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runme.log
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+ ./BitEpi.o -i sampleData/data.csv -o sampleData/out1 -t 1 -b1 10 -a1 0.001 -b2 0.502 -a2 35 -a3 0.003
runme.sh: line 5: ./BitEpi.o: No such file or directory
+ ./BitEpi.o -i sampleData/data.csv -o sampleData/out2 -t 2 -b3 0.505 -b4 40 -a4 30 -sort
runme.sh: line 6: ./BitEpi.o: No such file or directory
+ ./BitEpi.o -i sampleData/data.csv -o sampleData/out3 -t 1 -best
runme.sh: line 7: ./BitEpi.o: No such file or directory
+ bash GAMETES_2_EPI.sh sampleData/GAMETES_Example_Output
sampleData/GAMETES_Example_Output.txt exists
datamash is installed
plink is installed
>>>>> There are 100 SNPs and 2000 samples in the file
PLINK v1.90b6.10 64-bit (17 Jun 2019) www.cog-genomics.org/plink/1.9/
(C) 2005-2019 Shaun Purcell, Christopher Chang GNU General Public License v3
Logging to sampleData/GAMETES_Example_Output.log.
Options in effect:
--out sampleData/GAMETES_Example_Output
--pheno sampleData/GAMETES_Example_Output.pheno
--recode transpose
--vcf sampleData/GAMETES_Example_Output.vcf
3918 MB RAM detected; reserving 1959 MB for main workspace.
--vcf: sampleData/GAMETES_Example_Output-temporary.bed +
sampleData/GAMETES_Example_Output-temporary.bim +
sampleData/GAMETES_Example_Output-temporary.fam written.
100 variants loaded from .bim file.
2000 people (0 males, 0 females, 2000 ambiguous) loaded from .fam.
Ambiguous sex IDs written to sampleData/GAMETES_Example_Output.nosex .
2000 phenotype values present after --pheno.
Warning: Ignoring phenotypes of missing-sex samples. If you don't want those
phenotypes to be ignored, use the --allow-no-sex flag.
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 2000 founders and 0 nonfounders present.
Calculating allele frequencies... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99% done.
100 variants and 2000 people pass filters and QC.
Among remaining phenotypes, 1000 are cases and 1000 are controls.
--recode transpose to sampleData/GAMETES_Example_Output.tped +
sampleData/GAMETES_Example_Output.tfam ... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99%done.
+ bash VCF_2_EPI.sh sampleData/Hipster.vcf.bgz sampleData/Hipster.tsv 2
==============================================================
Argument 1: path to vcf or vcf.bgz file
Argument 2: path tab seprated (tsv) sample annotation file
Argument 3: isCase column number in sample annotation file
==============================================================
Argument 1: sampleData/Hipster.vcf.bgz
Argument 2: sampleData/Hipster.tsv
Argument 3: 2
==============================================================
***** This scripts uses bcftools.
***** This scripts uses vcf file rsid column as SNP id. It should be uniq id and should not be empty.
***** This scripts does not check if rsid exist and if it is uniqu for each snp
***** The order of samples in VCF file and sample annotation file should be the same.
***** The first line of the sample annotation file should be header line.
***** The sample annotation file should tab separated (tsv) file.
***** isCase column should only include 'True' and 'False'
***** The output is vcffile.epi.csv
***** This scripts does not check input arguments.
>>>>> Test if sampels are in the same order in vcf and sample annotation file
Sample list are matched
>>>>> Converting....
[W::vcf_parse] Contig '1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '2' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '4' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '5' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '6' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '8' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '9' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '10' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '11' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '12' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '13' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '14' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '15' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '16' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '18' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '19' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '21' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '22' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '2' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '4' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '5' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '6' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '8' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '9' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '10' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '11' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '12' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '13' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '14' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '15' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '16' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '18' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '19' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '21' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '22' is not defined in the header. (Quick workaround: index the file with tabix.)
>>>>> Done
>>>>> Remove temporary files
>>>>> Output: sampleData/Hipster.vcf.bgz.epi.csv
+ set +x
>>>>>>> Output files
-rw-r--r-- 1 arash arash 38 Nov 28 14:11 sampleData/out1.Alpha.1.csv
-rw-r--r-- 1 arash arash 617 Nov 28 14:11 sampleData/out1.Alpha.2.csv
-rw-r--r-- 1 arash arash 6543 Nov 28 14:11 sampleData/out1.Alpha.3.csv
-rw-r--r-- 1 arash arash 139 Nov 28 14:11 sampleData/out1.Beta.1.csv
-rw-r--r-- 1 arash arash 885 Nov 28 14:11 sampleData/out1.Beta.2.csv
-rw-r--r-- 1 arash arash 1597 Nov 28 14:11 sampleData/out2.Alpha.4.csv
-rw-r--r-- 1 arash arash 9058 Nov 28 14:11 sampleData/out2.Beta.3.csv
-rw-r--r-- 1 arash arash 2205 Nov 28 14:11 sampleData/out2.Beta.4.csv
-rw-r--r-- 1 arash arash 5210 Nov 28 14:11 sampleData/out3.best.csv
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