Process `OptiType_RNA (test_sample)` terminated with an error exit status (1)

[DecodeGenome]

Dear nextNEOpi developers:

I use the HPC to run nextNEOpi test sample, I got the error below and I checked the rna_mapped_1.bam and rna_mapped_2.bam file are empty. Please help to identify and solve this issue.

Thank you very much in advance

############################################## Error messages ####################### Error executing process > 'OptiType_RNA (test_sample)'

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

Command executed:

OPTITYPE="$(readlink -f $(which OptiTypePipeline.py))" MHC_MAPPED_R1=$(samtools view -c rna_mapped_1.bam) MHC_MAPPED_R2=$(samtools view -c rna_mapped_2.bam) MHC_MAPPED=$((MHC_MAPPED_R1+MHC_MAPPED_R2)) if [ "$MHC_MAPPED" != "0" ]; then $OPTITYPE -i rna_mapped_1.bam rna_mapped_2.bam -e 1 -b 0.009 --rna -o ./tmp &&
mv ./tmp//_result.tsv ./test_sample_optitype_RNA_result.tsv &&
mv ./tmp//_coverage_plot.pdf ./test_sample_optitype_RNA_coverage_plot.pdf &&
rm -rf ./tmp/ else touch test_sample_optitype_RNA_result.tsv echo "No result" > test_sample_optitype_RNA_coverage_plot.pdf fi

Command exit status: 1

Command output: (empty)

Command error: INFO: Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred INFO: Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred [main_samview] fail to read the header from "rna_mapped_1.bam".

Work dir: /wynton/group/bivona/Analytic_tools/NextNeoPi/nextNEOpi/work/10/dd9392940df5469d3ed8ef2b821f25

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line