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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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Output empty with test data #38

Closed tucano closed 10 months ago

tucano commented 10 months ago

Hello I am trying to run the example with this user_ini.path

[annovar]
convert2annovar = /home/davide.rambaldi/src/annovar/convert2annovar.pl
annotatevariation = /home/davide.rambaldi/src/annovar/annotate_variation.pl
coding_change = /home/davide.rambaldi/src/annovar/coding_change.pl
gene_table = /home/davide.rambaldi/src/annovar/humandb/hg19_refGene.txt
gene_fasta = /home/davide.rambaldi/src/annovar/humandb/hg19_refGeneMrna.fa
humandb = /home/davide.rambaldi/src/annovar/humandb
[netMHCpan]
netMHCpan = /home/davide.rambaldi/bin/netMHCpan-4.0/netMHCpan
[PeptideMatch]
peptidematch_jar = /home/davide.rambaldi/bin/PeptideMatchCMD_1.1.jar
reference_index = /scratch/davide.rambaldi/neo_pre_pipe_test/reference/uniprot/homosapiens/sprot_index
[blast]
blastp = /home/davide.rambaldi/miniconda4/envs/neo_pred_pipe/bin/blastp

Running with this command

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 hg38 were given, using this build for all analysis.
INFO: Begin.
INFO: Running convert2annovar.py on ./Example/input_vcfs/test2.vcf
INFO: ANNOVAR 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
Processing genotype information according to A (list of alleles) field.
INFO: Object size of neoantigens: 56 Kb
Processing genotype information according to A (list of alleles) field.
INFO: Running convert2annovar.py on ./Example/input_vcfs/test1.vcf
INFO: ANNOVAR 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: Running Epitope Predictions for test1 on epitopes of length 8.Indels
INFO: Running Epitope Predictions for test1 on epitopes of length 9
INFO: Running Epitope Predictions for test1 on epitopes of length 9.Indels
INFO: Running Epitope Predictions for test1 on epitopes of length 10
INFO: Running Epitope Predictions for test1 on epitopes of length 10.Indels
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
Processing genotype information according to A (list of alleles) field.
INFO: Digesting neoantigens for test1
INFO: Digesting neoantigens for test1
INFO: Digesting neoantigens for test1
INFO: Object size of neoantigens: 56 Kb
Processing genotype information according to A (list of alleles) field.
INFO: Summary Tables Complete.
INFO: Summary Tables Complete.
INFO: Complete

According to the log the test1 neoantigens file should contains some results?

Cuase in my environment the TestRun.neoantigens.txt file is empty.

Best Regards

Version used (commit hash): 54e14f99bb0e642de598bf2f6dce5e68905ac091

elakatos commented 10 months ago

Hi! Indeed, the output table should have some neoantigens, and the lines "INFO: Object size of neoantigens: 56 Kb" should have a much higher object size normally. We have seen this issue happen if netMHCpan didn't run properly. Can you run the test again with the -d option (to keep all intermediate files)? Then check in the tmp folder what is present in the netMHCpan-produced epitope predictions - if something is off with netMHCpan, you will see an error message output there instead of real predictions.

Eszter

tucano commented 10 months ago

Follow up:

Indeed I was missing the data for NetMHCpan 4.0

In the readme of NetMHCpan there is a broken link.

I have downloaded then the 4.1 version data from this page:

https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/

specifically from this link: https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/data.tar.gz

And the example runs neoantigens size is:

INFO: Object size of neoantigens: 792 Kb

Thanks for help.

Feel free to close the ISSUE.

May I suggest an update to the README about the location of data.tar.gz for NetMHCpan?

Best Regards

elakatos commented 10 months ago

Great! I'll update our instructions on netMHCpan. In the meantime keep in mind that output from version 4.1 will need to be processed manually as it has a slightly different format than what NeoPredPipe handles automatically. Best, Eszter