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Failed to call strelka2 #149

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marcogao2019 opened this issue Feb 24, 2021 · 0 comments
Open

Failed to call strelka2 #149

marcogao2019 opened this issue Feb 24, 2021 · 0 comments

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@marcogao2019
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marcogao2019 commented Feb 24, 2021

Hi, after calling /home/user/strelka/libexec/callSomaticVariants.pl, I got the "ERROR: Failed system call: '/home/user/strelka/libexec/strelka2 -clo...'".
Could u give any clue to fix it? thanks

this is my yaml example:
input:
id: tesla_melanoma_2_patient_4
mhc_alleles:
- HLA-A02:01
- HLA-B
15:01
normal:
- fragment_id: L001
type: single-end
r: /inputs_patient_4/patient04_normal.fastq.gz
tumor:
- fragment_id: L001
type: single-end
r: /inputs_patient_4/patient04_tumor.fastq.gz
rna:
- fragment_id: L001
type: paired-end
r1: /inputs_patient_4/patient04_tumor_rna_1.fastq.gz
r2: /inputs_patient_4/patient04_tumor_rna_2.fastq.gz
workdir:
/outputs_patient_4
reference:
genome: /reference-genome/b37decoy/b37decoy.fasta
dbsnp: /reference-genome/b37decoy/dbsnp.vcf
cosmic: /reference-genome/b37decoy/cosmic.vcf
transcripts: /reference-genome/b37decoy/transcripts.gtf
capture_kit_coverage_file: /reference-genome/b37decoy/S04380110_Covered_grch37_with_M.bed
parallel_indel_realigner: true
mhc_predictor: netmhcpan-iedb
variant_callers:

  • mutect
  • strelka
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