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[BUG] Mutect2 - Error with both 'intervals' and 'no-intervals' options #359
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Hi, Using the germline ressources fix the bug
Best |
A quick follow up on that. It seems that providing
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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 |
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
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