ValueError: not enough values to unpack (expected 2, got 1)

[Donbbit]

Thank you for writing such an excellent pipeline. I was using it and reached the final step to generate the neoantigen results when I run:
python workflow/scripts/prioritization/compile.py \
--SNV "results/test/annotation/somatic.snvs.vcf" \
--indels "results/test/annotation/somatic.short.indels.vcf" \
--long_indels "results/test/annotation/long.indels.vcf" \
--exitrons "results/test/annotation/exitrons.vcf" \
--altsplicing "results/test/annotation/altsplicing.vcf" \
--fusions "results/test/rnaseq/genefusion/rna_tumor_fusions.tsv" \
--custom "" \
--proteome resources/refs/peptide.fasta \
--anno resources/refs/genome_tmp.gtf \
--confidence medium \
--mhc_class I \
--mhcI "results/test/hla/mhc-I.tsv" \
--mhcI_len "8,9,10,11" \
--mhcII "" \
--mhcII_len "13,14,15" \
--counts "results/test/quantification/allcounts.txt" \
--threads 8 \
--output_dir results/test/prioritization \
--reference resources/refs/genome.fasta > logs/prioritization/test.log 2>&1

I got the error in the log:
Traceback (most recent call last):
File "/hsfscqjf1/ST_CQ/P24Z32300N0028/lvmeiqi/pipe_test/scanneo2/workflow/scripts/prioritization/compile.py", line 151, in
main()
File "/hsfscqjf1/ST_CQ/P24Z32300N0028/lvmeiqi/pipe_test/scanneo2/workflow/scripts/prioritization/compile.py", line 120, in main
comp = Compile(options)
^^^^^^^^^^^^^^^^
File "/hsfscqjf1/ST_CQ/P24Z32300N0028/lvmeiqi/pipe_test/scanneo2/workflow/scripts/prioritization/compile.py", line 23, in init
self.prioritize(options.indels, options, "somatic.short.indels")
File "/hsfscqjf1/ST_CQ/P24Z32300N0028/lvmeiqi/pipe_test/scanneo2/workflow/scripts/prioritization/compile.py", line 49, in prioritize
vars = variants.Variants(inputfile, options, vartype)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/hsfscqjf1/ST_CQ/P24Z32300N0028/lvmeiqi/pipe_test/scanneo2/workflow/scripts/prioritization/variants.py", line 125, in init
wt_aa_change, mt_aa_change = self.determine_aa_change(aa_change)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/hsfscqjf1/ST_CQ/P24Z32300N0028/lvmeiqi/pipe_test/scanneo2/workflow/scripts/prioritization/variants.py", line 196, in determine_aa_change
wt_aa_change, mt_aa_change = aa_change.split('/')
^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: not enough values to unpack (expected 2, got 1)

I think the error may be caused by results/test/annotation/somatic.short.indels.vcf But when I checked the results of this file, I couldn't find any issues. The first 200 lines of this file is attached.
somatic.short.indels_head200.vcf.txt

I really appreciate any help.

[riasc]

Hi,

sorry I missed this issue. I will look into this on the weekend. I see that you applied it directly on the script. Have you generated this VCF by yourself? The thing is that ScanNeo2 annotates the VCF using 'Variant Effect Predictor'. It seems like the VCF hasn't been annotated.

[riasc]

No it has been annotated. Will look into it. Thanks