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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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get no neoantigen when running with Example .vcf files #49

Closed Hupingdong closed 1 month ago

Hupingdong commented 4 months ago

Hi, I have run the NeoPredPipe.py as: python NeoPredPipe.py -I ./Example/input_vcfs -H ./Example/HLAtypes/hlatypes.txt -o ./ -n TestRun -c 1 2 -E 8 9 10 INFO: Annovar reference files of build hg19 were given, using this build for all analysis. INFO: Begin. INFO: Running convert2annovar.py on ./Example/input_vcfs/test1.vcf INFO: VCF Conversion Process complete ./Example/input_vcfs/test1.vcf INFO: Running annotate_variation.pl on ./avready/test1.avinput INFO: ANNOVAR annotation Process complete for ./avready/test1.avinput INFO: Running coding_change.pl on ./avannotated/test1.avannotated.exonic_variant_function INFO: Coding predictions complete for ./avannotated/test1.avannotated.exonic_variant_function INFO: Predicting neoantigens for test1 INFO: Running Epitope Predictions for test1 on epitopes of length 8 INFO: Skipping Sample! No peptides to predict for test1 INFO: Running Epitope Predictions for test1 on epitopes of length 9 INFO: Skipping Sample! No peptides to predict for test1 INFO: Running Epitope Predictions for test1 on epitopes of length 10 INFO: Skipping Sample! No peptides to predict for test1 INFO: Predictions complete for test1 on epitopes of length 10.Indels INFO: Digesting neoantigens for test1 INFO: Digesting neoantigens for test1 INFO: Digesting neoantigens for test1 INFO: Object size of neoantigens: 56 Kb INFO: Object size of neoantigens: 56 Kb INFO: Running convert2annovar.py on ./Example/input_vcfs/test2.vcf INFO: VCF Conversion Process complete ./Example/input_vcfs/test2.vcf INFO: Running annotate_variation.pl on ./avready/test2.avinput INFO: ANNOVAR annotation Process complete for ./avready/test2.avinput INFO: Running coding_change.pl on ./avannotated/test2.avannotated.exonic_variant_function INFO: Coding predictions complete for ./avannotated/test2.avannotated.exonic_variant_function INFO: Predicting neoantigens for test2 INFO: Running Epitope Predictions for test2 on epitopes of length 8 INFO: Skipping Sample! No peptides to predict for test2 INFO: Running Epitope Predictions for test2 on epitopes of length 9 INFO: Skipping Sample! No peptides to predict for test2 INFO: Running Epitope Predictions for test2 on epitopes of length 10 INFO: Skipping Sample! No peptides to predict for test2 INFO: Predictions complete for test2 on epitopes of length 10.Indels INFO: Digesting neoantigens for test2 INFO: Digesting neoantigens for test2 INFO: Digesting neoantigens for test2 INFO: Object size of neoantigens: 56 Kb INFO: Object size of neoantigens: 56 Kb INFO: Summary Tables Complete. INFO: Summary Tables Complete. INFO: Complete and get the results with all 0. I use the netMHCpan-4.1 and python3. Is there something wrong with it?

elakatos commented 1 month ago

Hi,

Based on the "Object size of neoantigens: 56 Kb", I suspect this might be a similar error to this issue, i.e. something might be wrong with the netMHCpan set-up: https://github.com/MathOnco/NeoPredPipe/issues/38#issue-1907126770 Run the test again with keeping intermediate files/folders (-d flag), and check the direct netMHCpan output in the tmp folder.