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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.
The text was updated successfully, but these errors were encountered:
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.
The text was updated successfully, but these errors were encountered: