I encountered the following error when running NeoPredPipe.py:
INFO: ANNOVAR Annotation files for mysample already present.
INFO: Coding change fasta files for mysample already present.
INFO: Coding change fasta files mysample has already been reformatted.
INFO: Predicting neoantigens for mysample
INFO: Running Epitope Predictions for mysample on epitopes of length 9.Indels
INFO: Running Epitope Predictions for mysample on epitopes of length 9
INFO: Running Epitope Predictions for mysample on epitopes of length 8
INFO: Running Epitope Predictions for mysample on epitopes of length 8.Indels
INFO: Running Epitope Predictions for mysample on epitopes of length 10
INFO: Running Epitope Predictions for mysample on epitopes of length 10.Indels
INFO: Predictions complete for mysample on epitopes of length 10.Indels
INFO: Digesting neoantigens for mysample
INFO: Digesting neoantigens for mysample
INFO: Digesting neoantigens for mysample
INFO: Object size of neoantigens: 87632 Kb
INFO: Strelka-specific format found, processing genotype information accordingly.
INFO: Digesting neoantigens for mysample
INFO: Digesting neoantigens for mysample
INFO: Digesting neoantigens for mysample
INFO: Object size of neoantigens: 13016 Kb
INFO: Strelka-specific format found, processing genotype information accordingly.
Traceback (most recent call last):
File "/SAN/colcc/driver_gene_TME/NeoPredPipe/NeoPredPipe.py", line 524, in
main()
File "/SAN/colcc/driver_gene_TME/NeoPredPipe/NeoPredPipe.py", line 505, in main
t.append(Sample(localpath, patname, patFile, hlas[patname], annPaths, netMHCpanPaths, pepmatchPaths, Options))
File "/SAN/colcc/driver_gene_TME/NeoPredPipe/NeoPredPipe.py", line 108, in init
self.digestIndSample(FilePath, pepmatchPaths, Options)
File "/SAN/colcc/driver_gene_TME/NeoPredPipe/NeoPredPipe.py", line 184, in digestIndSample
self.appendedEpitopesIndels, self.regionsPresentIndels = AppendDigestedEps(FilePath, self.digestedEpitopesIndels, self.patID, self.annotationReady, self.avReadyFile, Options)
File "/SAN/colcc/driver_gene_TME/NeoPredPipe/postprocessing.py", line 224, in AppendDigestedEps
present = int(sum([int(x) for x in match.split(',')]) > 0) #present if any is above zero, meaning sum is above 0
ValueError: invalid literal for int() with base 10: '0.86'
The error appears to be happening at line 224 of postprocessing.py. The input vcf is a Strelka output. I ran NeoPredPipe with the --manualproc option. The full genotype info field in the VCF is 35:35:24,25:5,5:6,5:30.73:0.86:0.00:0.00 (the literal that causes the error is in bold). May also be worth noting that this corresponds to an indel entry.
@elakatos @rschenck could you please help me figure out what's wrong?
Hello,
I encountered the following error when running NeoPredPipe.py:
INFO: ANNOVAR Annotation files for mysample already present. INFO: Coding change fasta files for mysample already present. INFO: Coding change fasta files mysample has already been reformatted. INFO: Predicting neoantigens for mysample INFO: Running Epitope Predictions for mysample on epitopes of length 9.Indels INFO: Running Epitope Predictions for mysample on epitopes of length 9 INFO: Running Epitope Predictions for mysample on epitopes of length 8 INFO: Running Epitope Predictions for mysample on epitopes of length 8.Indels INFO: Running Epitope Predictions for mysample on epitopes of length 10 INFO: Running Epitope Predictions for mysample on epitopes of length 10.Indels INFO: Predictions complete for mysample on epitopes of length 10.Indels INFO: Digesting neoantigens for mysample INFO: Digesting neoantigens for mysample INFO: Digesting neoantigens for mysample INFO: Object size of neoantigens: 87632 Kb INFO: Strelka-specific format found, processing genotype information accordingly. INFO: Digesting neoantigens for mysample INFO: Digesting neoantigens for mysample INFO: Digesting neoantigens for mysample INFO: Object size of neoantigens: 13016 Kb INFO: Strelka-specific format found, processing genotype information accordingly. Traceback (most recent call last): File "/SAN/colcc/driver_gene_TME/NeoPredPipe/NeoPredPipe.py", line 524, in
main()
File "/SAN/colcc/driver_gene_TME/NeoPredPipe/NeoPredPipe.py", line 505, in main
t.append(Sample(localpath, patname, patFile, hlas[patname], annPaths, netMHCpanPaths, pepmatchPaths, Options))
File "/SAN/colcc/driver_gene_TME/NeoPredPipe/NeoPredPipe.py", line 108, in init
self.digestIndSample(FilePath, pepmatchPaths, Options)
File "/SAN/colcc/driver_gene_TME/NeoPredPipe/NeoPredPipe.py", line 184, in digestIndSample
self.appendedEpitopesIndels, self.regionsPresentIndels = AppendDigestedEps(FilePath, self.digestedEpitopesIndels, self.patID, self.annotationReady, self.avReadyFile, Options)
File "/SAN/colcc/driver_gene_TME/NeoPredPipe/postprocessing.py", line 224, in AppendDigestedEps
present = int(sum([int(x) for x in match.split(',')]) > 0) #present if any is above zero, meaning sum is above 0
ValueError: invalid literal for int() with base 10: '0.86'
The error appears to be happening at line 224 of postprocessing.py. The input vcf is a Strelka output. I ran NeoPredPipe with the --manualproc option. The full genotype info field in the VCF is 35:35:24,25:5,5:6,5:30.73:0.86:0.00:0.00 (the literal that causes the error is in bold). May also be worth noting that this corresponds to an indel entry.
@elakatos @rschenck could you please help me figure out what's wrong?
Many thanks for your help,
Reda