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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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UnboundLocalError: local variable 'genoTypesPresent' referenced before assignment #1

Closed qindan2008 closed 5 years ago

qindan2008 commented 5 years ago

Hello, I run NeoPredPipe using the data in the Example directory with the flowing command:

python main_netMHCpan_pipe.py -I ./Example/input_vcfs -H ./Example/HLAtypes/hlatypes.txt -o ./ -n TestRun -c 1 2 -E 8 9 10

But an error occurred:

INFO: Begin. INFO: Proper directory already exists. Continue. INFO: Proper directory already exists. Continue. INFO: Proper directory already exists. Continue. INFO: Proper directory already exists. Continue. INFO: ANNOVAR Ready files for test1 already present. INFO: ANNOVAR Annotation files for test1 already present. INFO: Coding change fasta files for test1 already present. INFO: Coding change fasta files test1 has already been reformatted. INFO: Tmp fasta files test1 has already been created for netMHCpan length 8. INFO: Tmp fasta files test1 has already been created for netMHCpan length 9. INFO: Tmp fasta files test1 has already been created for netMHCpan length 10. INFO: Epitope prediction files test1 have already been created for netMHCpan length 8. INFO: Epitope prediction files test1 have already been created for netMHCpan length 9. INFO: Epitope prediction files test1 have already been created for netMHCpan length 10. INFO: Digesting neoantigens for test1 INFO: Digesting neoantigens for test1 INFO: Digesting neoantigens for test1 INFO: Object size of neoantigens: 72 Kb Traceback (most recent call last): File "main_netMHCpan_pipe.py", line 438, in main() File "main_netMHCpan_pipe.py", line 423, in main t.append(Sample(localpath, patname, patFile, hlas[patname], annPaths, netMHCpanPaths, pepmatchPaths, Options)) File "main_netMHCpan_pipe.py", line 89, in init self.digestIndSample(pepmatchPaths, Options) File "main_netMHCpan_pipe.py", line 149, in digestIndSample self.appendedEpitopes, self.regionsPresent = AppendDigestedEps(self.digestedEpitopes, self.patID, self.annotationReady, self.avReadyFile, Options) File "/DataProcess/softwares/NeoPredPipe-master/postprocessing.py", line 138, in AppendDigestedEps return(newLines, genoTypesPresent) UnboundLocalError: local variable 'genoTypesPresent' referenced before assignment

The pep fasta was downloaded from Ensembl, and pep index was build with the flowing command: java -jar PeptideMatchCMD_1.0.jar -a index -d Homo_sapiens.GRCh37.75.pep.all.fa -i LuceneIndex

How can I fix it ? Thank you.

rschenck commented 5 years ago

Just saw this. Will take a look into it.

rschenck commented 5 years ago

You are using a very outdated version of the scripts, line138 is not correct at all in the error you are reporting.

Can you please rerun with the latest version and let me know if you still have problems?