no output from GATK CombineGVCFs
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7 weeks ago
liyong ▴ 20

Hello All,

I am using GATK to do SNPs calling from 140 RNAseq data. After variant calling of each sample with HaplotypeCaller, I get 140 g.vcf.gz files. Before perform the final joint genotyping through GenotypeGVCFs, I need to combine these 140 g.vcf.gz files into one. Beforehand, I prepare a gvcf file list with ls hard_filtered/*_filtered.vcf.gz > gvcfs.list

And the command used for combining are: gatk CombineGVCFs -R genome.fa --variant gvcfs.list -O cohort.vcf.gz

After running a very long time (~8 hours), the job finished (telling from top command), and the log file didn't show any error. However, I didn't see any output file. Is there anything I can do to fix this?

Thanks a lot.

combineGVCFs gatk • 210 views
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and the log file didn't show any error.

which log file ?

Retry with

gatk   --java-options "-Xmx5g -Djava.io.tmpdir=." CombineGVCFs  -R genome.fa --variant gvcfs.list -O cohort.g.vcf.gz 2> log.stderr
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Thanks for your comments.

The CombineGVCFs commands are inside a shell script, when I run the script, I use nohup ./combine.sh >& combine.log &

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don't use nohup. nohup is bad, among other things it mixes stdout and stderr, you don't know how and why it exited . You'd better use screen or tmux .

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Thanks Pierre for the tips I will give it a try with screen later.

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