Skip to content

pVACseq related error #101

@SreeChai

Description

@SreeChai

Hi
I ran the pipeline's latest version on a file on which it had run successfully over 5 yrs ago.
The steps unto the fusion peptide generation were completed,
this is the subsequent error:

Error executing process > 'pVACseq (Sample25)'

Caused by:
Process pVACseq (Sample25) terminated with an error exit status (1)

Command executed:

pvacseq run
--iedb-install-directory /opt/iedb
-t 10
-p Sample25_vep_phased.vcf.gz
-e1 8,9,10,11
-e2 15,16,17,18,19,20,21,22,23,24,25
--normal-sample-name Sample25_normal
--tumor-purity 0.99

--netmhc-stab
--binding-threshold 500 --top-score-metric median --minimum-fold-change 0.0 --normal-cov 5 --tdna-cov 10 --trna-cov 10 --normal-vaf 0.02 --tdna-vaf 0.25 --trna-vaf 0.25 --expn-val 1 --maximum-transcript-support-level 1
Sample25_vep_somatic_gx.vcf.gz Sample25_tumor HLA-C*04:01 NetMHCpan MHCflurry NetMHCIIpan ./

if [ -e ./MHC_Class_I/Sample25_tumor.filtered.tsv ]; then
mv ./MHC_Class_I/Sample25_tumor.filtered.tsv ./MHC_Class_I/Sample25_tumor_HLA-C04:01.filtered.tsv
fi
if [ -e ./MHC_Class_I/Sample25_tumor.all_epitopes.tsv ]; then
mv ./MHC_Class_I/Sample25_tumor.all_epitopes.tsv ./MHC_Class_I/Sample25_tumor_HLA-C
04:01.all_epitopes.tsv
fi
if [ -e ./MHC_Class_II/Sample25_tumor.filtered.tsv ]; then
mv ./MHC_Class_II/Sample25_tumor.filtered.tsv ./MHC_Class_II/Sample25_tumor_HLA-C04:01.filtered.tsv
fi
if [ -e ./MHC_Class_II/Sample25_tumor.all_epitopes.tsv ]; then
mv ./MHC_Class_II/Sample25_tumor.all_epitopes.tsv ./MHC_Class_II/Sample25_tumor_HLA-C
04:01.all_epitopes.tsv
fi

Command exit status:
1

Command output:
(empty)

Command error:
INFO: Converting SIF file to temporary sandbox...
IEDB MHC I executable path doesn't exist /opt/iedb/mhc_i/src/predict_binding.py
INFO: Cleaning up image...

the path for the script is /Tools/neoAg_nextNeoPi/resources/databases/iedb/mhc_i/predict_binding.py
Where do I have to update this?

thanks in advance
Chai

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions