Closed YussAb closed 2 years ago
Hi,
I have the same issue.
I guess the -L
option is mandatory.
Using the germline ressources fix the bug
intervalsOptions = params.no_intervals ? "-L ${germlineResource}" : "-L ${intervalBed}"
Best N
A quick follow up on that. It seems that providing -L ${germlineResource}
requires a hugh amount of RAM ...
At least for exome data analysis, I think it would be better to use ;
intervalsOptions = params.no_intervals ? params.target_bed ? "-L ${params.target_bed}" : "-L ${germlineResource}" : "-L ${intervalBed}"
This is related to #299
In the GATK bundle they provide this ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/Mutect2/GetPileupSummaries/small_exac_common_3.hg38.vcf.gz.tbi
That one is just 1.3 MB. I need to test it, but I believe this may solve the memory issue.
I ran some samples (in another Mutect2 pipeline...) which were failing due to a memory issue in GetPileUpSummaries using this small_exac_common_3.hg38.vcf.gz
and they went through. I am unsure though how this may impact the results...
Closed by #592
Dear sarek community, I used the pipeline several times and I always found this bugs using Mutect2.
Description of the bug
GATK Mutect2
I found that among the pipeline there are two different bug using Mutect2 for somatic Tumor-Normal samples.
1- Mutect2 for Variantcalling using intervals option for parallelization; Even if the pipeline is executed correctly I get the following error;
**The exit status of the task that caused the workflow execution to fail was: null.
The full error message was:
No such property: variantcaller for class: Script_a7aea67c**
2- Mutect2 for Variantcalling with no intervals; there is a problem with the script in handling the "intervals (-L)" option:
**Error executing process > 'PileupSummariesForMutect2 (NIST7035_vs_NIST7086-no_intervals)'
Caused by: Process
PileupSummariesForMutect2 (NIST7035_vs_NIST7086-no_intervals)
terminated with an error exit status (1)Command executed: gatk --java-options "-Xmx25g" GetPileupSummaries
-I NIST7035.recal.bam -V somatic-hg38_af-only-gnomad.hg38.vcf.gz
-O no_intervals_NIST7035_pileupsummaries.table
Command exit status: 1
A USER ERROR has occurred: Argument intervals was missing: Argument 'intervals' is required.**
Steps to reproduce
Steps to reproduce the behaviour:
nextflow run main.nf --input /hpcshare/genomics/sarek_analyses/results/Preprocessing/TSV/recalibrated.tsv -profile base,singularity --step variantcalling --tools mutect2 --pon /homenfs/yabili/gatk_bundle/resources/somatic-hg38_1000g_pon.hg38.vcf.gz --pon_index /homenfs/yabili/gatk_bundle/resources/somatic-hg38_1000g_pon.hg38.vcf.gz.tbi --germline_resource /homenfs/yabili/gatk_bundle/resources/somatic-hg38_af-only-gnomad.hg38.vcf.gz --germline_resource_index /homenfs/yabili/gatk_bundle/resources/somatic-hg38_af-only-gnomad.hg38.vcf.gz.tbi
(to get the second error I disabled the intervals option in nextflow.config)
Nextflow Installation
Container engine