Open
Description
openedon Dec 29, 2022
Description of the bug
Hi,
This is about the GATK resource bundle but I am opening a bug report here because I encounter this while using this pipeline.
dbSNP138 has the wrong reference allele at position chr6:31236715.
Command used and terminal output
Command was:
nextflow run nf-core/sarek -profile docker --input WES_samplesheet.csv --outdir WES_output/ --genome GATK.GRCh37 --intervals GRCh37_exome_all_.bed --wes --save_reference --tools deepvariant,haplotypecaller --max_cpus 3 --max_memory 20.GB -with-trace --skip_tools baserecalibrator -resume
Terminal output looks like this:
-[nf-core/sarek] Pipeline completed with errors-
Error executing process > 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:VCF_VARIANT_FILTERING_GATK:FILTERVARIANTTRANCHES (mysample)'
Caused by:
Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:VCF_VARIANT_FILTERING_GATK:FILTERVARIANTTRANCHES (mysample)` terminated with an error exit status (2)
Command executed:
gatk --java-options "-Xmx12g" FilterVariantTranches \
--variant mysample.cnn.vcf.gz \
--resource dbsnp_138.b37.vcf.gz --resource 1000G_phase1.indels.b37.vcf.gz --resource Mills_and_1000G_gold_standard.indels.b37.vcf.gz --resource 1000G_phase1.snps.high_confidence.b37.vcf.gz \
--output mysample.haplotypecaller.filtered.vcf.gz \
--tmp-dir . \
--info-key CNN_1D
cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:VCF_VARIANT_FILTERING_GATK:FILTERVARIANTTRANCHES":
gatk4: $(echo $(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*$//')
END_VERSIONS
.
.
.
o retrieve a sequence dictionary from the associated index file
[95/1923] 16:07:11.173 WARN IntelInflater - Zero Bytes Written : 0
16:07:11.184 INFO FilterVariantTranches - Done initializing engine
16:07:11.294 INFO ProgressMeter - Starting traversal
16:07:11.295 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
16:07:11.296 INFO FilterVariantTranches - Starting pass 0 through the variants
16:07:24.653 INFO ProgressMeter - 1:150597890 0.2 3000 13476.1
16:07:39.146 INFO ProgressMeter - 2:68402012 0.5 6000 12926.4
16:07:54.029 INFO ProgressMeter - 3:44283525 0.7 9000 12636.6
16:08:04.120 INFO ProgressMeter - 4:762963 0.9 11000 12494.3
16:08:15.045 INFO ProgressMeter - 5:1216775 1.1 13000 12235.5
16:08:25.728 INFO ProgressMeter - 5:180235722 1.2 15000 12091.4
16:08:28.560 INFO FilterVariantTranches - Filtered 0 SNPs out of 14542 and filtered 0 indels out of 1233 with INFO score: CNN_1D.
16:08:28.563 INFO FilterVariantTranches - Shutting down engine
[December 20, 2022 at 4:08:28 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.FilterVariantTranches done. Elapsed time: 1.32 minutes. Runtime.totalMemory()=2260729856
***********************************************************************
A USER ERROR has occurred: Bad input: The provided variant file(s) have inconsistent references for the same position(s) at 6:31236715, GC* in input vs. GA* in resource
***********************************************************************
Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.
Work dir:
/home/owiepoc/work/37/f047461c745cbc3a799066d76ae620
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
Relevant files
No response
System information
nextflow version 22.10.3.5834
Container engine docker
Local executor
OS: Ubuntu 20.04.5 LTS x86_64
Host: VMware Virtual Platform None
Kernel: 5.4.0-135-generic
Uptime: 22 days, 15 mins
Packages: 775 (dpkg), 6 (snap)
Shell: bash 5.0.17
Resolution: preferred
Terminal: /dev/pts/0
CPU: Intel Xeon Platinum 8360Y (20) @ 2.394GHz
GPU: 00:0f.0 VMware SVGA II Adapter
Memory: 3377MiB / 140829MiB
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment