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-C04:01.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-C04:01.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
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-C04:01.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-C04:01.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