONE: Generated frequency of indel length in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.10000001.20000000.epacts.tmp.indel.frq ].
..............................................
... Anno(tation) ...
... Xiaowei Zhan, Goncalo Abecasis ...
... Speical Thanks: ...
... Hyun Ming Kang, Yanming Li ...
... zha...@umich.edu ...
... Sep 2011 ...
................................................
DONE: 1225 varaints are annotated.
DONE: Generated annotation output in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.10000001.20000000.epacts.tmp ].
Annotation succeed!
mv /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.10000001.20000000.epacts.tmp /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.10000001.20000000.epacts
..............................................
... Anno(tation) ...
... Xiaowei Zhan, Goncalo Abecasis ...
... Speical Thanks: ...
... Hyun Ming Kang, Yanming Li ...
... zha...@umich.edu ...
... Sep 2011 ...
................................................
DONE: 3245 varaints are annotated.
DONE: Generated annotation output in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.1.10000000.epacts.tmp ].
Annotation succeed!
mv /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.1.10000000.epacts.tmp /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.1.10000000.epacts
rm /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.10000001.20000000.epacts.tmp.log /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.10000001.20000000.epacts.tmp.top.anno.frq /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.10000001.20000000.epacts.tmp.anno.frq /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.10000001.20000000.epacts.tmp.base.frq /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.10000001.20000000.epacts.tmp.codon.frq /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.10000001.20000000.epacts.tmp.indel.frq
rm /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.1.10000000.epacts.tmp.log /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.1.10000000.epacts.tmp.top.anno.frq /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.1.10000000.epacts.tmp.anno.frq /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.1.10000000.epacts.tmp.base.frq /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.1.10000000.epacts.tmp.codon.frq /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.1.10000000.epacts.tmp.indel.frq
DONE: 92627 gene loaded.
NOTICE - Processing 3292 markers across 266 individuals...
DONE: Generated frequency of each annotype type in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.30000001.40000000.epacts.tmp.anno.frq ].
DONE: Generated frequency of each highest priority annotation type in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.30000001.40000000.epacts.tmp.top.anno.frq ].
Ts/Tv ratio: 2.96582
Ts observed: 3037 times; Tv observed: 1024 times.
DONE: Generated frequency of each base change in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.30000001.40000000.epacts.tmp.base.frq ].
DONE: Generated frequency of each codon change in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.30000001.40000000.epacts.tmp.codon.frq ].
DONE: Generated frequency of indel length in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.30000001.40000000.epacts.tmp.indel.frq ].
657 markers included
/home/bohuang/local/EPACTS/bin/epacts-anno --in /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.60000001.63025520.epacts --ref /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta
..............................................
... Anno(tation) ...
... Xiaowei Zhan, Goncalo Abecasis ...
... Speical Thanks: ...
... Hyun Ming Kang, Yanming Li ...
... zha...@umich.edu ...
... Sep 2011 ...
................................................
DONE: 4061 varaints are annotated.
DONE: Generated annotation output in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.30000001.40000000.epacts.tmp ].
Annotation succeed!
mv /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.30000001.40000000.epacts.tmp /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.30000001.40000000.epacts
rm /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.30000001.40000000.epacts.tmp.log /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.30000001.40000000.epacts.tmp.top.anno.frq /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.30000001.40000000.epacts.tmp.anno.frq /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.30000001.40000000.epacts.tmp.base.frq /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.30000001.40000000.epacts.tmp.codon.frq /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.30000001.40000000.epacts.tmp.indel.frq
/home/bohuang/local/EPACTS/bin/anno -i /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.60000001.63025520.epacts -r /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta -f refGene -g /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz -c /home/bohuang/local/EPACTS/share/EPACTS/codon.txt -o /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.60000001.63025520.epacts.tmp --inputFormat epacts -p /home/bohuang/local/EPACTS/share/EPACTS/priority.txt
The following parameters are available. Ones with "[]" are in effect:
Available Options
Required Parameters :
-i [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.60000001.63025520.epacts]
-o [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.60000001.63025520.epacts.tmp]
Gene Annotation
Parameters : -g [/home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz]
-r [/home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta]
--inputFormat [epacts], --checkReference, -f [refGene]
-p [/home/bohuang/local/EPACTS/share/EPACTS/priority.txt]
-c [/home/bohuang/local/EPACTS/share/EPACTS/codon.txt]
-u [], -d [], --se [], --si [], --outputFormat []
Other Annotation Tools : --genomeScore [], --bed [], --tabix []
Load reference genome /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta...
DONE: 84 chromosomes and 3101804739 bases are loaded.
Load codon file /home/bohuang/local/EPACTS/share/EPACTS/codon.txt...
DONE: codon file loaded.
Load priority file /home/bohuang/local/EPACTS/share/EPACTS/priority.txt...
DONE: 24 priority annotation types loaded.
Load gene file /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz...
DONE: 92627 gene loaded.
DONE: Generated frequency of each annotype type in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.60000001.63025520.epacts.tmp.anno.frq ].
DONE: Generated frequency of each highest priority annotation type in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.60000001.63025520.epacts.tmp.top.anno.frq ].
Ts/Tv ratio: 4.03364
Ts observed: 2638 times; Tv observed: 654 times.
DONE: Generated frequency of each base change in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.60000001.63025520.epacts.tmp.base.frq ].
DONE: Generated frequency of each codon change in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.60000001.63025520.epacts.tmp.codon.frq ].
DONE: Generated frequency of indel length in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.60000001.63025520.epacts.tmp.indel.frq ].
..............................................
... Anno(tation) ...
... Xiaowei Zhan, Goncalo Abecasis ...
... Speical Thanks: ...
... Hyun Ming Kang, Yanming Li ...
... zha...@umich.edu ...
... Sep 2011 ...
................................................
DONE: 3292 varaints are annotated.
DONE: Generated annotation output in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.60000001.63025520.epacts.tmp ].
Annotation succeed!
mv /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.60000001.63025520.epacts.tmp /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.60000001.63025520.epacts
rm /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.60000001.63025520.epacts.tmp.log /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.60000001.63025520.epacts.tmp.top.anno.frq /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.60000001.63025520.epacts.tmp.anno.frq /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.60000001.63025520.epacts.tmp.base.frq /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.60000001.63025520.epacts.tmp.codon.frq /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.60000001.63025520.epacts.tmp.indel.frq
DONE: 92627 gene loaded.
DONE: Generated frequency of each annotype type in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.50000001.60000000.epacts.tmp.anno.frq ].
DONE: Generated frequency of each highest priority annotation type in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.50000001.60000000.epacts.tmp.top.anno.frq ].
Ts/Tv ratio: 2.66173
Ts observed: 1259 times; Tv observed: 473 times.
DONE: Generated frequency of each base change in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.50000001.60000000.epacts.tmp.base.frq ].
DONE: Generated frequency of each codon change in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.50000001.60000000.epacts.tmp.codon.frq ].
DONE: Generated frequency of indel length in [ /home/bohuang/local/EPACTS/bin/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 ...
... zha...@umich.edu ...
... Sep 2011 ...
................................................
DONE: 1732 varaints are annotated.
DONE: Generated annotation output in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.50000001.60000000.epacts.tmp ].
Annotation succeed!
mv /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.50000001.60000000.epacts.tmp /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.50000001.60000000.epacts
rm /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.50000001.60000000.epacts.tmp.log /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.50000001.60000000.epacts.tmp.top.anno.frq /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.50000001.60000000.epacts.tmp.anno.frq /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.50000001.60000000.epacts.tmp.base.frq /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.50000001.60000000.epacts.tmp.codon.frq /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.50000001.60000000.epacts.tmp.indel.frq
/home/bohuang/local/EPACTS/bin/epacts-cat /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.1.10000000.epacts /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.10000001.20000000.epacts /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.20000001.30000000.epacts /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.30000001.40000000.epacts /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.40000001.50000000.epacts /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.50000001.60000000.epacts /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.60000001.63025520.epacts | /home/bohuang/local/EPACTS/bin/bgzip -c > /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.epacts.gz
/home/bohuang/local/EPACTS/bin/tabix -f -pbed /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.epacts.gz
rm -f /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.1.10000000.epacts /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.10000001.20000000.epacts /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.20000001.30000000.epacts /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.30000001.40000000.epacts /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.40000001.50000000.epacts /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.50000001.60000000.epacts /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.60000001.63025520.epacts
/home/bohuang/local/EPACTS/bin/epacts-plot --in /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.epacts.gz --region 20:0
nsnps = 3236
Rscript /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.epacts.R --vanilla
export GDFONTPATH=/home/bohuang/local/EPACTS/share/EPACTS; export GNUPLOT_FONTPATH=/home/bohuang/local/EPACTS/share/EPACTS; export GNUPLOT_PS_DIR=/home/bohuang/local/EPACTS/share/EPACTS; export PATH=$PATH:/home/bohuang/local/EPACTS/bin/; export GNUPLOT_PFBTOPFA="pfbtops %s"; gnuplot /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.epacts.cmd
export GDFONTPATH=/home/bohuang/local/EPACTS/share/EPACTS; export GNUPLOT_FONTPATH=/home/bohuang/local/EPACTS/share/EPACTS; export GNUPLOT_PS_DIR=/home/bohuang/local/EPACTS/share/EPACTS; export PATH=$PATH:/home/bohuang/local/EPACTS/bin/; export GNUPLOT_PFBTOPFA="pfbtops %s"; /home/bohuang/local/EPACTS/bin/epstopdf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.epacts.qq.eps
GPL Ghostscript 9.26: Unrecoverable error, exit code 1
Error: /undefined in LTB
Operand stack:
Execution stack:
%interp_exit .runexec2 --nostringval-- --nostringval-- --nostringval-- 2 %stopped_push --nostringval-- --nostringval-- --nostringval-- false 1 %stopped_push 2045 1 3 %oparray_pop 2044 1 3 %oparray_pop --nostringval-- 2025 1 3 %oparray_pop 1884 1 3 %oparray_pop --nostringval-- %errorexec_pop .runexec2 --nostringval-- --nostringval-- --nostringval-- 2 %stopped_push --nostringval--
Dictionary stack:
--dict:974/1684(ro)(G)-- --dict:0/20(G)-- --dict:87/200(L)-- --dict:205/256(L)--
Current allocation mode is local
export GDFONTPATH=/home/bohuang/local/EPACTS/share/EPACTS; export GNUPLOT_FONTPATH=/home/bohuang/local/EPACTS/share/EPACTS; export GNUPLOT_PS_DIR=/home/bohuang/local/EPACTS/share/EPACTS; export PATH=$PATH:/home/bohuang/local/EPACTS/bin/; export GNUPLOT_PFBTOPFA="pfbtops %s"; gnuplot /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.epacts.cmd
export GDFONTPATH=/home/bohuang/local/EPACTS/share/EPACTS; export GNUPLOT_FONTPATH=/home/bohuang/local/EPACTS/share/EPACTS; export GNUPLOT_PS_DIR=/home/bohuang/local/EPACTS/share/EPACTS; export PATH=$PATH:/home/bohuang/local/EPACTS/bin/; export GNUPLOT_PFBTOPFA="pfbtops %s"; /home/bohuang/local/EPACTS/bin/epstopdf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.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/bohuang/local/EPACTS/bin/out/test.single.q.emmax.epacts.cmd /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.epacts.qq.eps /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.epacts.mh.eps /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.epacts.*.dat
zcat /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.epacts.gz | awk '$11 != "NA" { print $0 }' | sort -g -k 11 | head -n 5000 > /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.epacts.top5000
touch /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.epacts.OK
Taking the site list from the VCF file
Annotate the VCF file
/home/bohuang/local/EPACTS/bin/anno -i out/1000G_exome_chr20_example_softFiltered.calls.sites.vcf.gz -r /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta -f refGene -g /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz -c /home/bohuang/local/EPACTS/share/EPACTS/codon.txt -o out/1000G_exome_chr20_example_softFiltered.calls.sites.anno.vcf.gz --inputFormat vcf -p /home/bohuang/local/EPACTS/share/EPACTS/priority.txt
The following parameters are available. Ones with "[]" are in effect:
Available Options
Required Parameters :
-i [out/1000G_exome_chr20_example_softFiltered.calls.sites.vcf.gz]
-o [out/1000G_exome_chr20_example_softFiltered.calls.sites.anno.vcf.gz]
Gene Annotation
Parameters : -g [/home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz]
-r [/home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta]
--inputFormat [vcf], --checkReference, -f [refGene]
-p [/home/bohuang/local/EPACTS/share/EPACTS/priority.txt]
-c [/home/bohuang/local/EPACTS/share/EPACTS/codon.txt]
-u [], -d [], --se [], --si [], --outputFormat []
Other Annotation Tools : --genomeScore [], --bed [], --tabix []
Load reference genome /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta...
DONE: 84 chromosomes and 3101804739 bases are loaded.
Load codon file /home/bohuang/local/EPACTS/share/EPACTS/codon.txt...
DONE: codon file loaded.
Load priority file /home/bohuang/local/EPACTS/share/EPACTS/priority.txt...
DONE: 24 priority annotation types loaded.
Load gene file /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz...
DONE: 92627 gene loaded.
DONE: Generated frequency of each annotype type in [ out/1000G_exome_chr20_example_softFiltered.calls.sites.anno.vcf.gz.anno.frq ].
DONE: Generated frequency of each highest priority annotation type in [ out/1000G_exome_chr20_example_softFiltered.calls.sites.anno.vcf.gz.top.anno.frq ].
Ts/Tv ratio: 2.9522
Ts observed: 14268 times; Tv observed: 4833 times.
DONE: Generated frequency of each base change in [ out/1000G_exome_chr20_example_softFiltered.calls.sites.anno.vcf.gz.base.frq ].
DONE: Generated frequency of each codon change in [ out/1000G_exome_chr20_example_softFiltered.calls.sites.anno.vcf.gz.codon.frq ].
DONE: Generated frequency of indel length in [ out/1000G_exome_chr20_example_softFiltered.calls.sites.anno.vcf.gz.indel.frq ].
..............................................
... Anno(tation) ...
... Xiaowei Zhan, Goncalo Abecasis ...
... Speical Thanks: ...
... Hyun Ming Kang, Yanming Li ...
... zha...@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
/home/bohuang/local/EPACTS/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
/home/bohuang/local/EPACTS/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
Detected phenotypes with more than 3 unique values -- considering as quantitative phenotypes.
Successfully written phenotypes and 2 covariates across 266 individuals
Finished generating EPACTS Makefile
Running 5 parallel jobs of EPACTS
forkExecWait(): make -f /home/bohuang/local/EPACTS/bin/out/test.gene.skat.Makefile -j 5
Rscript /home/bohuang/local/EPACTS/bin/out/test.gene.skat.0.R --vanilla
Rscript /home/bohuang/local/EPACTS/bin/out/test.gene.skat.1.R --vanilla
Rscript /home/bohuang/local/EPACTS/bin/out/test.gene.skat.2.R --vanilla
Rscript /home/bohuang/local/EPACTS/bin/out/test.gene.skat.3.R --vanilla
Rscript /home/bohuang/local/EPACTS/bin/out/test.gene.skat.4.R --vanilla
Loading required package: epactsR
Loading required package: epactsR
Loading required package: epactsR
Loading required package: epactsR
Loading required package: epactsR
Loading required package: mmSKAT
Loading required package: mmSKAT
Loading required package: mmSKAT
Loading required package: mmSKAT
Loading required package: mmSKAT
NULL
Sucessfully wrote ( 100 * 7 ) matrix
There were 17 warnings (use warnings() to see them)
Rscript /home/bohuang/local/EPACTS/bin/out/test.gene.skat.5.R --vanilla
Loading required package: epactsR
Loading required package: mmSKAT
NULL
Sucessfully wrote ( 8 * 7 ) matrix
Warning message:
Only one SNP in the SNP set!
NULL
Sucessfully wrote ( 100 * 7 ) matrix
There were 15 warnings (use warnings() to see them)
NULL
Sucessfully wrote ( 100 * 7 ) matrix
There were 11 warnings (use warnings() to see them)
NULL
Sucessfully wrote ( 100 * 7 ) matrix
There were 18 warnings (use warnings() to see them)
NULL
Sucessfully wrote ( 100 * 7 ) matrix
There were 12 warnings (use warnings() to see them)
(head -1 /home/bohuang/local/EPACTS/bin/out/test.gene.skat.0.epacts; cat /home/bohuang/local/EPACTS/bin/out/test.gene.skat.0.epacts /home/bohuang/local/EPACTS/bin/out/test.gene.skat.1.epacts /home/bohuang/local/EPACTS/bin/out/test.gene.skat.2.epacts /home/bohuang/local/EPACTS/bin/out/test.gene.skat.3.epacts /home/bohuang/local/EPACTS/bin/out/test.gene.skat.4.epacts /home/bohuang/local/EPACTS/bin/out/test.gene.skat.5.epacts | grep -v ^#;) > /home/bohuang/local/EPACTS/bin/out/test.gene.skat.epacts
rm /home/bohuang/local/EPACTS/bin/out/test.gene.skat.0.epacts /home/bohuang/local/EPACTS/bin/out/test.gene.skat.1.epacts /home/bohuang/local/EPACTS/bin/out/test.gene.skat.2.epacts /home/bohuang/local/EPACTS/bin/out/test.gene.skat.3.epacts /home/bohuang/local/EPACTS/bin/out/test.gene.skat.4.epacts /home/bohuang/local/EPACTS/bin/out/test.gene.skat.5.epacts /home/bohuang/local/EPACTS/bin/out/test.gene.skat.0.R /home/bohuang/local/EPACTS/bin/out/test.gene.skat.1.R /home/bohuang/local/EPACTS/bin/out/test.gene.skat.2.R /home/bohuang/local/EPACTS/bin/out/test.gene.skat.3.R /home/bohuang/local/EPACTS/bin/out/test.gene.skat.4.R /home/bohuang/local/EPACTS/bin/out/test.gene.skat.5.R
/home/bohuang/local/EPACTS/bin/epacts-plot --in /home/bohuang/local/EPACTS/bin/out/test.gene.skat.epacts
nsnps = 437
Rscript /home/bohuang/local/EPACTS/bin/out/test.gene.skat.epacts.R --vanilla
export GDFONTPATH=/home/bohuang/local/EPACTS/share/EPACTS; export GNUPLOT_FONTPATH=/home/bohuang/local/EPACTS/share/EPACTS; export GNUPLOT_PS_DIR=/home/bohuang/local/EPACTS/share/EPACTS; export PATH=$PATH:/home/bohuang/local/EPACTS/bin/; export GNUPLOT_PFBTOPFA="pfbtops %s"; gnuplot /home/bohuang/local/EPACTS/bin/out/test.gene.skat.epacts.cmd
export GDFONTPATH=/home/bohuang/local/EPACTS/share/EPACTS; export GNUPLOT_FONTPATH=/home/bohuang/local/EPACTS/share/EPACTS; export GNUPLOT_PS_DIR=/home/bohuang/local/EPACTS/share/EPACTS; export PATH=$PATH:/home/bohuang/local/EPACTS/bin/; export GNUPLOT_PFBTOPFA="pfbtops %s"; /home/bohuang/local/EPACTS/bin/epstopdf /home/bohuang/local/EPACTS/bin/out/test.gene.skat.epacts.qq.eps
GPL Ghostscript 9.26: Unrecoverable error, exit code 1
Error: /undefined in LTB
Operand stack:
Execution stack:
%interp_exit .runexec2 --nostringval-- --nostringval-- --nostringval-- 2 %stopped_push --nostringval-- --nostringval-- --nostringval-- false 1 %stopped_push 2045 1 3 %oparray_pop 2044 1 3 %oparray_pop --nostringval-- 2025 1 3 %oparray_pop 1884 1 3 %oparray_pop --nostringval-- %errorexec_pop .runexec2 --nostringval-- --nostringval-- --nostringval-- 2 %stopped_push --nostringval--
Dictionary stack:
--dict:974/1684(ro)(G)-- --dict:0/20(G)-- --dict:87/200(L)-- --dict:205/256(L)--
Current allocation mode is local
export GDFONTPATH=/home/bohuang/local/EPACTS/share/EPACTS; export GNUPLOT_FONTPATH=/home/bohuang/local/EPACTS/share/EPACTS; export GNUPLOT_PS_DIR=/home/bohuang/local/EPACTS/share/EPACTS; export PATH=$PATH:/home/bohuang/local/EPACTS/bin/; export GNUPLOT_PFBTOPFA="pfbtops %s"; gnuplot /home/bohuang/local/EPACTS/bin/out/test.gene.skat.epacts.cmd
export GDFONTPATH=/home/bohuang/local/EPACTS/share/EPACTS; export GNUPLOT_FONTPATH=/home/bohuang/local/EPACTS/share/EPACTS; export GNUPLOT_PS_DIR=/home/bohuang/local/EPACTS/share/EPACTS; export PATH=$PATH:/home/bohuang/local/EPACTS/bin/; export GNUPLOT_PFBTOPFA="pfbtops %s"; /home/bohuang/local/EPACTS/bin/epstopdf /home/bohuang/local/EPACTS/bin/out/test.gene.skat.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/bohuang/local/EPACTS/bin/out/test.gene.skat.epacts.cmd /home/bohuang/local/EPACTS/bin/out/test.gene.skat.epacts.qq.eps /home/bohuang/local/EPACTS/bin/out/test.gene.skat.epacts.mh.eps /home/bohuang/local/EPACTS/bin/out/test.gene.skat.epacts.*.dat
cat /home/bohuang/local/EPACTS/bin/out/test.gene.skat.epacts | awk '$10 != "NA" { print $0 }' | sort -g -k 10 | head -n 5000 > /home/bohuang/local/EPACTS/bin/out/test.gene.skat.epacts.top5000
touch /home/bohuang/local/EPACTS/bin/out/test.gene.skat.epacts.OK
----------------------------------------------------------------
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 2 covariates across 266 individuals
Processing chromosome 20...
Finished generating EPACTS Makefile
Running 5 parallel jobs of EPACTS
forkExecWait(): make -f /home/bohuang/local/EPACTS/bin/out/test.single.b.score.Makefile -j 5
Rscript /home/bohuang/local/EPACTS/share/EPACTS/epactsSingle.R --vanilla /home/bohuang/local/EPACTS /home/bohuang/local/EPACTS/bin/out/test.single.b.score.phe /home/bohuang/local/EPACTS/bin/out/test.single.b.score.cov /home/bohuang/local/EPACTS/bin/out/test.single.b.score.ind /home/bohuang/local/EPACTS/bin/./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz 20:1-10000000 /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.1.10000000.epacts GT 0.001 1 3 1000000000 0.5 0 FALSE single.b.score
Rscript /home/bohuang/local/EPACTS/share/EPACTS/epactsSingle.R --vanilla /home/bohuang/local/EPACTS /home/bohuang/local/EPACTS/bin/out/test.single.b.score.phe /home/bohuang/local/EPACTS/bin/out/test.single.b.score.cov /home/bohuang/local/EPACTS/bin/out/test.single.b.score.ind /home/bohuang/local/EPACTS/bin/./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz 20:10000001-20000000 /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.10000001.20000000.epacts GT 0.001 1 3 1000000000 0.5 0 FALSE single.b.score
Rscript /home/bohuang/local/EPACTS/share/EPACTS/epactsSingle.R --vanilla /home/bohuang/local/EPACTS /home/bohuang/local/EPACTS/bin/out/test.single.b.score.phe /home/bohuang/local/EPACTS/bin/out/test.single.b.score.cov /home/bohuang/local/EPACTS/bin/out/test.single.b.score.ind /home/bohuang/local/EPACTS/bin/./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz 20:20000001-30000000 /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.20000001.30000000.epacts GT 0.001 1 3 1000000000 0.5 0 FALSE single.b.score
Rscript /home/bohuang/local/EPACTS/share/EPACTS/epactsSingle.R --vanilla /home/bohuang/local/EPACTS /home/bohuang/local/EPACTS/bin/out/test.single.b.score.phe /home/bohuang/local/EPACTS/bin/out/test.single.b.score.cov /home/bohuang/local/EPACTS/bin/out/test.single.b.score.ind /home/bohuang/local/EPACTS/bin/./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz 20:30000001-40000000 /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.30000001.40000000.epacts GT 0.001 1 3 1000000000 0.5 0 FALSE single.b.score
Rscript /home/bohuang/local/EPACTS/share/EPACTS/epactsSingle.R --vanilla /home/bohuang/local/EPACTS /home/bohuang/local/EPACTS/bin/out/test.single.b.score.phe /home/bohuang/local/EPACTS/bin/out/test.single.b.score.cov /home/bohuang/local/EPACTS/bin/out/test.single.b.score.ind /home/bohuang/local/EPACTS/bin/./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz 20:40000001-50000000 /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.40000001.50000000.epacts GT 0.001 1 3 1000000000 0.5 0 FALSE single.b.score
Loading required package: epactsR
Loading required package: epactsR
Loading required package: epactsR
Loading required package: epactsR
Loading required package: epactsR
NULL
Sucessfully wrote ( 1248 * 10 ) matrix
NULL
NULL
Sucessfully wrote ( 1466 * 10 ) matrix
NULL
NULL
Sucessfully wrote ( 3367 * 10 ) matrix
NULL
/home/bohuang/local/EPACTS/bin/epacts-anno --in /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.10000001.20000000.epacts --ref /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta
/home/bohuang/local/EPACTS/bin/epacts-anno --in /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.20000001.30000000.epacts --ref /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta
/home/bohuang/local/EPACTS/bin/epacts-anno --in /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.1.10000000.epacts --ref /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta
NULL
Sucessfully wrote ( 4170 * 10 ) matrix
NULL
/home/bohuang/local/EPACTS/bin/epacts-anno --in /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.30000001.40000000.epacts --ref /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta
NULL
Sucessfully wrote ( 3662 * 10 ) matrix
NULL
/home/bohuang/local/EPACTS/bin/epacts-anno --in /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.40000001.50000000.epacts --ref /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta
/home/bohuang/local/EPACTS/bin/anno -i /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.30000001.40000000.epacts -r /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta -f refGene -g /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz -c /home/bohuang/local/EPACTS/share/EPACTS/codon.txt -o /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.30000001.40000000.epacts.tmp --inputFormat epacts -p /home/bohuang/local/EPACTS/share/EPACTS/priority.txt
/home/bohuang/local/EPACTS/bin/anno -i /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.20000001.30000000.epacts -r /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta -f refGene -g /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz -c /home/bohuang/local/EPACTS/share/EPACTS/codon.txt -o /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.20000001.30000000.epacts.tmp --inputFormat epacts -p /home/bohuang/local/EPACTS/share/EPACTS/priority.txt
The following parameters are available. Ones with "[]" are in effect:
Available Options
Required Parameters :
-i [/home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.30000001.40000000.epacts]
-o [/home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.30000001.40000000.epacts.tmp]
Gene Annotation
Parameters : -g [/home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz]
-r [/home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta]
--inputFormat [epacts], --checkReference, -f [refGene]
-p [/home/bohuang/local/EPACTS/share/EPACTS/priority.txt]
-c [/home/bohuang/local/EPACTS/share/EPACTS/codon.txt]
-u [], -d [], --se [], --si [], --outputFormat []
Other Annotation Tools : --genomeScore [], --bed [], --tabix []
/home/bohuang/local/EPACTS/bin/anno -i /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.10000001.20000000.epacts -r /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta -f refGene -g /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz -c /home/bohuang/local/EPACTS/share/EPACTS/codon.txt -o /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.10000001.20000000.epacts.tmp --inputFormat epacts -p /home/bohuang/local/EPACTS/share/EPACTS/priority.txt
Load reference genome /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta...
DONE: 84 chromosomes and 3101804739 bases are loaded.
Load codon file /home/bohuang/local/EPACTS/share/EPACTS/codon.txt...
The following parameters are available. Ones with "[]" are in effect:
DONE: codon file loaded.
Load priority file /home/bohuang/local/EPACTS/share/EPACTS/priority.txt...
Available Options
Required Parameters :
-i [/home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.20000001.30000000.epacts]
-o [/home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.20000001.30000000.epacts.tmp]
Gene Annotation
Parameters : -g [/home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz]
-r [/home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta]
--inputFormat [epacts], --checkReference, -f [refGene]
-p [/home/bohuang/local/EPACTS/share/EPACTS/priority.txt]
-c [/home/bohuang/local/EPACTS/share/EPACTS/codon.txt]
-u [], -d [], --se [], --si [], --outputFormat []
Other Annotation Tools : --genomeScore [], --bed [], --tabix []
Load reference genome /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta...
DONE: 84 chromosomes and 3101804739 bases are loaded.
Load codon file /home/bohuang/local/EPACTS/share/EPACTS/codon.txt...
DONE: codon file loaded.
Load priority file /home/bohuang/local/EPACTS/share/EPACTS/priority.txt...
DONE: 24 priority annotation types loaded.
DONE: 24 priority annotation types loaded.
Load gene file /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz...
Load gene file /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz...
The following parameters are available. Ones with "[]" are in effect:
Available Options
Required Parameters :
-i [/home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.10000001.20000000.epacts]
-o [/home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.10000001.20000000.epacts.tmp]
Gene Annotation
Parameters : -g [/home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz]
-r [/home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta]
--inputFormat [epacts], --checkReference, -f [refGene]
-p [/home/bohuang/local/EPACTS/share/EPACTS/priority.txt]
-c [/home/bohuang/local/EPACTS/share/EPACTS/codon.txt]
-u [], -d [], --se [], --si [], --outputFormat []
Other Annotation Tools : --genomeScore [], --bed [], --tabix []
Load reference genome /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta...
DONE: 84 chromosomes and 3101804739 bases are loaded.
Load codon file /home/bohuang/local/EPACTS/share/EPACTS/codon.txt...
DONE: codon file loaded.
Load priority file /home/bohuang/local/EPACTS/share/EPACTS/priority.txt...
DONE: 24 priority annotation types loaded.
Load gene file /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz...
/home/bohuang/local/EPACTS/bin/anno -i /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.1.10000000.epacts -r /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta -f refGene -g /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz -c /home/bohuang/local/EPACTS/share/EPACTS/codon.txt -o /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.1.10000000.epacts.tmp --inputFormat epacts -p /home/bohuang/local/EPACTS/share/EPACTS/priority.txt
The following parameters are available. Ones with "[]" are in effect:
Available Options
Required Parameters :
-i [/home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.1.10000000.epacts]
-o [/home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.1.10000000.epacts.tmp]
Gene Annotation
Parameters : -g [/home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz]
-r [/home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta]
--inputFormat [epacts], --checkReference, -f [refGene]
-p [/home/bohuang/local/EPACTS/share/EPACTS/priority.txt]
-c [/home/bohuang/local/EPACTS/share/EPACTS/codon.txt]
-u [], -d [], --se [], --si [], --outputFormat []
Other Annotation Tools : --genomeScore [], --bed [], --tabix []
Load reference genome /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta...
DONE: 84 chromosomes and 3101804739 bases are loaded.
Load codon file /home/bohuang/local/EPACTS/share/EPACTS/codon.txt...
DONE: codon file loaded.
Load priority file /home/bohuang/local/EPACTS/share/EPACTS/priority.txt...
DONE: 24 priority annotation types loaded.
Load gene file /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz...
/home/bohuang/local/EPACTS/bin/anno -i /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.40000001.50000000.epacts -r /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta -f refGene -g /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz -c /home/bohuang/local/EPACTS/share/EPACTS/codon.txt -o /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.40000001.50000000.epacts.tmp --inputFormat epacts -p /home/bohuang/local/EPACTS/share/EPACTS/priority.txt
The following parameters are available. Ones with "[]" are in effect:
Available Options
Required Parameters :
-i [/home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.40000001.50000000.epacts]
-o [/home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.40000001.50000000.epacts.tmp]
Gene Annotation
Parameters : -g [/home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz]
-r [/home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta]
--inputFormat [epacts], --checkReference, -f [refGene]
-p [/home/bohuang/local/EPACTS/share/EPACTS/priority.txt]
-c [/home/bohuang/local/EPACTS/share/EPACTS/codon.txt]
-u [], -d [], --se [], --si [], --outputFormat []
Other Annotation Tools : --genomeScore [], --bed [], --tabix []
Load reference genome /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta...
DONE: 84 chromosomes and 3101804739 bases are loaded.
Load codon file /home/bohuang/local/EPACTS/share/EPACTS/codon.txt...
DONE: codon file loaded.
Load priority file /home/bohuang/local/EPACTS/share/EPACTS/priority.txt...
DONE: 24 priority annotation types loaded.
Load gene file /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz...
DONE: 92627 gene loaded.
DONE: Generated frequency of each annotype type in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.10000001.20000000.epacts.tmp.anno.frq ].
DONE: Generated frequency of each highest priority annotation type in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.10000001.20000000.epacts.tmp.top.anno.frq ].
Ts/Tv ratio: 2.87578
Ts observed: 926 times; Tv observed: 322 times.
DONE: Generated frequency of each base change in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.10000001.20000000.epacts.tmp.base.frq ].
DONE: Generated frequency of each codon change in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.10000001.20000000.epacts.tmp.codon.frq ].
DONE: Generated frequency of indel length in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.10000001.20000000.epacts.tmp.indel.frq ].
..............................................
... Anno(tation) ...
... Xiaowei Zhan, Goncalo Abecasis ...
... Speical Thanks: ...
... Hyun Ming Kang, Yanming Li ...
... zha...@umich.edu ...
... Sep 2011 ...
................................................
DONE: 1248 varaints are annotated.
DONE: Generated annotation output in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.10000001.20000000.epacts.tmp ].
Annotation succeed!
mv /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.10000001.20000000.epacts.tmp /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.10000001.20000000.epacts
rm /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.10000001.20000000.epacts.tmp.log /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.10000001.20000000.epacts.tmp.top.anno.frq /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.10000001.20000000.epacts.tmp.anno.frq /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.10000001.20000000.epacts.tmp.base.frq /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.10000001.20000000.epacts.tmp.codon.frq /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.10000001.20000000.epacts.tmp.indel.frq
DONE: 92627 gene loaded.
Rscript /home/bohuang/local/EPACTS/share/EPACTS/epactsSingle.R --vanilla /home/bohuang/local/EPACTS /home/bohuang/local/EPACTS/bin/out/test.single.b.score.phe /home/bohuang/local/EPACTS/bin/out/test.single.b.score.cov /home/bohuang/local/EPACTS/bin/out/test.single.b.score.ind /home/bohuang/local/EPACTS/bin/./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz 20:50000001-60000000 /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.50000001.60000000.epacts GT 0.001 1 3 1000000000 0.5 0 FALSE single.b.score
DONE: 92627 gene loaded.
DONE: 92627 gene loaded.
DONE: 92627 gene loaded.
DONE: Generated frequency of each annotype type in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.40000001.50000000.epacts.tmp.anno.frq ].
DONE: Generated frequency of each highest priority annotation type in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.40000001.50000000.epacts.tmp.top.anno.frq ].
Ts/Tv ratio: 2.69153
Ts observed: 2670 times; Tv observed: 992 times.
DONE: Generated frequency of each base change in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.40000001.50000000.epacts.tmp.base.frq ].
DONE: Generated frequency of each codon change in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.40000001.50000000.epacts.tmp.codon.frq ].
DONE: Generated frequency of indel length in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.40000001.50000000.epacts.tmp.indel.frq ].
..............................................
... Anno(tation) ...
... Xiaowei Zhan, Goncalo Abecasis ...
... Speical Thanks: ...
... Hyun Ming Kang, Yanming Li ...
... zha...@umich.edu ...
... Sep 2011 ...
................................................
DONE: 3662 varaints are annotated.
DONE: Generated annotation output in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.40000001.50000000.epacts.tmp ].
Annotation succeed!
mv /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.40000001.50000000.epacts.tmp /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.40000001.50000000.epacts
rm /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.40000001.50000000.epacts.tmp.log /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.40000001.50000000.epacts.tmp.top.anno.frq /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.40000001.50000000.epacts.tmp.anno.frq /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.40000001.50000000.epacts.tmp.base.frq /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.40000001.50000000.epacts.tmp.codon.frq /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.40000001.50000000.epacts.tmp.indel.frq
Rscript /home/bohuang/local/EPACTS/share/EPACTS/epactsSingle.R --vanilla /home/bohuang/local/EPACTS /home/bohuang/local/EPACTS/bin/out/test.single.b.score.phe /home/bohuang/local/EPACTS/bin/out/test.single.b.score.cov /home/bohuang/local/EPACTS/bin/out/test.single.b.score.ind /home/bohuang/local/EPACTS/bin/./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz 20:60000001-63025520 /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.60000001.63025520.epacts GT 0.001 1 3 1000000000 0.5 0 FALSE single.b.score
DONE: Generated frequency of each annotype type in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.1.10000000.epacts.tmp.anno.frq ].
DONE: Generated frequency of each highest priority annotation type in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.1.10000000.epacts.tmp.top.anno.frq ].
Ts/Tv ratio: 2.8524
Ts observed: 2493 times; Tv observed: 874 times.
DONE: Generated frequency of each base change in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.1.10000000.epacts.tmp.base.frq ].
DONE: Generated frequency of each codon change in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.1.10000000.epacts.tmp.codon.frq ].
DONE: Generated frequency of indel length in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.1.10000000.epacts.tmp.indel.frq ].
..............................................
... Anno(tation) ...
... Xiaowei Zhan, Goncalo Abecasis ...
... Speical Thanks: ...
... Hyun Ming Kang, Yanming Li ...
... zha...@umich.edu ...
... Sep 2011 ...
................................................
DONE: 3367 varaints are annotated.
DONE: Generated annotation output in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.1.10000000.epacts.tmp ].
Annotation succeed!
mv /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.1.10000000.epacts.tmp /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.1.10000000.epacts
rm /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.1.10000000.epacts.tmp.log /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.1.10000000.epacts.tmp.top.anno.frq /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.1.10000000.epacts.tmp.anno.frq /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.1.10000000.epacts.tmp.base.frq /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.1.10000000.epacts.tmp.codon.frq /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.1.10000000.epacts.tmp.indel.frq
DONE: Generated frequency of each annotype type in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.20000001.30000000.epacts.tmp.anno.frq ].
DONE: Generated frequency of each highest priority annotation type in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.20000001.30000000.epacts.tmp.top.anno.frq ].
Ts/Tv ratio: 2.59314
Ts observed: 1058 times; Tv observed: 408 times.
DONE: Generated frequency of each base change in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.20000001.30000000.epacts.tmp.base.frq ].
DONE: Generated frequency of each codon change in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.20000001.30000000.epacts.tmp.codon.frq ].
DONE: Generated frequency of indel length in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.20000001.30000000.epacts.tmp.indel.frq ].
..............................................
... Anno(tation) ...
... Xiaowei Zhan, Goncalo Abecasis ...
... Speical Thanks: ...
... Hyun Ming Kang, Yanming Li ...
... zha...@umich.edu ...
... Sep 2011 ...
................................................
DONE: 1466 varaints are annotated.
DONE: Generated annotation output in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.20000001.30000000.epacts.tmp ].
Annotation succeed!
mv /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.20000001.30000000.epacts.tmp /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.20000001.30000000.epacts
rm /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.20000001.30000000.epacts.tmp.log /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.20000001.30000000.epacts.tmp.top.anno.frq /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.20000001.30000000.epacts.tmp.anno.frq /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.20000001.30000000.epacts.tmp.base.frq /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.20000001.30000000.epacts.tmp.codon.frq /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.20000001.30000000.epacts.tmp.indel.frq
Loading required package: epactsR
Loading required package: epactsR
DONE: Generated frequency of each annotype type in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.30000001.40000000.epacts.tmp.anno.frq ].
DONE: Generated frequency of each highest priority annotation type in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.30000001.40000000.epacts.tmp.top.anno.frq ].
Ts/Tv ratio: 2.90815
Ts observed: 3103 times; Tv observed: 1067 times.
DONE: Generated frequency of each base change in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.30000001.40000000.epacts.tmp.base.frq ].
DONE: Generated frequency of each codon change in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.30000001.40000000.epacts.tmp.codon.frq ].
DONE: Generated frequency of indel length in [ /home/bohuang/local/EPACTS/bin/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 ...
... zha...@umich.edu ...
... Sep 2011 ...
................................................
DONE: 4170 varaints are annotated.
DONE: Generated annotation output in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.30000001.40000000.epacts.tmp ].
Annotation succeed!
mv /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.30000001.40000000.epacts.tmp /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.30000001.40000000.epacts
rm /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.30000001.40000000.epacts.tmp.log /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.30000001.40000000.epacts.tmp.top.anno.frq /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.30000001.40000000.epacts.tmp.anno.frq /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.30000001.40000000.epacts.tmp.base.frq /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.30000001.40000000.epacts.tmp.codon.frq /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.30000001.40000000.epacts.tmp.indel.frq
NULL
Sucessfully wrote ( 1763 * 10 ) matrix
NULL
/home/bohuang/local/EPACTS/bin/epacts-anno --in /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.50000001.60000000.epacts --ref /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta
/home/bohuang/local/EPACTS/bin/anno -i /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.50000001.60000000.epacts -r /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta -f refGene -g /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz -c /home/bohuang/local/EPACTS/share/EPACTS/codon.txt -o /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.50000001.60000000.epacts.tmp --inputFormat epacts -p /home/bohuang/local/EPACTS/share/EPACTS/priority.txt
The following parameters are available. Ones with "[]" are in effect:
Available Options
Required Parameters :
-i [/home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.50000001.60000000.epacts]
-o [/home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.50000001.60000000.epacts.tmp]
Gene Annotation
Parameters : -g [/home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz]
-r [/home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta]
--inputFormat [epacts], --checkReference, -f [refGene]
-p [/home/bohuang/local/EPACTS/share/EPACTS/priority.txt]
-c [/home/bohuang/local/EPACTS/share/EPACTS/codon.txt]
-u [], -d [], --se [], --si [], --outputFormat []
Other Annotation Tools : --genomeScore [], --bed [], --tabix []
Load reference genome /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta...
DONE: 84 chromosomes and 3101804739 bases are loaded.
Load codon file /home/bohuang/local/EPACTS/share/EPACTS/codon.txt...
DONE: codon file loaded.
Load priority file /home/bohuang/local/EPACTS/share/EPACTS/priority.txt...
DONE: 24 priority annotation types loaded.
Load gene file /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz...
NULL
Sucessfully wrote ( 3425 * 10 ) matrix
NULL
/home/bohuang/local/EPACTS/bin/epacts-anno --in /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.60000001.63025520.epacts --ref /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta
/home/bohuang/local/EPACTS/bin/anno -i /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.60000001.63025520.epacts -r /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta -f refGene -g /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz -c /home/bohuang/local/EPACTS/share/EPACTS/codon.txt -o /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.60000001.63025520.epacts.tmp --inputFormat epacts -p /home/bohuang/local/EPACTS/share/EPACTS/priority.txt
The following parameters are available. Ones with "[]" are in effect:
Available Options
Required Parameters :
-i [/home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.60000001.63025520.epacts]
-o [/home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.60000001.63025520.epacts.tmp]
Gene Annotation
Parameters : -g [/home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz]
-r [/home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta]
--inputFormat [epacts], --checkReference, -f [refGene]
-p [/home/bohuang/local/EPACTS/share/EPACTS/priority.txt]
-c [/home/bohuang/local/EPACTS/share/EPACTS/codon.txt]
-u [], -d [], --se [], --si [], --outputFormat []
Other Annotation Tools : --genomeScore [], --bed [], --tabix []
Load reference genome /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta...
DONE: 84 chromosomes and 3101804739 bases are loaded.
Load codon file /home/bohuang/local/EPACTS/share/EPACTS/codon.txt...
DONE: codon file loaded.
Load priority file /home/bohuang/local/EPACTS/share/EPACTS/priority.txt...
DONE: 24 priority annotation types loaded.
Load gene file /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz...
DONE: 92627 gene loaded.
DONE: Generated frequency of each annotype type in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.50000001.60000000.epacts.tmp.anno.frq ].
DONE: Generated frequency of each highest priority annotation type in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.50000001.60000000.epacts.tmp.top.anno.frq ].
Ts/Tv ratio: 2.66528
Ts observed: 1282 times; Tv observed: 481 times.
DONE: Generated frequency of each base change in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.50000001.60000000.epacts.tmp.base.frq ].
DONE: Generated frequency of each codon change in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.50000001.60000000.epacts.tmp.codon.frq ].
DONE: Generated frequency of indel length in [ /home/bohuang/local/EPACTS/bin/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 ...
... zha...@umich.edu ...
... Sep 2011 ...
................................................
DONE: 1763 varaints are annotated.
DONE: Generated annotation output in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.50000001.60000000.epacts.tmp ].
Annotation succeed!
mv /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.50000001.60000000.epacts.tmp /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.50000001.60000000.epacts
rm /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.50000001.60000000.epacts.tmp.log /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.50000001.60000000.epacts.tmp.top.anno.frq /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.50000001.60000000.epacts.tmp.anno.frq /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.50000001.60000000.epacts.tmp.base.frq /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.50000001.60000000.epacts.tmp.codon.frq /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.50000001.60000000.epacts.tmp.indel.frq
DONE: 92627 gene loaded.
DONE: Generated frequency of each annotype type in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.60000001.63025520.epacts.tmp.anno.frq ].
DONE: Generated frequency of each highest priority annotation type in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.60000001.63025520.epacts.tmp.top.anno.frq ].
Ts/Tv ratio: 3.97097
Ts observed: 2736 times; Tv observed: 689 times.
DONE: Generated frequency of each base change in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.60000001.63025520.epacts.tmp.base.frq ].
DONE: Generated frequency of each codon change in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.60000001.63025520.epacts.tmp.codon.frq ].
DONE: Generated frequency of indel length in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.60000001.63025520.epacts.tmp.indel.frq ].
..............................................
... Anno(tation) ...
... Xiaowei Zhan, Goncalo Abecasis ...
... Speical Thanks: ...
... Hyun Ming Kang, Yanming Li ...
... zha...@umich.edu ...
... Sep 2011 ...
................................................
DONE: 3425 varaints are annotated.
DONE: Generated annotation output in [ /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.60000001.63025520.epacts.tmp ].
Annotation succeed!
mv /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.60000001.63025520.epacts.tmp /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.60000001.63025520.epacts
rm /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.60000001.63025520.epacts.tmp.log /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.60000001.63025520.epacts.tmp.top.anno.frq /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.60000001.63025520.epacts.tmp.anno.frq /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.60000001.63025520.epacts.tmp.base.frq /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.60000001.63025520.epacts.tmp.codon.frq /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.60000001.63025520.epacts.tmp.indel.frq
/home/bohuang/local/EPACTS/bin/epacts-cat /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.1.10000000.epacts /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.10000001.20000000.epacts /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.20000001.30000000.epacts /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.30000001.40000000.epacts /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.40000001.50000000.epacts /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.50000001.60000000.epacts /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.60000001.63025520.epacts | /home/bohuang/local/EPACTS/bin/bgzip -c > /home/bohuang/local/EPACTS/bin/out/test.single.b.score.epacts.gz
/home/bohuang/local/EPACTS/bin/tabix -f -pbed /home/bohuang/local/EPACTS/bin/out/test.single.b.score.epacts.gz
rm -f /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.1.10000000.epacts /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.10000001.20000000.epacts /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.20000001.30000000.epacts /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.30000001.40000000.epacts /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.40000001.50000000.epacts /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.50000001.60000000.epacts /home/bohuang/local/EPACTS/bin/out/test.single.b.score.20.60000001.63025520.epacts
/home/bohuang/local/EPACTS/bin/epacts-plot --in /home/bohuang/local/EPACTS/bin/out/test.single.b.score.epacts.gz --region 20:0
nsnps = 3331
Rscript /home/bohuang/local/EPACTS/bin/out/test.single.b.score.epacts.R --vanilla
export GDFONTPATH=/home/bohuang/local/EPACTS/share/EPACTS; export GNUPLOT_FONTPATH=/home/bohuang/local/EPACTS/share/EPACTS; export GNUPLOT_PS_DIR=/home/bohuang/local/EPACTS/share/EPACTS; export PATH=$PATH:/home/bohuang/local/EPACTS/bin/; export GNUPLOT_PFBTOPFA="pfbtops %s"; gnuplot /home/bohuang/local/EPACTS/bin/out/test.single.b.score.epacts.cmd
export GDFONTPATH=/home/bohuang/local/EPACTS/share/EPACTS; export GNUPLOT_FONTPATH=/home/bohuang/local/EPACTS/share/EPACTS; export GNUPLOT_PS_DIR=/home/bohuang/local/EPACTS/share/EPACTS; export PATH=$PATH:/home/bohuang/local/EPACTS/bin/; export GNUPLOT_PFBTOPFA="pfbtops %s"; /home/bohuang/local/EPACTS/bin/epstopdf /home/bohuang/local/EPACTS/bin/out/test.single.b.score.epacts.qq.eps
GPL Ghostscript 9.26: Unrecoverable error, exit code 1
Error: /undefined in LTB
Operand stack:
Execution stack:
%interp_exit .runexec2 --nostringval-- --nostringval-- --nostringval-- 2 %stopped_push --nostringval-- --nostringval-- --nostringval-- false 1 %stopped_push 2045 1 3 %oparray_pop 2044 1 3 %oparray_pop --nostringval-- 2025 1 3 %oparray_pop 1884 1 3 %oparray_pop --nostringval-- %errorexec_pop .runexec2 --nostringval-- --nostringval-- --nostringval-- 2 %stopped_push --nostringval--
Dictionary stack:
--dict:974/1684(ro)(G)-- --dict:0/20(G)-- --dict:87/200(L)-- --dict:205/256(L)--
Current allocation mode is local
export GDFONTPATH=/home/bohuang/local/EPACTS/share/EPACTS; export GNUPLOT_FONTPATH=/home/bohuang/local/EPACTS/share/EPACTS; export GNUPLOT_PS_DIR=/home/bohuang/local/EPACTS/share/EPACTS; export PATH=$PATH:/home/bohuang/local/EPACTS/bin/; export GNUPLOT_PFBTOPFA="pfbtops %s"; gnuplot /home/bohuang/local/EPACTS/bin/out/test.single.b.score.epacts.cmd
export GDFONTPATH=/home/bohuang/local/EPACTS/share/EPACTS; export GNUPLOT_FONTPATH=/home/bohuang/local/EPACTS/share/EPACTS; export GNUPLOT_PS_DIR=/home/bohuang/local/EPACTS/share/EPACTS; export PATH=$PATH:/home/bohuang/local/EPACTS/bin/; export GNUPLOT_PFBTOPFA="pfbtops %s"; /home/bohuang/local/EPACTS/bin/epstopdf /home/bohuang/local/EPACTS/bin/out/test.single.b.score.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/bohuang/local/EPACTS/bin/out/test.single.b.score.epacts.cmd /home/bohuang/local/EPACTS/bin/out/test.single.b.score.epacts.qq.eps /home/bohuang/local/EPACTS/bin/out/test.single.b.score.epacts.mh.eps /home/bohuang/local/EPACTS/bin/out/test.single.b.score.epacts.*.dat
zcat /home/bohuang/local/EPACTS/bin/out/test.single.b.score.epacts.gz | awk '$9 != "NA" { print $0 }' | sort -g -k 9 | head -n 5000 > /home/bohuang/local/EPACTS/bin/out/test.single.b.score.epacts.top5000
/home/bohuang/local/EPACTS/bin/epacts-zoom --vcf /home/bohuang/local/EPACTS/bin/./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz --prefix /home/bohuang/local/EPACTS/bin/out/test.single.b.score --top 1
SNP ID : 20:1610894
Examining +-300000 bp window
Examining genomic region 20:1310894-1910894
Index SNP's cM position is 5.854019
Unextended interval is 20:1610894-1610894 (0 bps)
Extending the intervals by .02 cM
export GDFONTPATH=/home/bohuang/local/EPACTS/share/EPACTS; export GNUPLOT_FONTPATH=/home/bohuang/local/EPACTS/share/EPACTS; export GNUPLOT_PS_DIR=/home/bohuang/local/EPACTS/share/EPACTS; export PATH=$PATH:/home/bohuang/local/EPACTS/bin/; export GNUPLOT_PFBTOPFA="pfbtops %s"; gnuplot /home/bohuang/local/EPACTS/bin/out/test.single.b.score.zoom.20.1610894.cmd
export GDFONTPATH=/home/bohuang/local/EPACTS/share/EPACTS; export GNUPLOT_FONTPATH=/home/bohuang/local/EPACTS/share/EPACTS; export GNUPLOT_PS_DIR=/home/bohuang/local/EPACTS/share/EPACTS; export PATH=$PATH:/home/bohuang/local/EPACTS/bin/; export GNUPLOT_PFBTOPFA="pfbtops %s"; /home/bohuang/local/EPACTS/bin/epstopdf /home/bohuang/local/EPACTS/bin/out/test.single.b.score.zoom.20.1610894.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
touch /home/bohuang/local/EPACTS/bin/out/test.single.b.score.epacts.OK
Creating Empirical Kinship matrix...
Kinship : Processing chromosome 20...
Finished generating EPACTS Makefile
Running 5 parallel jobs of EPACTS
make -f out/test.single.q.emmax.kinf.Makefile -j 5
The following parameters are available. Ones with "[]" are in effect:
Available Options
Input Options : --vcf [./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz],
--indf [out/test.single.q.emmax.kinf.ind],
The following parameters are available. Ones with "[]" are in effect:
Available Options
Input Options : --vcf [./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz],
--indf [out/test.single.q.emmax.kinf.ind],
--region [20:10000001-20000000], --unit [10000],
--field [GT], --rule [], --ignoreFilter [ON]
Filtering Options : --weight [], --minMAF [0.01],
--minCallRate [0.95], --minRSQ [0.00]
Empircial Kinship Method : --BN [ON], --IBS
Output Options : --out-kinf [out/test.single.q.emmax.kinf.20.10000001.20000000.kin],
--raw [ON], --adj-diag, --cov, --verbose
The following parameters are available. Ones with "[]" are in effect:
Available Options
Input Options : --vcf [./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz],
--indf [out/test.single.q.emmax.kinf.ind],
The following parameters are available. Ones with "[]" are in effect:
--region [20:20000001-30000000]
Available Options
Input Options : --vcf [./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz],
--region [20:30000001-40000000]NOTICE - nInds = 266 : HG00096 ..., --unit [10000]
,
--field [GT], --rule [], --ignoreFilter [ON]
Filtering Options : --weight [], --minMAF [0.01],
--minCallRate [0.95], --minRSQ [0.00]
Empircial Kinship Method : --BN [ON], --IBS
Output Options : --out-kinf [out/test.single.q.emmax.kinf.20.30000001.40000000.kin],
--raw [ON], --adj-diag, --cov, --verbose
The following parameters are available. Ones with "[]" are in effect:
Available Options
, --unit [10000],
--indf [out/test.single.q.emmax.kinf.ind],
--region [20:1-10000000], --unit [10000],
--field [GT], --rule [], --ignoreFilter [ON]
Filtering Options :
--weight [], --minMAF [0.01],
--minCallRate [0.95], --minRSQ [0.00]
Empircial Kinship Method :
--BN [ON], --IBS
Output Options : --out-kinf [out/test.single.q.emmax.kinf.20.1.10000000.kin],
--raw [ON], --adj-diag, --cov, --verbose
NOTICE - NOTICE - nInds = 266 : HG00096 ...nInds = 266 : HG00096 ...
Input Options : --vcf [./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz],
--indf [out/test.single.q.emmax.kinf.ind],
--region [20:40000001-50000000], --unit [10000],
--field [GT], --rule [], --ignoreFilter [ON]
Filtering Options : --weight [], --minMAF [0.01],
--minCallRate [0.95], --minRSQ [0.00]
Empircial Kinship Method : --BN [ON], --IBS
Output Options : --out-kinf [out/test.single.q.emmax.kinf.20.40000001.50000000.kin],
--raw [ON], --adj-diag, --cov, --verbose
NOTICE - nInds = 266 : HG00096 ...
--field [GT], --rule [], --ignoreFilter [ON]
Filtering Options : --weight [], --minMAF [0.01],
--minCallRate [0.95], --minRSQ [0.00]
Empircial Kinship Method : --BN [ON], --IBS
Output Options : --out-kinf [out/test.single.q.emmax.kinf.20.20000001.30000000.kin],
--raw [ON], --adj-diag, --cov, --verbose
NOTICE - nInds = 266 : HG00096 ...
NOTICE - Processing 1466 markers across 266 individuals...
192 markers included
NOTICE - Processing 3662 markers across 266 individuals...
493 markers included
NOTICE - Started writing kinship matrix into out/test.single.q.emmax.kinf.20.20000001.30000000.kin
NOTICE - Allocating a memory of size 284112
NOTICE - Finished writing kinship matrix into out/test.single.q.emmax.kinf.20.20000001.30000000.kin
The following parameters are available. Ones with "[]" are in effect:
Available Options
Input Options : --vcf [./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz],
--indf [out/test.single.q.emmax.kinf.ind],
--region [20:50000001-60000000], --unit [10000],
--field [GT], --rule [], --ignoreFilter [ON]
Filtering Options : --weight [], --minMAF [0.01],
--minCallRate [0.95], --minRSQ [0.00]NOTICE -
Empircial Kinship Method : --BN [ON], --IBS
Output Options : --out-kinf [out/test.single.q.emmax.kinf.20.50000001.60000000.kin],
--raw [ON], --adj-diag, --cov, --verbose
Started writing kinship matrix into out/test.single.q.emmax.kinf.20.40000001.50000000.kin
NOTICE - Allocating a memory of size 284112
NOTICE - Finished writing kinship matrix into out/test.single.q.emmax.kinf.20.40000001.50000000.kin
NOTICE - nInds = 266 : HG00096 ...
The following parameters are available. Ones with "[]" are in effect:
Available Options
Input Options : --vcf [./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz],
--indf [out/test.single.q.emmax.kinf.ind],
--region [20:60000001-63025520], --unit [10000],
--field [GT], --rule [], --ignoreFilter [ON]
Filtering Options : --weight [], --minMAF [0.01],
--minCallRate [0.95], --minRSQ [0.00]
Empircial Kinship Method : --BN [ON], --IBS
Output Options : --out-kinf [out/test.single.q.emmax.kinf.20.60000001.63025520.kin],
--raw [ON], --adj-diag, --cov, --verbose
NOTICE - nInds = 266 : HG00096 ...
NOTICE - Processing 3367 markers across 266 individuals...
582 markers included
NOTICE - Started writing kinship matrix into out/test.single.q.emmax.kinf.20.1.10000000.kin
NOTICE - Allocating a memory of size 284112
NOTICE - Finished writing kinship matrix into out/test.single.q.emmax.kinf.20.1.10000000.kin
NOTICE - Processing 1763 markers across 266 individuals...
256 markers included
NOTICE - Started writing kinship matrix into out/test.single.q.emmax.kinf.20.50000001.60000000.kin
NOTICE - Allocating a memory of size 284112
NOTICE - Finished writing kinship matrix into out/test.single.q.emmax.kinf.20.50000001.60000000.kin
NOTICE - Processing 1248 markers across 266 individuals...
191 markers included
NOTICE - Started writing kinship matrix into out/test.single.q.emmax.kinf.20.10000001.20000000.kin
NOTICE - Allocating a memory of size 284112
NOTICE - Finished writing kinship matrix into out/test.single.q.emmax.kinf.20.10000001.20000000.kin
NOTICE - Processing 3425 markers across 266 individuals...
557 markers included
NOTICE - Started writing kinship matrix into out/test.single.q.emmax.kinf.20.60000001.63025520.kin
NOTICE - Allocating a memory of size 284112
NOTICE - Finished writing kinship matrix into out/test.single.q.emmax.kinf.20.60000001.63025520.kin
NOTICE - Processing 4170 markers across 266 individuals...
442 markers included
NOTICE - Started writing kinship matrix into out/test.single.q.emmax.kinf.20.30000001.40000000.kin
NOTICE - Allocating a memory of size 284112
NOTICE - Finished writing kinship matrix into out/test.single.q.emmax.kinf.20.30000001.40000000.kin
The following parameters are available. Ones with "[]" are in effect:
Available Options
Input Options : --raw, --cov
Empircial Kinship Method : --BN [ON], --IBS, --YV
Output Options : --out-kinf [out/test.single.q.emmax.kinf],
--verbose
NOTICE - Merging the following kinship matrices
NOTICE - Allocating size 284088 bytes..
NOTICE - Allocating size 284088 bytes..
NOTICE - Allocating size 284088 bytes..
NOTICE - Allocating size 284088 bytes..
NOTICE - Allocating size 284088 bytes..
NOTICE - Allocating size 284088 bytes..
NOTICE - Allocating size 284088 bytes..
NOTICE - Allocating a memory of size 284112
/home/bohuang/local/EPACTS/bin/pEmmax gen-kin --vcf ./../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
/home/bohuang/local/EPACTS/bin/pEmmax gen-kin --vcf ./../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
/home/bohuang/local/EPACTS/bin/pEmmax gen-kin --vcf ./../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
/home/bohuang/local/EPACTS/bin/pEmmax gen-kin --vcf ./../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
/home/bohuang/local/EPACTS/bin/pEmmax gen-kin --vcf ./../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
/home/bohuang/local/EPACTS/bin/pEmmax gen-kin --vcf ./../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
/home/bohuang/local/EPACTS/bin/pEmmax gen-kin --vcf ./../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
/home/bohuang/local/EPACTS/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...
Detected phenotypes with more than 3 unique values -- considering as quantitative phenotypes.
Successfully written phenotypes and 2 covariates across 266 individuals
Processing chromosome 20...
Finished generating EPACTS Makefile
Running 5 parallel jobs of EPACTS
forkExecWait(): make -f /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.Makefile -j 5
/home/bohuang/local/EPACTS/bin/pEmmax assoc --vcf /home/bohuang/local/EPACTS/bin/./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz --region 20:1-10000000 --phenof /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.phe --field GT --indf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.ind --eigf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.eigR --remlf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.reml --out-assocf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.1.10000000.epacts --minMAF 0.001 --maxMAF 1 --maxMAC 1000000000 --minRSQ 0 --minCallRate 0.5 --minMAC 3
/home/bohuang/local/EPACTS/bin/pEmmax assoc --vcf /home/bohuang/local/EPACTS/bin/./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz --region 20:10000001-20000000 --phenof /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.phe --field GT --indf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.ind --eigf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.eigR --remlf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.reml --out-assocf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.10000001.20000000.epacts --minMAF 0.001 --maxMAF 1 --maxMAC 1000000000 --minRSQ 0 --minCallRate 0.5 --minMAC 3
/home/bohuang/local/EPACTS/bin/pEmmax assoc --vcf /home/bohuang/local/EPACTS/bin/./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz --region 20:20000001-30000000 --phenof /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.phe --field GT --indf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.ind --eigf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.eigR --remlf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.reml --out-assocf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.20000001.30000000.epacts --minMAF 0.001 --maxMAF 1 --maxMAC 1000000000 --minRSQ 0 --minCallRate 0.5 --minMAC 3
/home/bohuang/local/EPACTS/bin/pEmmax assoc --vcf /home/bohuang/local/EPACTS/bin/./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz --region 20:30000001-40000000 --phenof /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.phe --field GT --indf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.ind --eigf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.eigR --remlf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.reml --out-assocf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.30000001.40000000.epacts --minMAF 0.001 --maxMAF 1 --maxMAC 1000000000 --minRSQ 0 --minCallRate 0.5 --minMAC 3
/home/bohuang/local/EPACTS/bin/pEmmax assoc --vcf /home/bohuang/local/EPACTS/bin/./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz --region 20:40000001-50000000 --phenof /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.phe --field GT --indf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.ind --eigf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.eigR --remlf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.reml --out-assocf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.40000001.50000000.epacts --minMAF 0.001 --maxMAF 1 --maxMAC 1000000000 --minRSQ 0 --minCallRate 0.5 --minMAC 3
The following parameters are available. Ones with "[]" are in effect:
Available Options
VCF Input Options : --vcf [/home/bohuang/local/EPACTS/bin/./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz],
--region [20:1-10000000], --unit [10000],
--indf [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.ind],
--field [GT], --rule []
The following parameters are available. Ones with "[]" are in effect:
Available Options
VCF Input Options : --vcf [/home/bohuang/local/EPACTS/bin/./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz], --minMAF [1.0e-03],
--maxMAF [1.00], --minMAC [3], --maxMAC [1000000000],
--minCallRate [0.50], --minRSQ [0.00], --ignoreFilter
Other Input Options : --phenof [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.phe],
,
--region [20:30000001-40000000], --unit [10000],
--indf [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.ind],
--field [GT], --rule [], --minMAF [1.0e-03],
--maxMAF [1.00], --minMAC [3], --maxMAC [1000000000],
--minCallRate [0.50]
The following parameters are available. Ones with "[]" are in effect:
--eigf [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.eigR],
--remlf [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.reml], --minRSQ [0.00]
Output Options : --out-assocf [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.1.10000000.epacts], --ignoreFilter,
--verbose
Other Input Options : --phenof [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.phe],
--eigf [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.eigR],
--remlf [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.reml]
Output Options : --out-assocf [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.30000001.40000000.epacts],
--verbose
NOTICE -
Reading eigenvectors
Available Options
VCF Input Options : --vcf [/home/bohuang/local/EPACTS/bin/./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz],
--region [20:20000001-30000000], --unit [10000],
--indf [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.ind],
--field [GT], --rule [], --minMAF [1.0e-03],
--maxMAF [1.00], --minMAC [3], --maxMAC [1000000000],
--minCallRate [0.50], --minRSQ [0.00], --ignoreFilter
Other Input Options : --phenof [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.phe],
--eigf [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.eigR],
--remlf [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.reml]
Output Options : --out-assocf [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.20000001.30000000.epacts],
--verbose
The following parameters are available. Ones with "[]" are in effect:
NOTICE - Reading eigenvectors
Available Options
VCF Input Options : --vcf [/home/bohuang/local/EPACTS/bin/./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz],
--region [20:10000001-20000000], --unit [10000],
--indf [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.ind],
--field [GT], --rule [], --minMAF [1.0e-03],
--maxMAF [1.00], --minMAC [3], --maxMAC [1000000000],
--minCallRate [0.50], --minRSQ [0.00], --ignoreFilter
Other Input Options : --phenof [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.phe],
--eigf [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.eigR],
--remlf [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.reml]
Output Options : --out-assocf [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.10000001.20000000.epacts],
--verbose
NOTICE - Reading eigenvectors
NOTICE - NOTICE - Allocating a size 70221 bytes
NOTICE - Allocating a size 70221 bytes
The following parameters are available. Ones with "[]" are in effect:
Available Options
VCF Input Options : --vcf [/home/bohuang/local/EPACTS/bin/./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz],
--region [20:40000001-50000000], --unit [10000],
--indf [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.ind],
--field [GT], --rule [], --minMAF [1.0e-03],
--maxMAF [1.00], --minMAC [3], --maxMAC [1000000000],
--minCallRate [0.50], --minRSQ [0.00], --ignoreFilter
Other Input Options : --phenof [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.phe],
--eigf [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.eigR],
--remlf [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.reml]
Output Options : --out-assocf [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.40000001.50000000.epacts],
--verbose
NOTICE - Reading eigenvectors
NOTICE - Allocating a size 70221 bytes
Reading eigenvectors
NOTICE - Allocating a size 70221 bytes
NOTICE - Finished loading phenotypes across 266 individuals with 1 covariates (including interception)
NOTICE - NOTICE - Finished loading phenotypes across 266 individuals with 1 covariates (including interception)
NOTICE - NOTICE - Finished loading phenotypes across 266 individuals with 1 covariates (including interception)
Finished loading phenotypes across 266 individuals with 1 covariates (including interception)
NOTICE - Reading delta = 50.118679
NOTICE - Reading delta = 50.118679
NOTICE - Reading delta = 50.118679
Allocating a size 70221 bytes
NOTICE - Finished loading phenotypes across 266 individuals with 1 covariates (including interception)
NOTICE - Reading delta = 50.118679
NOTICE - Reading delta = 50.118679
NOTICE - Processing 1225 markers across 266 individuals...
243 markers included
/home/bohuang/local/EPACTS/bin/epacts-anno --in /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.10000001.20000000.epacts --ref /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta
/home/bohuang/local/EPACTS/bin/anno -i /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.10000001.20000000.epacts -r /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta -f refGene -g /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz -c /home/bohuang/local/EPACTS/share/EPACTS/codon.txt -o /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.10000001.20000000.epacts.tmp --inputFormat epacts -p /home/bohuang/local/EPACTS/share/EPACTS/priority.txt
The following parameters are available. Ones with "[]" are in effect:
Available Options
Required Parameters :
-i [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.10000001.20000000.epacts]
-o [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.10000001.20000000.epacts.tmp]
Gene Annotation
Parameters : -g [/home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz]
-r [/home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta]
--inputFormat [epacts], --checkReference, -f [refGene]
-p [/home/bohuang/local/EPACTS/share/EPACTS/priority.txt]
-c [/home/bohuang/local/EPACTS/share/EPACTS/codon.txt]
-u [], -d [], --se [], --si [], --outputFormat []
Other Annotation Tools : --genomeScore [], --bed [], --tabix []
Load reference genome /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta...
DONE: 84 chromosomes and 3101804739 bases are loaded.
Load codon file /home/bohuang/local/EPACTS/share/EPACTS/codon.txt...
DONE: codon file loaded.
Load priority file /home/bohuang/local/EPACTS/share/EPACTS/priority.txt...
DONE: 24 priority annotation types loaded.
Load gene file /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz...
NOTICE - Processing 1423 markers across 266 individuals...
231 markers included
/home/bohuang/local/EPACTS/bin/epacts-anno --in /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.20000001.30000000.epacts --ref /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta
/home/bohuang/local/EPACTS/bin/anno -i /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.20000001.30000000.epacts -r /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta -f refGene -g /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz -c /home/bohuang/local/EPACTS/share/EPACTS/codon.txt -o /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.20000001.30000000.epacts.tmp --inputFormat epacts -p /home/bohuang/local/EPACTS/share/EPACTS/priority.txt
The following parameters are available. Ones with "[]" are in effect:
Available Options
Required Parameters :
-i [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.20000001.30000000.epacts]
-o [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.20000001.30000000.epacts.tmp]
Gene Annotation
Parameters : -g [/home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz]
-r [/home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta]
--inputFormat [epacts], --checkReference, -f [refGene]
-p [/home/bohuang/local/EPACTS/share/EPACTS/priority.txt]
-c [/home/bohuang/local/EPACTS/share/EPACTS/codon.txt]
-u [], -d [], --se [], --si [], --outputFormat []
Other Annotation Tools : --genomeScore [], --bed [], --tabix []
Load reference genome /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta...
DONE: 84 chromosomes and 3101804739 bases are loaded.
Load codon file /home/bohuang/local/EPACTS/share/EPACTS/codon.txt...
DONE: codon file loaded.
Load priority file /home/bohuang/local/EPACTS/share/EPACTS/priority.txt...
DONE: 24 priority annotation types loaded.
Load gene file /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz...
NOTICE - Processing 4061 markers across 266 individuals...
NOTICE - Processing 3578 markers across 266 individuals...
NOTICE - Processing 3245 markers across 266 individuals...
550 markers included
/home/bohuang/local/EPACTS/bin/epacts-anno --in /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.30000001.40000000.epacts --ref /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta
634 markers included
/home/bohuang/local/EPACTS/bin/epacts-anno --in /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.1.10000000.epacts --ref /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta
612 markers included
/home/bohuang/local/EPACTS/bin/epacts-anno --in /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.40000001.50000000.epacts --ref /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta
/home/bohuang/local/EPACTS/bin/anno -i /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.1.10000000.epacts -r /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta -f refGene -g /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz -c /home/bohuang/local/EPACTS/share/EPACTS/codon.txt -o /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.1.10000000.epacts.tmp --inputFormat epacts -p /home/bohuang/local/EPACTS/share/EPACTS/priority.txt
/home/bohuang/local/EPACTS/bin/anno -i /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.30000001.40000000.epacts -r /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta -f refGene -g /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz -c /home/bohuang/local/EPACTS/share/EPACTS/codon.txt -o /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.30000001.40000000.epacts.tmp --inputFormat epacts -p /home/bohuang/local/EPACTS/share/EPACTS/priority.txt
The following parameters are available. Ones with "[]" are in effect:
Available Options
Required Parameters :
-i [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.30000001.40000000.epacts]
-o [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.30000001.40000000.epacts.tmp]
Gene Annotation
Parameters : -g [/home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz]
-r [/home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta]
--inputFormat [epacts], --checkReference, -f [refGene]
-p [/home/bohuang/local/EPACTS/share/EPACTS/priority.txt]
-c [/home/bohuang/local/EPACTS/share/EPACTS/codon.txt]
-u [], -d [], --se [], --si [], --outputFormat []
Other Annotation Tools : --genomeScore [], --bed [], --tabix []
Load reference genome /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta...
DONE: 84 chromosomes and 3101804739 bases are loaded.
Load codon file /home/bohuang/local/EPACTS/share/EPACTS/codon.txt...
DONE: codon file loaded.
Load priority file /home/bohuang/local/EPACTS/share/EPACTS/priority.txt...
DONE: 24 priority annotation types loaded.
Load gene file /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz...
The following parameters are available. Ones with "[]" are in effect:
Available Options
Required Parameters :
-i [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.1.10000000.epacts]
-o [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.1.10000000.epacts.tmp]
Gene Annotation
Parameters : -g [/home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz]
-r [/home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta]
--inputFormat [epacts], --checkReference, -f [refGene]
-p [/home/bohuang/local/EPACTS/share/EPACTS/priority.txt]
-c [/home/bohuang/local/EPACTS/share/EPACTS/codon.txt]
-u [], -d [], --se [], --si [], --outputFormat []
Other Annotation Tools : --genomeScore [], --bed [], --tabix []
Load reference genome /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta...
DONE: 84 chromosomes and 3101804739 bases are loaded.
Load codon file /home/bohuang/local/EPACTS/share/EPACTS/codon.txt...
DONE: codon file loaded.
Load priority file /home/bohuang/local/EPACTS/share/EPACTS/priority.txt...
DONE: 24 priority annotation types loaded.
Load gene file /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz...
/home/bohuang/local/EPACTS/bin/anno -i /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.40000001.50000000.epacts -r /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta -f refGene -g /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz -c /home/bohuang/local/EPACTS/share/EPACTS/codon.txt -o /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.40000001.50000000.epacts.tmp --inputFormat epacts -p /home/bohuang/local/EPACTS/share/EPACTS/priority.txt
The following parameters are available. Ones with "[]" are in effect:
Available Options
Required Parameters :
-i [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.40000001.50000000.epacts]
-o [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.40000001.50000000.epacts.tmp]
Gene Annotation
Parameters : -g [/home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz]
-r [/home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta]
--inputFormat [epacts], --checkReference, -f [refGene]
-p [/home/bohuang/local/EPACTS/share/EPACTS/priority.txt]
-c [/home/bohuang/local/EPACTS/share/EPACTS/codon.txt]
-u [], -d [], --se [], --si [], --outputFormat []
Other Annotation Tools : --genomeScore [], --bed [], --tabix []
Load reference genome /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta...
DONE: 84 chromosomes and 3101804739 bases are loaded.
Load codon file /home/bohuang/local/EPACTS/share/EPACTS/codon.txt...
DONE: codon file loaded.
Load priority file /home/bohuang/local/EPACTS/share/EPACTS/priority.txt...
DONE: 24 priority annotation types loaded.
Load gene file /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz...
DONE: 92627 gene loaded.
DONE: Generated frequency of each annotype type in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.20000001.30000000.epacts.tmp.anno.frq ].
DONE: Generated frequency of each highest priority annotation type in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.20000001.30000000.epacts.tmp.top.anno.frq ].
Ts/Tv ratio: 2.6581
Ts observed: 1034 times; Tv observed: 389 times.
DONE: Generated frequency of each base change in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.20000001.30000000.epacts.tmp.base.frq ].
DONE: Generated frequency of each codon change in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.20000001.30000000.epacts.tmp.codon.frq ].
DONE: Generated frequency of indel length in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.20000001.30000000.epacts.tmp.indel.frq ].
..............................................
... Anno(tation) ...
... Xiaowei Zhan, Goncalo Abecasis ...
... Speical Thanks: ...
... Hyun Ming Kang, Yanming Li ...
... zha...@umich.edu ...
... Sep 2011 ...
................................................
DONE: 1423 varaints are annotated.
DONE: Generated annotation output in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.20000001.30000000.epacts.tmp ].
Annotation succeed!
mv /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.20000001.30000000.epacts.tmp /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.20000001.30000000.epacts
rm /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.20000001.30000000.epacts.tmp.log /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.20000001.30000000.epacts.tmp.top.anno.frq /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.20000001.30000000.epacts.tmp.anno.frq /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.20000001.30000000.epacts.tmp.base.frq /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.20000001.30000000.epacts.tmp.codon.frq /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.20000001.30000000.epacts.tmp.indel.frq
/home/bohuang/local/EPACTS/bin/pEmmax assoc --vcf /home/bohuang/local/EPACTS/bin/./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz --region 20:50000001-60000000 --phenof /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.phe --field GT --indf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.ind --eigf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.eigR --remlf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.reml --out-assocf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.50000001.60000000.epacts --minMAF 0.001 --maxMAF 1 --maxMAC 1000000000 --minRSQ 0 --minCallRate 0.5 --minMAC 3
The following parameters are available. Ones with "[]" are in effect:
Available Options
VCF Input Options : --vcf [/home/bohuang/local/EPACTS/bin/./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz],
--region [20:50000001-60000000], --unit [10000],
--indf [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.ind],
--field [GT], --rule [], --minMAF [1.0e-03],
--maxMAF [1.00], --minMAC [3], --maxMAC [1000000000],
--minCallRate [0.50], --minRSQ [0.00], --ignoreFilter
Other Input Options : --phenof [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.phe],
--eigf [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.eigR],
--remlf [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.reml]
Output Options : --out-assocf [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.50000001.60000000.epacts],
--verbose
NOTICE - Reading eigenvectors
NOTICE - Allocating a size 70221 bytes
NOTICE - Finished loading phenotypes across 266 individuals with 1 covariates (including interception)
NOTICE - Reading delta = 50.118679
DONE: 92627 gene loaded.
DONE: 92627 gene loaded.
NOTICE - Processing 1732 markers across 266 individuals...
309 markers included
/home/bohuang/local/EPACTS/bin/epacts-anno --in /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.50000001.60000000.epacts --ref /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta
DONE: Generated frequency of each annotype type in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.40000001.50000000.epacts.tmp.anno.frq ].
DONE: Generated frequency of each highest priority annotation type in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.40000001.50000000.epacts.tmp.top.anno.frq ].
Ts/Tv ratio: 2.73486
Ts observed: 2620 times; Tv observed: 958 times.
DONE: Generated frequency of each base change in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.40000001.50000000.epacts.tmp.base.frq ].
DONE: Generated frequency of each codon change in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.40000001.50000000.epacts.tmp.codon.frq ].
DONE: Generated frequency of indel length in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.40000001.50000000.epacts.tmp.indel.frq ].
/home/bohuang/local/EPACTS/bin/anno -i /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.50000001.60000000.epacts -r /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta -f refGene -g /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz -c /home/bohuang/local/EPACTS/share/EPACTS/codon.txt -o /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.50000001.60000000.epacts.tmp --inputFormat epacts -p /home/bohuang/local/EPACTS/share/EPACTS/priority.txt
..............................................
... Anno(tation) ...
... Xiaowei Zhan, Goncalo Abecasis ...
... Speical Thanks: ...
... Hyun Ming Kang, Yanming Li ...
... zha...@umich.edu ...
... Sep 2011 ...
................................................
DONE: 3578 varaints are annotated.
DONE: Generated annotation output in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.40000001.50000000.epacts.tmp ].
Annotation succeed!
mv /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.40000001.50000000.epacts.tmp /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.40000001.50000000.epacts
The following parameters are available. Ones with "[]" are in effect:
Available Options
Required Parameters :
-i [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.50000001.60000000.epacts]
-o [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.50000001.60000000.epacts.tmp]
Gene Annotation
Parameters : -g [/home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz]
-r [/home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta]
--inputFormat [epacts], --checkReference, -f [refGene]
-p [/home/bohuang/local/EPACTS/share/EPACTS/priority.txt]
-c [/home/bohuang/local/EPACTS/share/EPACTS/codon.txt]
-u [], -d [], --se [], --si [], --outputFormat []
Other Annotation Tools : --genomeScore [], --bed [], --tabix []
rm /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.40000001.50000000.epacts.tmp.log /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.40000001.50000000.epacts.tmp.top.anno.frq /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.40000001.50000000.epacts.tmp.anno.frq /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.40000001.50000000.epacts.tmp.base.frq /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.40000001.50000000.epacts.tmp.codon.frq /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.40000001.50000000.epacts.tmp.indel.frq
Load reference genome /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta...
DONE: 84 chromosomes and 3101804739 bases are loaded.
Load codon file /home/bohuang/local/EPACTS/share/EPACTS/codon.txt...
DONE: codon file loaded.
Load priority file /home/bohuang/local/EPACTS/share/EPACTS/priority.txt...
DONE: 24 priority annotation types loaded.
Load gene file /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz...
/home/bohuang/local/EPACTS/bin/pEmmax assoc --vcf /home/bohuang/local/EPACTS/bin/./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz --region 20:60000001-63025520 --phenof /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.phe --field GT --indf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.ind --eigf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.eigR --remlf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.reml --out-assocf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.60000001.63025520.epacts --minMAF 0.001 --maxMAF 1 --maxMAC 1000000000 --minRSQ 0 --minCallRate 0.5 --minMAC 3
The following parameters are available. Ones with "[]" are in effect:
Available Options
VCF Input Options : --vcf [/home/bohuang/local/EPACTS/bin/./../share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz],
--region [20:60000001-63025520], --unit [10000],
--indf [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.ind],
--field [GT], --rule [], --minMAF [1.0e-03],
--maxMAF [1.00], --minMAC [3], --maxMAC [1000000000],
--minCallRate [0.50], --minRSQ [0.00], --ignoreFilter
Other Input Options : --phenof [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.phe],
--eigf [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.eigR],
--remlf [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.reml]
Output Options : --out-assocf [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.60000001.63025520.epacts],
--verbose
NOTICE - Reading eigenvectors
NOTICE - Allocating a size 70221 bytes
DONE: 92627 gene loaded.
NOTICE - Finished loading phenotypes across 266 individuals with 1 covariates (including interception)
NOTICE - Reading delta = 50.118679
DONE: Generated frequency of each annotype type in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.1.10000000.epacts.tmp.anno.frq ].
DONE: Generated frequency of each highest priority annotation type in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.1.10000000.epacts.tmp.top.anno.frq ].
Ts/Tv ratio: 2.96215
Ts observed: 2426 times; Tv observed: 819 times.
DONE: Generated frequency of each base change in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.1.10000000.epacts.tmp.base.frq ].
DONE: Generated frequency of each codon change in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.1.10000000.epacts.tmp.codon.frq ].
DONE: Generated frequency of indel length in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.1.10000000.epacts.tmp.indel.frq ].
DONE: Generated frequency of each annotype type in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.10000001.20000000.epacts.tmp.anno.frq ].
DONE: Generated frequency of each highest priority annotation type in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.10000001.20000000.epacts.tmp.top.anno.frq ].
Ts/Tv ratio: 2.91374
Ts observed: 912 times; Tv observed: 313 times.
DONE: Generated frequency of each base change in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.10000001.20000000.epacts.tmp.base.frq ].
DONE: Generated frequency of each codon change in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.10000001.20000000.epacts.tmp.codon.frq ].
DONE: Generated frequency of indel length in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.10000001.20000000.epacts.tmp.indel.frq ].
..............................................
... Anno(tation) ...
... Xiaowei Zhan, Goncalo Abecasis ...
... Speical Thanks: ...
... Hyun Ming Kang, Yanming Li ...
... zha...@umich.edu ...
... Sep 2011 ...
................................................
DONE: 1225 varaints are annotated.
DONE: Generated annotation output in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.10000001.20000000.epacts.tmp ].
Annotation succeed!
mv /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.10000001.20000000.epacts.tmp /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.10000001.20000000.epacts
..............................................
... Anno(tation) ...
... Xiaowei Zhan, Goncalo Abecasis ...
... Speical Thanks: ...
... Hyun Ming Kang, Yanming Li ...
... zha...@umich.edu ...
... Sep 2011 ...
................................................
DONE: 3245 varaints are annotated.
DONE: Generated annotation output in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.1.10000000.epacts.tmp ].
Annotation succeed!
mv /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.1.10000000.epacts.tmp /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.1.10000000.epacts
rm /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.10000001.20000000.epacts.tmp.log /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.10000001.20000000.epacts.tmp.top.anno.frq /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.10000001.20000000.epacts.tmp.anno.frq /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.10000001.20000000.epacts.tmp.base.frq /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.10000001.20000000.epacts.tmp.codon.frq /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.10000001.20000000.epacts.tmp.indel.frq
rm /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.1.10000000.epacts.tmp.log /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.1.10000000.epacts.tmp.top.anno.frq /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.1.10000000.epacts.tmp.anno.frq /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.1.10000000.epacts.tmp.base.frq /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.1.10000000.epacts.tmp.codon.frq /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.1.10000000.epacts.tmp.indel.frq
DONE: 92627 gene loaded.
NOTICE - Processing 3292 markers across 266 individuals...
DONE: Generated frequency of each annotype type in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.30000001.40000000.epacts.tmp.anno.frq ].
DONE: Generated frequency of each highest priority annotation type in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.30000001.40000000.epacts.tmp.top.anno.frq ].
Ts/Tv ratio: 2.96582
Ts observed: 3037 times; Tv observed: 1024 times.
DONE: Generated frequency of each base change in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.30000001.40000000.epacts.tmp.base.frq ].
DONE: Generated frequency of each codon change in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.30000001.40000000.epacts.tmp.codon.frq ].
DONE: Generated frequency of indel length in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.30000001.40000000.epacts.tmp.indel.frq ].
657 markers included
/home/bohuang/local/EPACTS/bin/epacts-anno --in /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.60000001.63025520.epacts --ref /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta
..............................................
... Anno(tation) ...
... Xiaowei Zhan, Goncalo Abecasis ...
... Speical Thanks: ...
... Hyun Ming Kang, Yanming Li ...
... zha...@umich.edu ...
... Sep 2011 ...
................................................
DONE: 4061 varaints are annotated.
DONE: Generated annotation output in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.30000001.40000000.epacts.tmp ].
Annotation succeed!
mv /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.30000001.40000000.epacts.tmp /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.30000001.40000000.epacts
rm /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.30000001.40000000.epacts.tmp.log /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.30000001.40000000.epacts.tmp.top.anno.frq /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.30000001.40000000.epacts.tmp.anno.frq /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.30000001.40000000.epacts.tmp.base.frq /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.30000001.40000000.epacts.tmp.codon.frq /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.30000001.40000000.epacts.tmp.indel.frq
/home/bohuang/local/EPACTS/bin/anno -i /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.60000001.63025520.epacts -r /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta -f refGene -g /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz -c /home/bohuang/local/EPACTS/share/EPACTS/codon.txt -o /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.60000001.63025520.epacts.tmp --inputFormat epacts -p /home/bohuang/local/EPACTS/share/EPACTS/priority.txt
The following parameters are available. Ones with "[]" are in effect:
Available Options
Required Parameters :
-i [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.60000001.63025520.epacts]
-o [/home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.60000001.63025520.epacts.tmp]
Gene Annotation
Parameters : -g [/home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz]
-r [/home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta]
--inputFormat [epacts], --checkReference, -f [refGene]
-p [/home/bohuang/local/EPACTS/share/EPACTS/priority.txt]
-c [/home/bohuang/local/EPACTS/share/EPACTS/codon.txt]
-u [], -d [], --se [], --si [], --outputFormat []
Other Annotation Tools : --genomeScore [], --bed [], --tabix []
Load reference genome /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta...
DONE: 84 chromosomes and 3101804739 bases are loaded.
Load codon file /home/bohuang/local/EPACTS/share/EPACTS/codon.txt...
DONE: codon file loaded.
Load priority file /home/bohuang/local/EPACTS/share/EPACTS/priority.txt...
DONE: 24 priority annotation types loaded.
Load gene file /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz...
DONE: 92627 gene loaded.
DONE: Generated frequency of each annotype type in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.60000001.63025520.epacts.tmp.anno.frq ].
DONE: Generated frequency of each highest priority annotation type in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.60000001.63025520.epacts.tmp.top.anno.frq ].
Ts/Tv ratio: 4.03364
Ts observed: 2638 times; Tv observed: 654 times.
DONE: Generated frequency of each base change in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.60000001.63025520.epacts.tmp.base.frq ].
DONE: Generated frequency of each codon change in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.60000001.63025520.epacts.tmp.codon.frq ].
DONE: Generated frequency of indel length in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.60000001.63025520.epacts.tmp.indel.frq ].
..............................................
... Anno(tation) ...
... Xiaowei Zhan, Goncalo Abecasis ...
... Speical Thanks: ...
... Hyun Ming Kang, Yanming Li ...
... zha...@umich.edu ...
... Sep 2011 ...
................................................
DONE: 3292 varaints are annotated.
DONE: Generated annotation output in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.60000001.63025520.epacts.tmp ].
Annotation succeed!
mv /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.60000001.63025520.epacts.tmp /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.60000001.63025520.epacts
rm /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.60000001.63025520.epacts.tmp.log /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.60000001.63025520.epacts.tmp.top.anno.frq /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.60000001.63025520.epacts.tmp.anno.frq /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.60000001.63025520.epacts.tmp.base.frq /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.60000001.63025520.epacts.tmp.codon.frq /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.60000001.63025520.epacts.tmp.indel.frq
DONE: 92627 gene loaded.
DONE: Generated frequency of each annotype type in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.50000001.60000000.epacts.tmp.anno.frq ].
DONE: Generated frequency of each highest priority annotation type in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.50000001.60000000.epacts.tmp.top.anno.frq ].
Ts/Tv ratio: 2.66173
Ts observed: 1259 times; Tv observed: 473 times.
DONE: Generated frequency of each base change in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.50000001.60000000.epacts.tmp.base.frq ].
DONE: Generated frequency of each codon change in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.50000001.60000000.epacts.tmp.codon.frq ].
DONE: Generated frequency of indel length in [ /home/bohuang/local/EPACTS/bin/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 ...
... zha...@umich.edu ...
... Sep 2011 ...
................................................
DONE: 1732 varaints are annotated.
DONE: Generated annotation output in [ /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.50000001.60000000.epacts.tmp ].
Annotation succeed!
mv /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.50000001.60000000.epacts.tmp /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.50000001.60000000.epacts
rm /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.50000001.60000000.epacts.tmp.log /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.50000001.60000000.epacts.tmp.top.anno.frq /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.50000001.60000000.epacts.tmp.anno.frq /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.50000001.60000000.epacts.tmp.base.frq /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.50000001.60000000.epacts.tmp.codon.frq /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.50000001.60000000.epacts.tmp.indel.frq
/home/bohuang/local/EPACTS/bin/epacts-cat /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.1.10000000.epacts /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.10000001.20000000.epacts /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.20000001.30000000.epacts /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.30000001.40000000.epacts /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.40000001.50000000.epacts /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.50000001.60000000.epacts /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.60000001.63025520.epacts | /home/bohuang/local/EPACTS/bin/bgzip -c > /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.epacts.gz
/home/bohuang/local/EPACTS/bin/tabix -f -pbed /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.epacts.gz
rm -f /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.1.10000000.epacts /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.10000001.20000000.epacts /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.20000001.30000000.epacts /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.30000001.40000000.epacts /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.40000001.50000000.epacts /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.50000001.60000000.epacts /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.20.60000001.63025520.epacts
/home/bohuang/local/EPACTS/bin/epacts-plot --in /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.epacts.gz --region 20:0
nsnps = 3236
Rscript /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.epacts.R --vanilla
export GDFONTPATH=/home/bohuang/local/EPACTS/share/EPACTS; export GNUPLOT_FONTPATH=/home/bohuang/local/EPACTS/share/EPACTS; export GNUPLOT_PS_DIR=/home/bohuang/local/EPACTS/share/EPACTS; export PATH=$PATH:/home/bohuang/local/EPACTS/bin/; export GNUPLOT_PFBTOPFA="pfbtops %s"; gnuplot /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.epacts.cmd
export GDFONTPATH=/home/bohuang/local/EPACTS/share/EPACTS; export GNUPLOT_FONTPATH=/home/bohuang/local/EPACTS/share/EPACTS; export GNUPLOT_PS_DIR=/home/bohuang/local/EPACTS/share/EPACTS; export PATH=$PATH:/home/bohuang/local/EPACTS/bin/; export GNUPLOT_PFBTOPFA="pfbtops %s"; /home/bohuang/local/EPACTS/bin/epstopdf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.epacts.qq.eps
GPL Ghostscript 9.26: Unrecoverable error, exit code 1
Error: /undefined in LTB
Operand stack:
Execution stack:
%interp_exit .runexec2 --nostringval-- --nostringval-- --nostringval-- 2 %stopped_push --nostringval-- --nostringval-- --nostringval-- false 1 %stopped_push 2045 1 3 %oparray_pop 2044 1 3 %oparray_pop --nostringval-- 2025 1 3 %oparray_pop 1884 1 3 %oparray_pop --nostringval-- %errorexec_pop .runexec2 --nostringval-- --nostringval-- --nostringval-- 2 %stopped_push --nostringval--
Dictionary stack:
--dict:974/1684(ro)(G)-- --dict:0/20(G)-- --dict:87/200(L)-- --dict:205/256(L)--
Current allocation mode is local
export GDFONTPATH=/home/bohuang/local/EPACTS/share/EPACTS; export GNUPLOT_FONTPATH=/home/bohuang/local/EPACTS/share/EPACTS; export GNUPLOT_PS_DIR=/home/bohuang/local/EPACTS/share/EPACTS; export PATH=$PATH:/home/bohuang/local/EPACTS/bin/; export GNUPLOT_PFBTOPFA="pfbtops %s"; gnuplot /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.epacts.cmd
export GDFONTPATH=/home/bohuang/local/EPACTS/share/EPACTS; export GNUPLOT_FONTPATH=/home/bohuang/local/EPACTS/share/EPACTS; export GNUPLOT_PS_DIR=/home/bohuang/local/EPACTS/share/EPACTS; export PATH=$PATH:/home/bohuang/local/EPACTS/bin/; export GNUPLOT_PFBTOPFA="pfbtops %s"; /home/bohuang/local/EPACTS/bin/epstopdf /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.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/bohuang/local/EPACTS/bin/out/test.single.q.emmax.epacts.cmd /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.epacts.qq.eps /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.epacts.mh.eps /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.epacts.*.dat
zcat /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.epacts.gz | awk '$11 != "NA" { print $0 }' | sort -g -k 11 | head -n 5000 > /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.epacts.top5000
touch /home/bohuang/local/EPACTS/bin/out/test.single.q.emmax.epacts.OK
Taking the site list from the VCF file
Annotate the VCF file
/home/bohuang/local/EPACTS/bin/anno -i out/1000G_exome_chr20_example_softFiltered.calls.sites.vcf.gz -r /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta -f refGene -g /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz -c /home/bohuang/local/EPACTS/share/EPACTS/codon.txt -o out/1000G_exome_chr20_example_softFiltered.calls.sites.anno.vcf.gz --inputFormat vcf -p /home/bohuang/local/EPACTS/share/EPACTS/priority.txt
The following parameters are available. Ones with "[]" are in effect:
Available Options
Required Parameters :
-i [out/1000G_exome_chr20_example_softFiltered.calls.sites.vcf.gz]
-o [out/1000G_exome_chr20_example_softFiltered.calls.sites.anno.vcf.gz]
Gene Annotation
Parameters : -g [/home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz]
-r [/home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta]
--inputFormat [vcf], --checkReference, -f [refGene]
-p [/home/bohuang/local/EPACTS/share/EPACTS/priority.txt]
-c [/home/bohuang/local/EPACTS/share/EPACTS/codon.txt]
-u [], -d [], --se [], --si [], --outputFormat []
Other Annotation Tools : --genomeScore [], --bed [], --tabix []
Load reference genome /home/bohuang/local/EPACTS/share/EPACTS/human_g1k_v37.fasta...
DONE: 84 chromosomes and 3101804739 bases are loaded.
Load codon file /home/bohuang/local/EPACTS/share/EPACTS/codon.txt...
DONE: codon file loaded.
Load priority file /home/bohuang/local/EPACTS/share/EPACTS/priority.txt...
DONE: 24 priority annotation types loaded.
Load gene file /home/bohuang/local/EPACTS/share/EPACTS/hg19_gencodeV14.txt.gz...
DONE: 92627 gene loaded.
DONE: Generated frequency of each annotype type in [ out/1000G_exome_chr20_example_softFiltered.calls.sites.anno.vcf.gz.anno.frq ].
DONE: Generated frequency of each highest priority annotation type in [ out/1000G_exome_chr20_example_softFiltered.calls.sites.anno.vcf.gz.top.anno.frq ].
Ts/Tv ratio: 2.9522
Ts observed: 14268 times; Tv observed: 4833 times.
DONE: Generated frequency of each base change in [ out/1000G_exome_chr20_example_softFiltered.calls.sites.anno.vcf.gz.base.frq ].
DONE: Generated frequency of each codon change in [ out/1000G_exome_chr20_example_softFiltered.calls.sites.anno.vcf.gz.codon.frq ].
DONE: Generated frequency of indel length in [ out/1000G_exome_chr20_example_softFiltered.calls.sites.anno.vcf.gz.indel.frq ].
..............................................
... Anno(tation) ...
... Xiaowei Zhan, Goncalo Abecasis ...
... Speical Thanks: ...
... Hyun Ming Kang, Yanming Li ...
... zha...@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
/home/bohuang/local/EPACTS/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
/home/bohuang/local/EPACTS/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
Detected phenotypes with more than 3 unique values -- considering as quantitative phenotypes.
Successfully written phenotypes and 2 covariates across 266 individuals
Finished generating EPACTS Makefile
Running 5 parallel jobs of EPACTS
forkExecWait(): make -f /home/bohuang/local/EPACTS/bin/out/test.gene.skat.Makefile -j 5
Rscript /home/bohuang/local/EPACTS/bin/out/test.gene.skat.0.R --vanilla
Rscript /home/bohuang/local/EPACTS/bin/out/test.gene.skat.1.R --vanilla
Rscript /home/bohuang/local/EPACTS/bin/out/test.gene.skat.2.R --vanilla
Rscript /home/bohuang/local/EPACTS/bin/out/test.gene.skat.3.R --vanilla
Rscript /home/bohuang/local/EPACTS/bin/out/test.gene.skat.4.R --vanilla
Loading required package: epactsR
Loading required package: epactsR
Loading required package: epactsR
Loading required package: epactsR
Loading required package: epactsR
Loading required package: mmSKAT
Loading required package: mmSKAT
Loading required package: mmSKAT
Loading required package: mmSKAT
Loading required package: mmSKAT
NULL
Sucessfully wrote ( 100 * 7 ) matrix
There were 17 warnings (use warnings() to see them)
Rscript /home/bohuang/local/EPACTS/bin/out/test.gene.skat.5.R --vanilla
Loading required package: epactsR
Loading required package: mmSKAT
NULL
Sucessfully wrote ( 8 * 7 ) matrix
Warning message:
Only one SNP in the SNP set!
NULL
Sucessfully wrote ( 100 * 7 ) matrix
There were 15 warnings (use warnings() to see them)
NULL
Sucessfully wrote ( 100 * 7 ) matrix
There were 11 warnings (use warnings() to see them)
NULL
Sucessfully wrote ( 100 * 7 ) matrix
There were 18 warnings (use warnings() to see them)
NULL
Sucessfully wrote ( 100 * 7 ) matrix
There were 12 warnings (use warnings() to see them)
(head -1 /home/bohuang/local/EPACTS/bin/out/test.gene.skat.0.epacts; cat /home/bohuang/local/EPACTS/bin/out/test.gene.skat.0.epacts /home/bohuang/local/EPACTS/bin/out/test.gene.skat.1.epacts /home/bohuang/local/EPACTS/bin/out/test.gene.skat.2.epacts /home/bohuang/local/EPACTS/bin/out/test.gene.skat.3.epacts /home/bohuang/local/EPACTS/bin/out/test.gene.skat.4.epacts /home/bohuang/local/EPACTS/bin/out/test.gene.skat.5.epacts | grep -v ^#;) > /home/bohuang/local/EPACTS/bin/out/test.gene.skat.epacts
rm /home/bohuang/local/EPACTS/bin/out/test.gene.skat.0.epacts /home/bohuang/local/EPACTS/bin/out/test.gene.skat.1.epacts /home/bohuang/local/EPACTS/bin/out/test.gene.skat.2.epacts /home/bohuang/local/EPACTS/bin/out/test.gene.skat.3.epacts /home/bohuang/local/EPACTS/bin/out/test.gene.skat.4.epacts /home/bohuang/local/EPACTS/bin/out/test.gene.skat.5.epacts /home/bohuang/local/EPACTS/bin/out/test.gene.skat.0.R /home/bohuang/local/EPACTS/bin/out/test.gene.skat.1.R /home/bohuang/local/EPACTS/bin/out/test.gene.skat.2.R /home/bohuang/local/EPACTS/bin/out/test.gene.skat.3.R /home/bohuang/local/EPACTS/bin/out/test.gene.skat.4.R /home/bohuang/local/EPACTS/bin/out/test.gene.skat.5.R
/home/bohuang/local/EPACTS/bin/epacts-plot --in /home/bohuang/local/EPACTS/bin/out/test.gene.skat.epacts
nsnps = 437
Rscript /home/bohuang/local/EPACTS/bin/out/test.gene.skat.epacts.R --vanilla
export GDFONTPATH=/home/bohuang/local/EPACTS/share/EPACTS; export GNUPLOT_FONTPATH=/home/bohuang/local/EPACTS/share/EPACTS; export GNUPLOT_PS_DIR=/home/bohuang/local/EPACTS/share/EPACTS; export PATH=$PATH:/home/bohuang/local/EPACTS/bin/; export GNUPLOT_PFBTOPFA="pfbtops %s"; gnuplot /home/bohuang/local/EPACTS/bin/out/test.gene.skat.epacts.cmd
export GDFONTPATH=/home/bohuang/local/EPACTS/share/EPACTS; export GNUPLOT_FONTPATH=/home/bohuang/local/EPACTS/share/EPACTS; export GNUPLOT_PS_DIR=/home/bohuang/local/EPACTS/share/EPACTS; export PATH=$PATH:/home/bohuang/local/EPACTS/bin/; export GNUPLOT_PFBTOPFA="pfbtops %s"; /home/bohuang/local/EPACTS/bin/epstopdf /home/bohuang/local/EPACTS/bin/out/test.gene.skat.epacts.qq.eps
GPL Ghostscript 9.26: Unrecoverable error, exit code 1
Error: /undefined in LTB
Operand stack:
Execution stack:
%interp_exit .runexec2 --nostringval-- --nostringval-- --nostringval-- 2 %stopped_push --nostringval-- --nostringval-- --nostringval-- false 1 %stopped_push 2045 1 3 %oparray_pop 2044 1 3 %oparray_pop --nostringval-- 2025 1 3 %oparray_pop 1884 1 3 %oparray_pop --nostringval-- %errorexec_pop .runexec2 --nostringval-- --nostringval-- --nostringval-- 2 %stopped_push --nostringval--
Dictionary stack:
--dict:974/1684(ro)(G)-- --dict:0/20(G)-- --dict:87/200(L)-- --dict:205/256(L)--
Current allocation mode is local
export GDFONTPATH=/home/bohuang/local/EPACTS/share/EPACTS; export GNUPLOT_FONTPATH=/home/bohuang/local/EPACTS/share/EPACTS; export GNUPLOT_PS_DIR=/home/bohuang/local/EPACTS/share/EPACTS; export PATH=$PATH:/home/bohuang/local/EPACTS/bin/; export GNUPLOT_PFBTOPFA="pfbtops %s"; gnuplot /home/bohuang/local/EPACTS/bin/out/test.gene.skat.epacts.cmd
export GDFONTPATH=/home/bohuang/local/EPACTS/share/EPACTS; export GNUPLOT_FONTPATH=/home/bohuang/local/EPACTS/share/EPACTS; export GNUPLOT_PS_DIR=/home/bohuang/local/EPACTS/share/EPACTS; export PATH=$PATH:/home/bohuang/local/EPACTS/bin/; export GNUPLOT_PFBTOPFA="pfbtops %s"; /home/bohuang/local/EPACTS/bin/epstopdf /home/bohuang/local/EPACTS/bin/out/test.gene.skat.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/bohuang/local/EPACTS/bin/out/test.gene.skat.epacts.cmd /home/bohuang/local/EPACTS/bin/out/test.gene.skat.epacts.qq.eps /home/bohuang/local/EPACTS/bin/out/test.gene.skat.epacts.mh.eps /home/bohuang/local/EPACTS/bin/out/test.gene.skat.epacts.*.dat
cat /home/bohuang/local/EPACTS/bin/out/test.gene.skat.epacts | awk '$10 != "NA" { print $0 }' | sort -g -k 10 | head -n 5000 > /home/bohuang/local/EPACTS/bin/out/test.gene.skat.epacts.top5000
touch /home/bohuang/local/EPACTS/bin/out/test.gene.skat.epacts.OK
----------------------------------------------------------------
END
Syed M. Ijlal Haider
Jan 24, 2019, 5:36:23 AM1/24/19
to EPACTS
Hello,
Just wondering if you were able to solve this error?? I am having exactly the same problem and trying to figure it out from last 2 days but in-vein. would be nice if you can explain a bit if you have solved the problem?
Kind Regards,
Haider
黄博
Jan 25, 2019, 5:38:20 PM1/25/19
to epa...@googlegroups.com
Sorry. I have not solve the problem in my Ubuntu. Now I am using the soft on the server. Good luck.
Best,
Bo
Syed M. Ijlal Haider <ijlalhy...@gmail.com> 于2019年1月24日周四 上午5:36写道：
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Victor de Jager
Jun 5, 2020, 5:28:56 AM6/5/20
to EPACTS
I have exactly the same issue, any solutions are welcome
Valentina Cipriani
Oct 14, 2020, 7:26:18 AM10/14/20
to EPACTS
I received the same error
I see that no solutions were suggested at the time
Is anyone able to help please?
Many thanks
Valentina Cipriani
Oct 20, 2020, 5:26:44 AM10/20/20
to EPACTS
Hello everyone
I received some help from my IT department - below is a workaround rather than a root-cause fix, but it solved the issue for me.
It is a one line (plus one comment) change to prologue.ps as shown below:
git diff HEAD^ HEAD
diff --git a/data/prologue.ps b/data/prologue.ps
index 6777ee6..e9a8bc6 100644
--- a/data/prologue.ps
+++ b/data/prologue.ps
@@ -48,6 +48,8 @@
% Default Line Types
/LTw {PL [] 1 setgray} def /LTb {BL [] LCb DL} def
+% Workaround to avoid epstopdf failure
+/LTB {LTb} def
/LTa {AL [1 udl mul 2 udl mul] 0 setdash LCa setrgbcolor} def
/LT0 {PL [] LC0 DL} def
/LT1 {PL [4 dl1 2 dl2] LC1 DL} def
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