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gagneurlab / drop

Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders
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error in MAE rule mae_createSNVs #417

Closed agomez700 closed 1 year ago

agomez700 commented 1 year ago

Hi all,

Successfully ran aberrant expression and aberrant splicing modules, but am running to this issue with MAE and wondering if you have any suggestions.

rule mae_createSNVs: input: /lab-share/Neph-Sampson-e2/Public/AC/drop_6/Scripts/Pipeline/chr_NCBI_UCSC.txt, /lab-share/Neph-Sampson-e2/Public/AC/drop_6/Scripts/Pipeline/chr_UCSC_NCBI.txt, /home/ch222985/CRDC_data/rna_seq/resource/qc_vcf_1000G_hg38.vcf.gz, /home/ch222985/CRDC_data/rna_seq/hg38/BCH-22-95062-01_R38/BCH-22-95062-01_R38_dupmarked_with_ReadGroup.bam, /lab-share/Neph-Sampson-e2/Public/AC/drop_6/Scripts/MonoallelicExpression/pipeline/MAE/filterSNVs.sh, /home/ch222985/Public/AC/drop_6/processed_data/mae/params/snvs/BCH-22-95062-01_snvParams.csv output: /home/ch222985/Public/AC/drop_6/processed_data/mae/snvs/BCH-22-95062-01_G38--BCH-22-95062-01.vcf.gz, /home/ch222985/Public/AC/drop_6/processed_data/mae/snvs/BCH-22-95062-01_G38--BCH-22-95062-01.vcf.gz.tbi jobid: 90 reason: Missing output files: /home/ch222985/Public/AC/drop_6/processed_data/mae/snvs/BCH-22-95062-01_G38--BCH-22-95062-01.vcf.gz wildcards: vcf=BCH-22-95062-01_G38, rna=BCH-22-95062-01 resources: tmpdir=/tmp

Filter SNVs Error: subset called for sample that does not exist in header: "BCH-22-95062-01_G38". Use "--force-samples" to ignore this error. [Fri Dec 16 08:23:06 2022] Error in rule mae_createSNVs: jobid: 90 output: /home/ch222985/Public/AC/drop_6/processed_data/mae/snvs/BCH-22-95062-01_G38--BCH-22-95062-01.vcf.gz, /home/ch222985/Public/AC/drop_6/processed_data/mae/snvs/BCH-22-95062-01_G38--BCH-22-95062-01.vcf.gz.tbi shell:

    /lab-share/Neph-Sampson-e2/Public/AC/drop_6/Scripts/MonoallelicExpression/pipeline/MAE/filterSNVs.sh /lab-share/Neph-Sampson-e2/Public/AC/drop_6/Scripts/Pipeline/chr_NCBI_UCSC.txt /lab-share/Neph-Sampson-e2/Public/AC/drop_6/Scripts/Pipeline/chr_UCSC_NCBI.txt /home/ch222985/CRDC_data/rna_seq/resource/qc_vcf_1000G_hg38.vcf.gz         BCH-22-95062-01_G38 /home/ch222985/CRDC_data/rna_seq/hg38/BCH-22-95062-01_R38/BCH-22-95062-01_R38_dupmarked_with_ReadGroup.bam /home/ch222985/Public/AC/drop_6/processed_data/mae/snvs/BCH-22-95062-01_G38--BCH-22-95062-01.vcf.gz         bcftools samtools

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: .snakemake/log/2022-12-16T082259.853430.snakemake.log

nickhsmith commented 1 year ago

Sorry for the mistake with the DROP 1.2.4 permissions, those should be updated now.

As for your first error, could you please check that the sample name you designate in your sample annotation DNA_ID is the same as the the sampleID in the VCF itself.

zgrep "^#CHROM" <VCF_FILE>

Could you also share your sample annotation file, please?

agomez700 commented 1 year ago

yes sorry you are spot on I was calling the wrong VCF file in the sample annotation so the sample names did not match the one in the annotation. file.

Sorry for the bother - you guys are always so helpful. I am trying again now that they match and will let you know if that does not fix the problem (and will close this out if it does).

agomez700 commented 1 year ago

fixed! thank you and closing issue now.