Could not find vcf.stats file after Mutect2
I executed Mutect2 to do a variant calling. The command ran successfully however, when I tried to do the FilterMutectCalls, I got the error message stating the following:
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A USER ERROR has occurred: Mutect stats table somatic_1t.vcf.stats not found. When Mutect2 outputs a file calls.vcf it also creates a calls.vcf.stats file. Perhaps this file was not moved along with the vcf, or perhaps it was not delocalized from a virtual machine while running in the cloud.
When I tried to look for a solution, I found out similar issues were brought up earlier but the bug has been addressed in newer versions. As I am using GATK 4.2.4.0 I wonder what could be the reason now. Clearly, my Mutect2 command did not generate the 'stats' file. Please suggest a solution to this.
REQUIRED for all errors and issues:
a) GATK version used: gatk/4.2.4.0
b) Exact command used:
#!/bin/bash
#SBATCH --time=23:30:00
#SBATCH --account=def-kar
#SBATCH --mem-per-cpu=3G
#SBATCH --cpus-per-task=16
module load StdEnv/2020
module load gatk/4.2.4.0
gatk Mutect2 \
-R ../ref/GRCh38.d1.vd1.fa \
-I recal_reads_1_n.bam \
-I recal_reads_1_t.bam \
-normal 20 \
--germline-resource ../cloudRes/af-only-gnomad.hg38.vcf.gz \
--panel-of-normals ../cloudRes/1000g_pon.hg38.vcf.gz \
-O somatic_1t.vcf
gatk FilterMutectCalls \
-R ../ref/GRCh38.d1.vd1.fa \
-V somatic_1t.vcf \
-O somatic_1t_filtered.vcf
c) Entire program log:
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1091)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:140)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
at org.broadinstitute.hellbender.Main.main(Main.java:289)
Using GATK jar /cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/gatk/4.2.4.0/gatk-package-4.2.4.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/gatk/4.2.4.0/gatk-package-4.2.4.0-local.jar Mutect2 -R ../ref/GRCh38.d1.vd1.fa -I recal_reads_1_n.bam -I recal_reads_1_t.bam -normal 20 --germline-resource ../cloudRes/af-only-gnomad.hg38.vcf.gz --panel-of-normals ../cloudRes/1000g_pon.hg38.vcf.gz -O somatic_1t.vcf
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Hi Seke Keretsu,
Thank you for your much-appreciated patience and for writing to the GATK forum!
I reviewed the error you encountered with our developers and received some feedback on your next steps.
The cluster you are using doesn't seem to be saving your stats table properly when running the tool. Have you tried running the tool locally?
I'd recommend the following: firstly, ensure that your stats table is, in fact, being generated. If it is being generated and isn't being saved, our hypothesis is likely correct. In that case, go ahead and re-try running the tool on your local computer instead of a cluster.
I hope this helps! Please let me know if this leads you to success. If you have any further questions/issues in the meantime, please do not hesitate to reach out.
Best,
Anthony
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Hi Seke Keretsu,
We haven't heard from you in a while so we're going to close out this ticket. If you still require assistance, simply respond to this email and we'll be happy to pick up where we left off!
Kind regards,
Anthony
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