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MathOnco / NeoPredPipe

Neoantigens prediction pipeline for multi- or single-region vcf files using ANNOVAR and netMHCpan.
GNU Lesser General Public License v3.0
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new error in postprocess #4

Closed ChengYunazhi closed 5 years ago

ChengYunazhi commented 5 years ago

INFO: Annovar reference files of build hg19 were given, using this build for all analysis. INFO: Begin. INFO: Proper directory already exists. Continue. INFO: Proper directory already exists. Continue. INFO: Proper directory already exists. Continue. INFO: Running convert2annovar.py on /DataProcess/standar_workflow/neoantigen/somatic_vcfs_varscan2_with_chr/WFGT.vcf INFO: VCF Conversion Process complete /DataProcess/standar_workflow/neoantigen/somatic_vcfs_varscan2_with_chr/WFGT.vcf INFO: ANNOVAR Annotation files for WFGT already present. INFO: Coding change fasta files for WFGT already present. INFO: Coding change fasta files WFGT has already been reformatted. INFO: Predicting neoantigens for WFGT INFO: Running Epitope Predictions for WFGT on epitopes of length 8 INFO: Running Epitope Predictions for WFGT on epitopes of length 9 INFO: Running Epitope Predictions for WFGT on epitopes of length 10 INFO: Predictions complete for WFGT on epitopes of length 10 INFO: Digesting neoantigens for WFGT INFO: Digesting neoantigens for WFGT INFO: Digesting neoantigens for WFGT INFO: Object size of neoantigens: 824472 Kb Traceback (most recent call last): File "/DataProcess/softwares/NeoPredPipe-1.0/main_netMHCpan_pipe.py", line 456, in main() File "/DataProcess/softwares/NeoPredPipe-1.0/main_netMHCpan_pipe.py", line 441, in main t.append(Sample(localpath, patname, patFile, hlas[patname], annPaths, netMHCpanPaths, pepmatchPaths, Options)) File "/DataProcess/softwares/NeoPredPipe-1.0/main_netMHCpan_pipe.py", line 96, in init self.digestIndSample(pepmatchPaths, Options) File "/DataProcess/softwares/NeoPredPipe-1.0/main_netMHCpan_pipe.py", line 156, in digestIndSample self.appendedEpitopes, self.regionsPresent = AppendDigestedEps(self.digestedEpitopes, self.patID, self.annotationReady, self.avReadyFile, Options) File "/DataProcess/softwares/NeoPredPipe-1.0/postprocessing.py", line 159, in AppendDigestedEps present = int(int(match.split(',')[1]) > 0) #present if depth for variant allele > 0 IndexError: list index out of range

rschenck commented 5 years ago

Please see other comment for the issue you have raised. We will look into this error.

ChengYunazhi commented 5 years ago

error was fixed. AD fields in varscan2 (somatic was called) is different, which cause split error. AD in varscan2 means variant allele depth, howere neoPredPipe supposed AD was "(Reference allele depth, Variant allele depth)". Thanks!

rschenck commented 5 years ago

Good to know. Will need to add more robustness for this