pVACseq (test_sample)` terminated with an error exit status (1)

[DecodeGenome]

Hi nextNEOpi developers:

Thank you very much for your previous support. I am running the test sample using nextNEOpi, it appears to create results, but at the end, there is an error:

Error executing process > 'pVACseq (test_sample)'

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

Command executed:

pvacseq run \ --iedb-install-directory /opt/iedb \ -t 10 \ -p test_sample_vep_phased.vcf.gz \ -e1 8,9,10,11 \ -e2 15,16,17,18,19,20,21,22,23,24,25 \ --normal-sample-name test_sample_normal \ --tumor-purity 0.53 \ \ --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 \ test_sample_vep_somatic_gx.vcf.gz test_sample_tumor HLA-C*06:02 NetMHCpan NetMHCpanEL MHCflurry MHCflurryEL NetMHCIIpan NetMHCIIpanEL ./

if [ -e ./MHC_Class_I/test_sample_tumor.filtered.tsv ]; then mv ./MHC_Class_I/test_sample_tumor.filtered.tsv ./MHC_Class_I/test_sample_tumor_HLA-C06:02.filtered.tsv fi if [ -e ./MHC_Class_I/test_sample_tumor.all_epitopes.tsv ]; then mv ./MHC_Class_I/test_sample_tumor.all_epitopes.tsv ./MHC_Class_I/test_sample_tumor_HLA-C06:02.all_epitopes.tsv fi if [ -e ./MHC_Class_II/test_sample_tumor.filtered.tsv ]; then mv ./MHC_Class_II/test_sample_tumor.filtered.tsv ./MHC_Class_II/test_sample_tumor_HLA-C06:02.filtered.tsv fi if [ -e ./MHC_Class_II/test_sample_tumor.all_epitopes.tsv ]; then mv ./MHC_Class_II/test_sample_tumor.all_epitopes.tsv ./MHC_Class_II/test_sample_tumor_HLA-C06:02.all_epitopes.tsv fi ..............................................

Work dir: /wynton/group/bivona/Analytic_tools/NextNeoPi/nextNEOpi/work/f6/58dc606a49d04d69929dfb59b386d5

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named .command.sh

As usual, I aattached the compressed file from Word dir for your information, hopefully, you can provide suggestions or solutions.

Best,

Wei 58dc_contents.tar.gz

[riederd]

This should be fixed now by nextNEOpi v1.4.1 which uses now pVACtools 4.1.1(see also #43, #60, #66)