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TRON-Bioinformatics / neofox

Annotation of mutated peptide sequences with published or novel potential neoantigen descriptors
GNU General Public License v3.0
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Not working for the test data #12

Open xtmgah opened 1 year ago

xtmgah commented 1 year ago

Hello

thanks for devolving the neofox alogirhtem. I am trying to build a singularity container and then test the data sets. However, i can't figure out why the test data failed. Can you help to check? Also, can you let me know how can i prepare the candidate file based on my mutations data from normal-tumor paied WES or WGS studies? Thanks.

singularity exec --pwd /test --bind $(pwd):/test neofox.sif neofox --input-file /test/test_data.tsv --patient-data /test/test_patients.tsv --output-folder /test/output --output-prefix test

[I 230109 13:07:18 neofox:59] Loading reference data... [I 230109 13:07:18 neofox:127] Reference data loaded [I 230109 13:07:18 neofox:190] Starting NeoFox annotations... [E 230109 13:07:55 prime:86] Results from PRIME are empty, something went wrong [E 230109 13:07:59 runner:51] Finished command with return code 1 [E 230109 13:07:59 runner:52] [E 230109 13:07:59 runner:53] Loading required package: Biostrings Warning message: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called ‘Biostrings’ Error in AAStringSet(epitope) : could not find function "AAStringSet" Execution halted

[E 230109 13:07:59 neofox:266] Error processing neoantigen {'patientIdentifier': 'Ptx', 'gene': 'BRCA2', 'position': [14], 'wildTypeXmer': 'AAAAAAAAAAAAAFAAAAAAAAAAAAA', 'mutatedXmer': 'AAAAAAAAAAAAALAAAAAAAAAAAAA', 'rnaExpression': 0.519506894, 'imputedGeneExpression': 0.53659963 17, 'dnaVariantAlleleFrequency': 0.857, 'rnaVariantAlleleFrequency': None, 'neofoxAnnotations': {'annotations': [{'name': 'NetMHCpan_MHCI_bestRank_rank', 'value': '4.389'}, {'name': 'NetMHCpan_bestRank_peptide', 'value': 'AAALAAAAA'}, {'name': 'NetMHCpan_bestRank_allele', 'value': 'HLA-B07:02'}, {'name': 'NetMHCpan_bestRank_rankWT', 'value': '5.068'}, {'name': 'NetMHCpan_bestRank_peptideWT', 'value': 'AAAFAAAAA'}, {'name': 'NetMHCpan_bestAffinity_affinity', 'value': '1018.2'}, {'name': 'NetMHCpan_bestAffinity_peptide', 'value': 'AALAAAAAAA'}, {'name': 'Ne tMHCpan_bestAffinity_allele', 'value': 'HLA-A02:01'}, {'name': 'NetMHCpan_bestAffinity_affinityWT', 'value': '8184.1'}, {'name': 'NetMHCpan_bestAffinity_peptideWT', 'value': 'AAFAAAAAAA'}, {'name': 'NetMHCpan_bestRank9mer_rank', 'value': '4.389'}, {'name': 'NetMHCpan_bestRank9mer _peptide', 'value': 'AAALAAAAA'}, {'name': 'NetMHCpan_bestRank9mer_allele', 'value': 'HLA-B07:02'}, {'name': 'NetMHCpan_bestRank9mer_rankWT', 'value': '5.068'}, {'name': 'NetMHCpan_bestRank9mer_peptideWT', 'value': 'AAAFAAAAA'}, {'name': 'NetMHCpan_bestAffinity9mer_affinity', 'va lue': '1534.8'}, {'name': 'NetMHCpan_bestAffinity9mer_allele', 'value': 'HLA-C03:04'}, {'name': 'NetMHCpan_bestAffinity9mer_peptide', 'value': 'AAALAAAAA'}, {'name': 'NetMHCpan_bestAffinity9mer_affinityWT', 'value': '1180.8'}, {'name': 'NetMHCpan_bestAffinity9mer_peptideWT', 'val ue': 'AAAFAAAAA'}, {'name': 'PHBR_I', 'value': '8.5743'}, {'name': 'GeneratorRate_MHCI', 'value': '0'}, {'name': 'GeneratorRate_CDN_MHCI', 'value': '0'}, {'name': 'GeneratorRate_ADN_MHCI', 'value': '0'}, {'name': 'NetMHCpan_bestAffinity9mer_positionMutation', 'value': '4'}, {'name ': 'NetMHCpan_bestAffinity9mer_anchorMutated', 'value': '0'}, {'name': 'NetMHCIIpan_bestRank_rank', 'value': '0.03'}, {'name': 'NetMHCIIpan_bestRank_peptide', 'value': 'AAAAAAAAALAAAAA'}, {'name': 'NetMHCIIpan_bestRank_allele', 'value': 'HLA-DQA101:02-DQB106:02'}, {'name': 'NetM HCIIpan_bestRank_rankWT', 'value': '0.27'}, {'name': 'NetMHCIIpan_bestRank_peptideWT', 'value': 'AAAAAAAAAFAAAAA'}, {'name': 'NetMHCIIpan_bestAffinity_affinity', 'value': '15.65'}, {'name': 'NetMHCIIpan_bestAffinity_peptide', 'value': 'AAAAAAAALAAAAAA'}, {'name': 'NetMHCIIpan_best Affinity_allele', 'value': 'HLA-DQA101:02-DQB106:02'}, {'name': 'NetMHCIIpan_bestAffinity_affinityWT', 'value': '22.47'}, {'name': 'NetMHCIIpan_bestAffinity_peptideWT', 'value': 'AAAAAAAAFAAAAAA'}, {'name': 'PHBR_II', 'value': 'NA'}, {'name': 'GeneratorRate_MHCII', 'value': '25' }, {'name': 'GeneratorRate_CDN_MHCII', 'value': '21'}, {'name': 'GeneratorRate_ADN_MHCII', 'value': '4'}, {'name': 'MixMHCpred_bestScore_peptide', 'value': 'NA'}, {'name': 'MixMHCpred_bestScore_score', 'value': 'NA'}, {'name': 'MixMHCpred_bestScore_rank', 'value': 'NA'}, {'name': 'MixMHCpred_bestScore_allele', 'value': 'NA'}, {'name': 'PRIME_best_peptide', 'value': 'NA'}, {'name': 'PRIME_best_score', 'value': 'NA'}, {'name': 'PRIME_best_rank', 'value': 'NA'}, {'name': 'PRIME_best_allele', 'value': 'NA'}, {'name': 'MixMHC2pred_bestRank_peptide', 'value': 'A AAALAAAAAAAAAAA'}, {'name': 'MixMHC2pred_bestRank_rank', 'value': '0.296'}, {'name': 'MixMHC2pred_bestRank_allele', 'value': 'HLA-DPA101:03-DPB106:01'}, {'name': 'Expression_mutated_transcript', 'value': '0.44522'}, {'name': 'mutation_not_found_in_proteome', 'value': '1'}, {'nam e': 'Amplitude_MHCI_bestAffinity9mer', 'value': '0.56811'}, {'name': 'Amplitude_MHCI_bestAffinity', 'value': '2.3262'}, {'name': 'Amplitude_MHCII_bestRank', 'value': '9'}, {'name': 'Pathogensimiliarity_MHCI_bestAffinity9mer', 'value': '0'}, {'name': 'RecognitionPotential_MHCI_best Affinity9mer', 'value': '0'}, {'name': 'Pathogensimiliarity_MHCII_bestAffinity', 'value': '0'}, {'name': 'Pathogensimiliarity_MHCI_bestAffinity', 'value': '0'}, {'name': 'RecognitionPotential_MHCI_bestAffinity', 'value': '0'}, {'name': 'DAI_MHCI_bestAffinity', 'value': '7165.9'}, {'name': 'Classically_defined_neopeptide_MHCI', 'value': '0'}, {'name': 'Alternatively_defined_neopeptide_MHCI', 'value': '0'}, {'name': 'Classically_defined_neopeptide_MHCII', 'value': '1'}, {'name': 'Alternatively_defined_neopeptide_MHCII', 'value': '1'}, {'name': 'Tcell_predict or', 'value': '0.39121828442992074'}, {'name': 'Improved_Binder_MHCI', 'value': '0'}, {'name': 'Selfsimilarity_MHCII', 'value': '0.981263768075705'}, {'name': 'Selfsimilarity_MHCI', 'value': '0.9763465205057597'}, {'name': 'Selfsimilarity_MHCI_conserved_binder', 'value': '0.976346 5205057597'}, {'name': 'Number_of_mismatches_MCHI', 'value': '1'}, {'name': 'Priority_score', 'value': '0'}, {'name': 'Neoag_immunogenicity', 'value': '13.16998'}, {'name': 'IEDB_Immunogenicity_MHCI', 'value': '0.18182'}, {'name': 'IEDB_Immunogenicity_MHCII', 'value': '0.36258'}, {'name': 'Dissimilarity_MHCI', 'value': '1'}, {'name': 'Dissimilarity_MHCII', 'value': '3e-05'}, {'name': 'Vaxrank_bindingScore', 'value': '0.01301'}, {'name': 'Vaxrank_totalScore', 'value': '0.00579'}], 'annotator': 'NeoFox', 'annotatorVersion': '1.0.2', 'timestamp': '20230109130 720985999', 'resources': [{'name': 'netMHCpan', 'version': '4.1'}, {'name': 'netMHCIIpan', 'version': '4.0'}, {'name': 'mixMHCpred', 'version': '2.1'}, {'name': 'mixMHC2pred', 'version': '1.2'}, {'name': 'IEDB', 'url': 'http://www.iedb.org/downloader.php?file_name=doc/tcell_full_v 3.zip', 'hash': 'eec05e51ecaaf56b43bb3ff264ec544c', 'downloadTimestamp': '20230104175159'}, {'name': 'IMGT/HLA database', 'version': '3.50.0', 'url': 'https://raw.githubusercontent.com/ANHIG/IMGTHLA/Latest/Allelelist.txt', 'hash': 'd65afa8e62ec064edda1ad3d39b88b0b', 'downloadTimes tamp': '20230104175159'}, {'name': 'Human Uniprot proteome', 'version': '2022_05', 'url': 'https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/reference_proteomes/Eukaryota/UP000005640/UP000005640_9606.fasta.gz', 'hash': '5c9dd16f61273c60be34a70f2a4ea16c', 'downloadTimestamp': '20230104175159'}, {'name': 'Human Uniprot proteome isoforms', 'version': '2022_05', 'url': 'https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/reference_proteomes/Eukaryota/UP000005640/UP000005640_9606_additional.fasta.gz', 'hash': '8 7e4e371119013fa5c9ef27b52a4281b', 'downloadTimestamp': '20230104175159'}, {'name': 'Mouse Uniprot proteome', 'version': '2022_05', 'url': 'https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/reference_proteomes/Eukaryota/UP000000589/UP000000589_10090.fasta. gz', 'hash': '5171a152853097eee107d244141cad45', 'downloadTimestamp': '20230104175159'}, {'name': 'Mouse Uniprot proteome isoforms', 'version': '2022_05', 'url': 'https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/reference_proteomes/Eukaryota/UP000000589/ UP000000589_10090_additional.fasta.gz', 'hash': '4422263a1fdbabe3c04f7f40d8b9e622', 'downloadTimestamp': '20230104175159'}]}, 'neoepitopesMhcII': [{'position': 5, 'mutatedPeptide': 'AAAAAAAAALAAAAA', 'wildTypePeptide': 'AAAAAAAAAFAAAAA', 'isoformMhcII': {'name': 'HLA-DQA103:01-DQ B106:02', 'alphaChain': {'fullName': 'HLA-DQA103:01', 'name': 'HLA-DQA103:01', 'gene': 'DQA1', 'group': '03', 'protein': '01'}, 'betaChain': {'fullName': 'HLA-DQB106:02', 'name': 'HLA-DQB106:02', 'gene': 'DQB1', 'group': '06', 'protein': '02'}}, 'affinityMutated': 775.74, 'ra nkMutated': 0.4, 'affinityWildType': 778.08, 'rankWildType': 0.8}, {'position': 6, 'mutatedPeptide': 'AAAAAAAALAAAAAA', 'wildTypePeptide': 'AAAAAAAAFAAAAAA', 'isoformMhcII': {'name': 'HLA-DQA103:01-DQB106:02', 'alphaChain': {'fullName': 'HLA-DQA103:01', 'name': 'HLA-DQA103:01' , 'gene': 'DQA1', 'group': '03', 'protein': '01'}, 'betaChain': {'fullName': 'HLA-DQB106:02', 'name': 'HLA-DQB106:02', 'gene': 'DQB1', 'group': '06', 'protein': '02'}}, 'affinityMutated': 812.22, 'rankMutated': 0.39, 'affinityWildType': 812.51, 'rankWildType': 1.61}, {'position' : 7, 'mutatedPeptide': 'AAAAAAALAAAAAAA', 'wildTypePeptide': 'AAAAAAAFAAAAAAA', 'isoformMhcII': {'name': 'HLA-DQA103:01-DQB106:02', 'alphaChain': {'fullName': 'HLA-DQA103:01', 'name': 'HLA-DQA103:01', 'gene': 'DQA1', 'group': '03', 'protein': '01'}, 'betaChain': {'fullName': ' HLA-DQB106:02', 'name': 'HLA-DQB106:02', 'gene': 'DQB1', 'group': '06', 'protein': '02'}}, 'affinityMutated': 817.84, 'rankMutated': 0.34, 'affinityWildType': 831.29, 'rankWildType': 0.97}, {'position': 8, 'mutatedPeptide': 'AAAAAALAAAAAAAA', 'wildTypePeptide': 'AAAAAAFAAAAAAAA' , 'isoformMhcII': {'name': 'HLA-DQA103:01-DQB106:02', 'alphaChain': {'fullName': 'HLA-DQA103:01', 'name': 'HLA-DQA103:01', 'gene': 'DQA1', 'group': '03', 'protein': '01'}, 'betaChain': {'fullName': 'HLA-DQB106:02', 'name': 'HLA-DQB106:02', 'gene': 'DQB1', 'group': '06', 'pro tein': '02'}}, 'affinityMutated': 769.27, 'rankMutated': 0.79, 'affinityWildType': 617.85, 'rankWildType': 0.33}, {'position': 9, 'mutatedPeptide': 'AAAAALAAAAAAAAA', 'wildTypePeptide': 'AAAAAFAAAAAAAAA', 'isoformMhcII': {'name': 'HLA-DQA103:01-DQB106:02', 'alphaChain': {'fullNa me': 'HLA-DQA103:01', 'name': 'HLA-DQA103:01', 'gene': 'DQA1', 'group': '03', 'protein': '01'}, 'betaChain': {'fullName': 'HLA-DQB106:02', 'name': 'HLA-DQB106:02', 'gene': 'DQB1', 'group': '06', 'protein': '02'}}, 'affinityMutated': 707.77, 'rankMutated': 0.37, 'affinityWildTy pe': 543.14, 'rankWildType': 0.05}, {'position': 10, 'mutatedPeptide': 'AAAALAAAAAAAAAA', 'wildTypePeptide': 'AAAAFAAAAAAAAAA', 'isoformMhcII': {'name': 'HLA-DQA103:01-DQB106:02', 'alphaChain': {'fullName': 'HLA-DQA103:01', 'name': 'HLA-DQA103:01', 'gene': 'DQA1', 'group': '03 ', 'protein': '01'}, 'betaChain': {'fullName': 'HLA-DQB106:02', 'name': 'HLA-DQB106:02', 'gene': 'DQB1', 'group': '06', 'protein': '02'}}, 'affinityMutated': 667.61, 'rankMutated': 0.1, 'affinityWildType': 505.19, 'rankWildType': 0.01}, {'position': 11, 'mutatedPeptide': 'AAALAA AAAAAAAAA', 'wildTypePeptide': 'AAAFAAAAAAAAAAA', 'isoformMhcII': {'name': 'HLA-DQA103:01-DQB106:02', 'alphaChain': {'fullName': 'HLA-DQA103:01', 'name': 'HLA-DQA103:01', 'gene': 'DQA1', 'group': '03', 'protein': '01'}, 'betaChain': {'fullName': 'HLA-DQB106:02', 'name': 'HLA- DQB106:02', 'gene': 'DQB1', 'group': '06', 'protein': '02'}}, 'affinityMutated': 612.72, 'rankMutated': 0.04, 'affinityWildType': 465.8}, {'position': 12, 'mutatedPeptide': 'AALAAAAAAAAAAAA', 'wildTypePeptide': 'AAFAAAAAAAAAAAA', 'isoformMhcII': {'name': 'HLA-DQA103:01-DQB106:0 2', 'alphaChain': {'fullName': 'HLA-DQA103:01', 'name': 'HLA-DQA103:01', 'gene': 'DQA1', 'group': '03', 'protein': '01'}, 'betaChain': {'fullName': 'HLA-DQB106:02', 'name': 'HLA-DQB106:02', 'gene': 'DQB1', 'group': '06', 'protein': '02'}}, 'affinityMutated': 703.69, 'rankMutat ed': 0.18, 'affinityWildType': 560.78, 'rankWildType': 0.04}, {'position': 13, 'mutatedPeptide': 'ALAAAAAAAAAAAAA', 'wildTypePeptide': 'AFAAAAAAAAAAAAA', 'isoformMhcII': {'name': 'HLA-DQA103:01-DQB106:02', 'alphaChain': {'fullName': 'HLA-DQA103:01', 'name': 'HLA-DQA103:01', 'g ene': 'DQA1', 'group': '03', 'protein': '01'}, 'betaChain': {'fullName': 'HLA-DQB106:02', 'name': 'HLA-DQB106:02', 'gene': 'DQB1', 'group': '06', 'protein': '02'}}, 'affinityMutated': 824.45, 'rankMutated': 0.56, 'affinityWildType': 678.63, 'rankWildType': 0.28}, {'position': 9, 'mutatedPeptide': 'AAAAALAAAAAAAAA', 'wildTypePeptide': 'AAAAAFAAAAAAAAA', 'isoformMhcII': {'name': 'HLA-DQA101:02-DQB103:02', 'alphaChain': {'fullName': 'HLA-DQA101:02', 'name': 'HLA-DQA101:02', 'gene': 'DQA1', 'group': '01', 'protein': '02'}, 'betaChain': {'fullName': 'HLA- DQB103:02', 'name': 'HLA-DQB103:02', 'gene': 'DQB1', 'group': '03', 'protein': '02'}}, 'affinityMutated': 584.81, 'rankMutated': 3.23, 'affinityWildType': 467.56, 'rankWildType': 1.3}, {'position': 10, 'mutatedPeptide': 'AAAALAAAAAAAAAA', 'wildTypePeptide': 'AAAAFAAAAAAAAAA', 'i soformMhcII': {'name': 'HLA-DQA101:02-DQB103:02', 'alphaChain': {'fullName': 'HLA-DQA101:02', 'name': 'HLA-DQA101:02', 'gene': 'DQA1', 'group': '01', 'protein': '02'}, 'betaChain': {'fullName': 'HLA-DQB103:02', 'name': 'HLA-DQB103:02', 'gene': 'DQB1', 'group': '03', 'protein ': '02'}}, 'affinityMutated': 524.6, 'rankMutated': 1.23, 'affinityWildType': 443.41, 'rankWildType': 0.67}, {'position': 11, 'mutatedPeptide': 'AAALAAAAAAAAAAA', 'wildTypePeptide': 'AAAFAAAAAAAAAAA', 'isoformMhcII': {'name': 'HLA-DQA101:02-DQB103:02', 'alphaChain': {'fullName': 'HLA-DQA101:02', 'name': 'HLA-DQA101:02', 'gene': 'DQA1', 'group': '01', 'protein': '02'}, 'betaChain': {'fullName': 'HLA-DQB103:02', 'name': 'HLA-DQB103:02', 'gene': 'DQB1', 'group': '03', 'protein': '02'}}, 'affinityMutated': 495.4, 'rankMutated': 0.78, 'affinityWildType': 452.64, 'rankWildType': 0.47}, {'position': 12, 'mutatedPeptide': 'AALAAAAAAAAAAAA', 'wildTypePeptide': 'AAFAAAAAAAAAAAA', 'isoformMhcII': {'name': 'HLA-DQA101:02-DQB103:02', 'alphaChain': {'fullName': 'HLA-DQA101:02', 'name': 'HLA-DQA101:02', 'gene': 'DQA1', 'group': '01', 'p rotein': '02'}, 'betaChain': {'fullName': 'HLA-DQB103:02', 'name': 'HLA-DQB103:02', 'gene': 'DQB1', 'group': '03', 'protein': '02'}}, 'affinityMutated': 593.48, 'rankMutated': 2.6, 'affinityWildType': 553.29, 'rankWildType': 1.57}, {'position': 5, 'mutatedPeptide': 'AAAAAAAAALAA AAA', 'wildTypePeptide': 'AAAAAAAAAFAAAAA', 'isoformMhcII': {'name': 'HLA-DPA101:03-DPB106:01', 'alphaChain': {'fullName': 'HLA-DPA101:03', 'name': 'HLA-DPA101:03', 'gene': 'DPA1', 'group': '01', 'protein': '03'}, 'betaChain': {'fullName': 'HLA-DPB106:01', 'name': 'HLA-DPB10 6:01', 'gene': 'DPB1', 'group': '06', 'protein': '01'}}, 'affinityMutated': 3415.63, 'rankMutated': 2.93, 'affinityWildType': 2585.77, 'rankWildType': 2.12}, {'position': 6, 'mutatedPeptide': 'AAAAAAAALAAAAAA', 'wildTypePeptide': 'AAAAAAAAFAAAAAA', 'isoformMhcII': {'name': 'HLA-DP A101:03-DPB106:01', 'alphaChain': {'fullName': 'HLA-DPA101:03', 'name': 'HLA-DPA101:03', 'gene': 'DPA1', 'group': '01', 'protein': '03'}, 'betaChain': {'fullName': 'HLA-DPB106:01', 'name': 'HLA-DPB106:01', 'gene': 'DPB1', 'group': '06', 'protein': '01'}}, 'affinityMutated': 2958.8, 'rankMutated': 1.55, 'affinityWildType': 2154.78, 'rankWildType': 0.99}, {'position': 7, 'mutatedPeptide': 'AAAAAAALAAAAAAA', 'wildTypePeptide': 'AAAAAAAFAAAAAAA', 'isoformMhcII': {'name': 'HLA-DPA101:03-DPB106:01', 'alphaChain': {'fullName': 'HLA-DPA101:03', 'name': 'H LA-DPA101:03', 'gene': 'DPA1', 'group': '01', 'protein': '03'}, 'betaChain': {'fullName': 'HLA-DPB106:01', 'name': 'HLA-DPB106:01', 'gene': 'DPB1', 'group': '06', 'protein': '01'}}, 'affinityMutated': 2710.11, 'rankMutated': 1.53, 'affinityWildType': 2144.94, 'rankWildType': 1. 06}, {'position': 8, 'mutatedPeptide': 'AAAAAALAAAAAAAA', 'wildTypePeptide': 'AAAAAAFAAAAAAAA', 'isoformMhcII': {'name': 'HLA-DPA101:03-DPB106:01', 'alphaChain': {'fullName': 'HLA-DPA101:03', 'name': 'HLA-DPA101:03', 'gene': 'DPA1', 'group': '01', 'protein': '03'}, 'betaChain' : {'fullName': 'HLA-DPB106:01', 'name': 'HLA-DPB106:01', 'gene': 'DPB1', 'group': '06', 'protein': '01'}}, 'affinityMutated': 2459.74, 'rankMutated': 3.18, 'affinityWildType': 1299.57, 'rankWildType': 0.73}, {'position': 9, 'mutatedPeptide': 'AAAAALAAAAAAAAA', 'wildTypePeptide': 'AAAAAFAAAAAAAAA', 'isoformMhcII': {'name': 'HLA-DPA101:03-DPB106:01', 'alphaChain': {'fullName': 'HLA-DPA101:03', 'name': 'HLA-DPA101:03', 'gene': 'DPA1', 'group': '01', 'protein': '03'}, 'betaChain': {'fullName': 'HLA-DPB106:01', 'name': 'HLA-DPB106:01', 'gene': 'DPB1', ' group': '06', 'protein': '01'}}, 'affinityMutated': 1990.01, 'rankMutated': 1.81, 'affinityWildType': 940.81, 'rankWildType': 0.32}, {'position': 10, 'mutatedPeptide': 'AAAALAAAAAAAAAA', 'wildTypePeptide': 'AAAAFAAAAAAAAAA', 'isoformMhcII': {'name': 'HLA-DPA101:03-DPB106:01', 'a lphaChain': {'fullName': 'HLA-DPA101:03', 'name': 'HLA-DPA101:03', 'gene': 'DPA1', 'group': '01', 'protein': '03'}, 'betaChain': {'fullName': 'HLA-DPB106:01', 'name': 'HLA-DPB106:01', 'gene': 'DPB1', 'group': '06', 'protein': '01'}}, 'affinityMutated': 1561.25, 'rankMutated': 0.83, 'affinityWildType': 698.42, 'rankWildType': 0.16}, {'position': 11, 'mutatedPeptide': 'AAALAAAAAAAAAAA', 'wildTypePeptide': 'AAAFAAAAAAAAAAA', 'isoformMhcII': {'name': 'HLA-DPA101:03-DPB106:01', 'alphaChain': {'fullName': 'HLA-DPA101:03', 'name': 'HLA-DPA101:03', 'gene': 'DPA1', 'group': '01', 'protein': '03'}, 'betaChain': {'fullName': 'HLA-DPB106:01', 'name': 'HLA-DPB106:01', 'gene': 'DPB1', 'group': '06', 'protein': '01'}}, 'affinityMutated': 1308.41, 'rankMutated': 0.62, 'affinityWildType': 542.44, 'rankWildType': 0.12}, {'position': 12, 'm utatedPeptide': 'AALAAAAAAAAAAAA', 'wildTypePeptide': 'AAFAAAAAAAAAAAA', 'isoformMhcII': {'name': 'HLA-DPA101:03-DPB106:01', 'alphaChain': {'fullName': 'HLA-DPA101:03', 'name': 'HLA-DPA101:03', 'gene': 'DPA1', 'group': '01', 'protein': '03'}, 'betaChain': {'fullName': 'HLA-DPB 106:01', 'name': 'HLA-DPB106:01', 'gene': 'DPB1', 'group': '06', 'protein': '01'}}, 'affinityMutated': 1572.88, 'rankMutated': 1.72, 'affinityWildType': 671.31, 'rankWildType': 0.5}, {'position': 13, 'mutatedPeptide': 'ALAAAAAAAAAAAAA', 'wildTypePeptide': 'AFAAAAAAAAAAAAA', 'iso formMhcII': {'name': 'HLA-DPA101:03-DPB106:01', 'alphaChain': {'fullName': 'HLA-DPA101:03', 'name': 'HLA-DPA101:03', 'gene': 'DPA1', 'group': '01', 'protein': '03'}, 'betaChain': {'fullName': 'HLA-DPB106:01', 'name': 'HLA-DPB106:01', 'gene': 'DPB1', 'group': '06', 'protein': '01'}}, 'affinityMutated': 2211.13, 'rankMutated': 4.46, 'affinityWildType': 929.37, 'rankWildType': 2.68}, {'position': 5, 'mutatedPeptide': 'AAAAAAAAALAAAAA', 'wildTypePeptide': 'AAAAAAAAAFAAAAA', 'isoformMhcII': {'name': 'HLA-DQA103:01-DQB103:02', 'alphaChain': {'fullName': 'HLA-DQA103:01', 'name': 'HLA-DQA103:01', 'gene': 'DQA1', 'group': '03', 'protein': '01'}, 'betaChain': {'fullName': 'HLA-DQB103:02', 'name': 'HLA-DQB103:02', 'gene': 'DQB1', 'group': '03', 'protein': '02'}}, 'affinityMutated': 988.63, 'rankMutated': 4.52, 'affinityWildType': 658.16, 'rankWildType': 3.67}, {'position': 6, 'mutatedPeptide': 'AAAAAAAALAAAAAA', 'wildTypePeptide': 'AAAAAAAAFAAAAAA', 'isoformMhcII': {'name': 'HLA-DQA103:01-DQB103:02', 'alphaChain': {'fullName': 'HLA-DQA103:01', 'name': 'HLA-DQA103:01', 'gene': 'DQA1', 'group': '03', 'pr otein': '01'}, 'betaChain': {'fullName': 'HLA-DQB103:02', 'name': 'HLA-DQB103:02', 'gene': 'DQB1', 'group': '03', 'protein': '02'}}, 'affinityMutated': 1040.53, 'rankMutated': 4.39, 'affinityWildType': 702.02, 'rankWildType': 2.95}, {'position': 7, 'mutatedPeptide': 'AAAAAAALAAA AAAA', 'wildTypePeptide': 'AAAAAAAFAAAAAAA', 'isoformMhcII': {'name': 'HLA-DQA103:01-DQB103:02', 'alphaChain': {'fullName': 'HLA-DQA103:01', 'name': 'HLA-DQA103:01', 'gene': 'DQA1', 'group': '03', 'protein': '01'}, 'betaChain': {'fullName': 'HLA-DQB103:02', 'name': 'HLA-DQB1 03:02', 'gene': 'DQB1', 'group': '03', 'protein': '02'}}, 'affinityMutated': 998.08, 'rankMutated': 3.75, 'affinityWildType': 717.94, 'rankWildType': 2.67}, {'position': 10, 'mutatedPeptide': 'AAAALAAAAAAAAAA', 'wildTypePeptide': 'AAAAFAAAAAAAAAA', 'isoformMhcII': {'name': 'HLA-DQ A103:01-DQB103:02', 'alphaChain': {'fullName': 'HLA-DQA103:01', 'name': 'HLA-DQA103:01', 'gene': 'DQA1', 'group': '03', 'protein': '01'}, 'betaChain': {'fullName': 'HLA-DQB103:02', 'name': 'HLA-DQB103:02', 'gene': 'DQB1', 'group': '03', 'protein': '02'}}, 'affinityMutated': 1119.5, 'rankMutated': 4.0, 'affinityWildType': 768.85, 'rankWildType': 0.61}, {'position': 11, 'mutatedPeptide': 'AAALAAAAAAAAAAA', 'wildTypePeptide': 'AAAFAAAAAAAAAAA', 'isoformMhcII': {'name': 'HLA-DQA103:01-DQB103:02', 'alphaChain': {'fullName': 'HLA-DQA103:01', 'name': 'HL A-DQA103:01', 'gene': 'DQA1', 'group': '03', 'protein': '01'}, 'betaChain': {'fullName': 'HLA-DQB103:02', 'name': 'HLA-DQB103:02', 'gene': 'DQB1', 'group': '03', 'protein': '02'}}, 'affinityMutated': 1106.38, 'rankMutated': 2.76, 'affinityWildType': 834.87, 'rankWildType': 0.37 }, {'position': 12, 'mutatedPeptide': 'AALAAAAAAAAAAAA', 'wildTypePeptide': 'AAFAAAAAAAAAAAA', 'isoformMhcII': {'name': 'HLA-DQA103:01-DQB103:02', 'alphaChain': {'fullName': 'HLA-DQA103:01', 'name': 'HLA-DQA103:01', 'gene': 'DQA1', 'group': '03', 'protein': '01'}, 'betaChain': {'fullName': 'HLA-DQB103:02', 'name': 'HLA-DQB103:02', 'gene': 'DQB1', 'group': '03', 'protein': '02'}}, 'affinityMutated': 1248.22, 'rankMutated': 4.25, 'affinityWildType': 1005.79, 'rankWildType': 1.58}, {'position': 10, 'mutatedPeptide': 'AAAALAAAAAAAAAA', 'wildTypePeptide': 'AAAAFAAAAAAAAAA', 'isoformMhcII': {'name': 'HLA-DRB104:04', 'betaChain': {'fullName': 'HLA-DRB104:04', 'name': 'HLA-DRB104:04', 'gene': 'DRB1', 'group': '04', 'protein': '04'}}, 'affinityMutated': 179.85, 'rankMutated': 4.6, 'affinityWildType': 199.63, 'rankWildType': 7.28}, {'position': 11, 'mutatedPeptide': 'AAALAAAAAAAAAAA', 'wildTypePeptide': 'AAAFAAAAAAAAAAA', 'isoformMhcII': {'name': 'HLA-DRB104:04', 'betaChain': {'fullName': 'HLA-DRB104:04', 'name': 'HLA-DRB104:04', 'gene': 'DRB1', 'group': '04', 'protein': '04'}}, 'affinityMutated': 142.15, 'rankMutated': 3.57, 'affinityWildType': 169.07, 'rankWildType': 5.85}, {'position': 5, 'mutatedPeptide': 'AAAAAAAAALAAAAA', 'wildTypePeptide': 'AAAAAAAAAFAAAAA', 'isoformMhcII': {'name': 'HLA-DQA101:02-DQB106:02', 'alphaChain': {'fullName': 'HLA-DQA101:02', 'name': 'HLA-DQA1 01:02', 'gene': 'DQA1', 'group': '01', 'protein': '02'}, 'betaChain': {'fullName': 'HLA-DQB106:02', 'name': 'HLA-DQB106:02', 'gene': 'DQB1', 'group': '06', 'protein': '02'}}, 'affinityMutated': 15.77, 'rankMutated': 0.03, 'affinityWildType': 20.72, 'rankWildType': 0.27}, {'posit ion': 6, 'mutatedPeptide': 'AAAAAAAALAAAAAA', 'wildTypePeptide': 'AAAAAAAAFAAAAAA', 'isoformMhcII': {'name': 'HLA-DQA101:02-DQB106:02', 'alphaChain': {'fullName': 'HLA-DQA101:02', 'name': 'HLA-DQA101:02', 'gene': 'DQA1', 'group': '01', 'protein': '02'}, 'betaChain': {'fullName ': 'HLA-DQB106:02', 'name': 'HLA-DQB106:02', 'gene': 'DQB1', 'group': '06', 'protein': '02'}}, 'affinityMutated': 15.65, 'rankMutated': 0.04, 'affinityWildType': 22.47, 'rankWildType': 0.41}, {'position': 7, 'mutatedPeptide': 'AAAAAAALAAAAAAA', 'wildTypePeptide': 'AAAAAAAFAAAAAA A', 'isoformMhcII': {'name': 'HLA-DQA101:02-DQB106:02', 'alphaChain': {'fullName': 'HLA-DQA101:02', 'name': 'HLA-DQA101:02', 'gene': 'DQA1', 'group': '01', 'protein': '02'}, 'betaChain': {'fullName': 'HLA-DQB106:02', 'name': 'HLA-DQB106:02', 'gene': 'DQB1', 'group': '06', 'p rotein': '02'}}, 'affinityMutated': 17.14, 'rankMutated': 0.07, 'affinityWildType': 23.89, 'rankWildType': 0.35}, {'position': 8, 'mutatedPeptide': 'AAAAAALAAAAAAAA', 'wildTypePeptide': 'AAAAAAFAAAAAAAA', 'isoformMhcII': {'name': 'HLA-DQA101:02-DQB106:02', 'alphaChain': {'fullNa me': 'HLA-DQA101:02', 'name': 'HLA-DQA101:02', 'gene': 'DQA1', 'group': '01', 'protein': '02'}, 'betaChain': {'fullName': 'HLA-DQB106:02', 'name': 'HLA-DQB106:02', 'gene': 'DQB1', 'group': '06', 'protein': '02'}}, 'affinityMutated': 21.13, 'rankMutated': 0.39, 'affinityWildTyp e': 27.61, 'rankWildType': 0.4}, {'position': 9, 'mutatedPeptide': 'AAAAALAAAAAAAAA', 'wildTypePeptide': 'AAAAAFAAAAAAAAA', 'isoformMhcII': {'name': 'HLA-DQA101:02-DQB106:02', 'alphaChain': {'fullName': 'HLA-DQA101:02', 'name': 'HLA-DQA101:02', 'gene': 'DQA1', 'group': '01', ' protein': '02'}, 'betaChain': {'fullName': 'HLA-DQB106:02', 'name': 'HLA-DQB106:02', 'gene': 'DQB1', 'group': '06', 'protein': '02'}}, 'affinityMutated': 22.5, 'rankMutated': 0.33, 'affinityWildType': 29.02, 'rankWildType': 0.29}, {'position': 10, 'mutatedPeptide': 'AAAALAAAAAAA AAA', 'wildTypePeptide': 'AAAAFAAAAAAAAAA', 'isoformMhcII': {'name': 'HLA-DQA101:02-DQB106:02', 'alphaChain': {'fullName': 'HLA-DQA101:02', 'name': 'HLA-DQA101:02', 'gene': 'DQA1', 'group': '01', 'protein': '02'}, 'betaChain': {'fullName': 'HLA-DQB106:02', 'name': 'HLA-DQB10 6:02', 'gene': 'DQB1', 'group': '06', 'protein': '02'}}, 'affinityMutated': 22.35, 'rankMutated': 0.13, 'affinityWildType': 27.86, 'rankWildType': 0.22}, {'position': 11, 'mutatedPeptide': 'AAALAAAAAAAAAAA', 'wildTypePeptide': 'AAAFAAAAAAAAAAA', 'isoformMhcII': {'name': 'HLA-DQA1 01:02-DQB106:02', 'alphaChain': {'fullName': 'HLA-DQA101:02', 'name': 'HLA-DQA101:02', 'gene': 'DQA1', 'group': '01', 'protein': '02'}, 'betaChain': {'fullName': 'HLA-DQB106:02', 'name': 'HLA-DQB106:02', 'gene': 'DQB1', 'group': '06', 'protein': '02'}}, 'affinityMutated': 21. 21, 'rankMutated': 0.07, 'affinityWildType': 26.86, 'rankWildType': 0.11}, {'position': 12, 'mutatedPeptide': 'AALAAAAAAAAAAAA', 'wildTypePeptide': 'AAFAAAAAAAAAAAA', 'isoformMhcII': {'name': 'HLA-DQA101:02-DQB106:02', 'alphaChain': {'fullName': 'HLA-DQA101:02', 'name': 'HLA-DQ A101:02', 'gene': 'DQA1', 'group': '01', 'protein': '02'}, 'betaChain': {'fullName': 'HLA-DQB106:02', 'name': 'HLA-DQB106:02', 'gene': 'DQB1', 'group': '06', 'protein': '02'}}, 'affinityMutated': 23.24, 'rankMutated': 0.08, 'affinityWildType': 27.69, 'rankWildType': 0.08}, {'po sition': 13, 'mutatedPeptide': 'ALAAAAAAAAAAAAA', 'wildTypePeptide': 'AFAAAAAAAAAAAAA', 'isoformMhcII': {'name': 'HLA-DQA101:02-DQB106:02', 'alphaChain': {'fullName': 'HLA-DQA101:02', 'name': 'HLA-DQA101:02', 'gene': 'DQA1', 'group': '01', 'protein': '02'}, 'betaChain': {'full Name': 'HLA-DQB106:02', 'name': 'HLA-DQB106:02', 'gene': 'DQB1', 'group': '06', 'protein': '02'}}, 'affinityMutated': 28.07, 'rankMutated': 0.1, 'affinityWildType': 29.39, 'rankWildType': 0.09}]} [E 230109 13:07:59 neofox:267] Error processing patient {'identifier': 'Ptx', 'isRnaAvailable': True, 'tumorType': 'SKCM', 'mhc1': [{'zygosity': 'HETEROZYGOUS', 'alleles': [{'fullName': 'HLA-A03:01', 'name': 'HLA-A03:01', 'gene': 'A', 'group': '03', 'protein': '01'}, {'fullName' : 'HLA-A02:01', 'name': 'HLA-A02:01', 'gene': 'A', 'group': '02', 'protein': '01'}]}, {'name': 'B', 'zygosity': 'HETEROZYGOUS', 'alleles': [{'fullName': 'HLA-B07:02', 'name': 'HLA-B07:02', 'gene': 'B', 'group': '07', 'protein': '02'}, {'fullName': 'HLA-B40:01', 'name': 'HLA-B 40:01', 'gene': 'B', 'group': '40', 'protein': '01'}]}, {'name': 'C', 'zygosity': 'HETEROZYGOUS', 'alleles': [{'fullName': 'HLA-C07:02', 'name': 'HLA-C07:02', 'gene': 'C', 'group': '07', 'protein': '02'}, {'fullName': 'HLA-C03:04', 'name': 'HLA-C03:04', 'gene': 'C', 'group': '03', 'protein': '04'}]}], 'mhc2': [{'name': 'DP', 'genes': [{'name': 'DPA1', 'alleles': [{'fullName': 'HLA-DPA101:03', 'name': 'HLA-DPA101:03', 'gene': 'DPA1', 'group': '01', 'protein': '03'}]}, {'name': 'DPB1', 'zygosity': 'HETEROZYGOUS', 'alleles': [{'fullName': 'HLA-DPB102: 01', 'name': 'HLA-DPB102:01', 'gene': 'DPB1', 'group': '02', 'protein': '01'}, {'fullName': 'HLA-DPB106:01', 'name': 'HLA-DPB106:01', 'gene': 'DPB1', 'group': '06', 'protein': '01'}]}], 'isoforms': [{'name': 'HLA-DPA101:03-DPB102:01', 'alphaChain': {'fullName': 'HLA-DPA101:0 3', 'name': 'HLA-DPA101:03', 'gene': 'DPA1', 'group': '01', 'protein': '03'}, 'betaChain': {'fullName': 'HLA-DPB102:01', 'name': 'HLA-DPB102:01', 'gene': 'DPB1', 'group': '02', 'protein': '01'}}, {'name': 'HLA-DPA101:03-DPB106:01', 'alphaChain': {'fullName': 'HLA-DPA101:03', 'name': 'HLA-DPA101:03', 'gene': 'DPA1', 'group': '01', 'protein': '03'}, 'betaChain': {'fullName': 'HLA-DPB106:01', 'name': 'HLA-DPB106:01', 'gene': 'DPB1', 'group': '06', 'protein': '01'}}]}, {'name': 'DQ', 'genes': [{'name': 'DQA1', 'zygosity': 'HETEROZYGOUS', 'alleles': [{ 'fullName': 'HLA-DQA101:02', 'name': 'HLA-DQA101:02', 'gene': 'DQA1', 'group': '01', 'protein': '02'}, {'fullName': 'HLA-DQA103:01', 'name': 'HLA-DQA103:01', 'gene': 'DQA1', 'group': '03', 'protein': '01'}]}, {'name': 'DQB1', 'zygosity': 'HETEROZYGOUS', 'alleles': [{'fullName' : 'HLA-DQB106:02', 'name': 'HLA-DQB106:02', 'gene': 'DQB1', 'group': '06', 'protein': '02'}, {'fullName': 'HLA-DQB103:02', 'name': 'HLA-DQB103:02', 'gene': 'DQB1', 'group': '03', 'protein': '02'}]}], 'isoforms': [{'name': 'HLA-DQA101:02-DQB106:02', 'alphaChain': {'fullName': 'HLA-DQA101:02', 'name': 'HLA-DQA101:02', 'gene': 'DQA1', 'group': '01', 'protein': '02'}, 'betaChain': {'fullName': 'HLA-DQB106:02', 'name': 'HLA-DQB106:02', 'gene': 'DQB1', 'group': '06', 'protein': '02'}}, {'name': 'HLA-DQA101:02-DQB103:02', 'alphaChain': {'fullName': 'H LA-DQA101:02', 'name': 'HLA-DQA101:02', 'gene': 'DQA1', 'group': '01', 'protein': '02'}, 'betaChain': {'fullName': 'HLA-DQB103:02', 'name': 'HLA-DQB103:02', 'gene': 'DQB1', 'group': '03', 'protein': '02'}}, {'name': 'HLA-DQA103:01-DQB106:02', 'alphaChain': {'fullName': 'HLA- DQA103:01', 'name': 'HLA-DQA103:01', 'gene': 'DQA1', 'group': '03', 'protein': '01'}, 'betaChain': {'fullName': 'HLA-DQB106:02', 'name': 'HLA-DQB106:02', 'gene': 'DQB1', 'group': '06', 'protein': '02'}}, {'name': 'HLA-DQA103:01-DQB103:02', 'alphaChain': {'fullName': 'HLA-DQA 103:01', 'name': 'HLA-DQA103:01', 'gene': 'DQA1', 'group': '03', 'protein': '01'}, 'betaChain': {'fullName': 'HLA-DQB103:02', 'name': 'HLA-DQB103:02', 'gene': 'DQB1', 'group': '03', 'protein': '02'}}]}, {'genes': [{'zygosity': 'HETEROZYGOUS', 'alleles': [{'fullName': 'HLA-DRB1 04:04', 'name': 'HLA-DRB104:04', 'gene': 'DRB1', 'group': '04', 'protein': '04'}, {'fullName': 'HLA-DRB115:01', 'name': 'HLA-DRB115:01', 'gene': 'DRB1', 'group': '15', 'protein': '01'}]}], 'isoforms': [{'name': 'HLA-DRB104:04', 'betaChain': {'fullName': 'HLA-DRB104:04', 'nam e': 'HLA-DRB104:04', 'gene': 'DRB1', 'group': '04', 'protein': '04'}}, {'name': 'HLA-DRB115:01', 'betaChain': {'fullName': 'HLA-DRB115:01', 'name': 'HLA-DRB115:01', 'gene': 'DRB1', 'group': '15', 'protein': '01'}}]}]} [E 230109 13:07:59 command_line:192] Error running command '/usr/bin/Rscript /usr/local/lib/python3.7/site-packages/neofox/published_features/hex/hex.R AALAAAAAAA /app/neofox-reference/iedb/IEDB_homo_sapiens.fasta /usr/local/lib/python3.7/site-packages/neofox/published_features/he x' Traceback (most recent call last): File "/usr/local/lib/python3.7/site-packages/neofox/command_line.py", line 182, in neofox_cli with_all_neoepitopes=with_all_neoepitopes File "/usr/local/lib/python3.7/site-packages/neofox/neofox.py", line 194, in get_annotations annotations = self.send_to_client(dask_client) File "/usr/local/lib/python3.7/site-packages/neofox/neofox.py", line 230, in send_to_client annotated_neoantigens = dask_client.gather(futures) File "/usr/local/lib/python3.7/site-packages/distributed/client.py", line 2152, in gather asynchronous=asynchronous, File "/usr/local/lib/python3.7/site-packages/distributed/utils.py", line 310, in sync self.loop, func, *args, callback_timeout=callback_timeout, **kwargs File "/usr/local/lib/python3.7/site-packages/distributed/utils.py", line 376, in sync raise exc.with_traceback(tb) File "/usr/local/lib/python3.7/site-packages/distributed/utils.py", line 349, in f result = yield future File "/usr/local/lib/python3.7/site-packages/tornado/gen.py", line 769, in run value = future.result() File "/usr/local/lib/python3.7/site-packages/distributed/client.py", line 2009, in _gather raise exception.with_traceback(traceback) File "/usr/local/lib/python3.7/site-packages/neofox/neofox.py", line 268, in annotate_neoantigen raise e File "/usr/local/lib/python3.7/site-packages/neofox/neofox.py", line 264, in annotate_neoantigen ).get_annotated_neoantigen(neoantigen, patient, with_all_neoepitopes=with_all_neoepitopes) File "/usr/local/lib/python3.7/site-packages/neofox/annotator/neoantigen_annotator.py", line 233, in get_annotated_neoantigen mutated_peptide_mhcii=netmhc2pan.best_predicted_epitope_affinity if netmhc2pan else None) File "/usr/local/lib/python3.7/site-packages/neofox/published_features/hex/hex.py", line 60, in get_annotation hex_aln_score_mhci = self.apply_hex(mutated_peptide_mhci.mutated_peptide) File "/usr/local/lib/python3.7/site-packages/neofox/published_features/hex/hex.py", line 44, in applyhex output, = self.runner.run_command(cmd) File "/usr/local/lib/python3.7/site-packages/neofox/helpers/runner.py", line 55, in run_command "Error running command '{}'".format(" ".join(cmd)) neofox.exceptions.NeofoxCommandException: Error running command '/usr/bin/Rscript /usr/local/lib/python3.7/site-packages/neofox/published_features/hex/hex.R AALAAAAAAA /app/neofox-reference/iedb/IEDB_homo_sapiens.fasta /usr/local/lib/python3.7/site-packages/neofox/published_fe atures/hex'

xtmgah commented 1 year ago

@priesgo priesgo Any suggestion for the testing? I really interested in testing this algorithm. Really appreciated your help here. Thanks.

priesgo commented 1 year ago

Hi @xtmgah thanks for your feedback. On a quick check it seems like the HEX config is wrong for some reason. I will come back to you, but first, let me ask which version are you using?

xtmgah commented 1 year ago

@priesgo Thanks for your explanation. Please let me know how to fix the issue. We really want to estimate our data as soon as possible. I think I pulled out the "NeoFox 1.0.2" from Github. BTW, I do see some different parameters between the version I used and the documentation online. For example, I my version, i see the parameter "--input-file", but the documentation i saw in the github page or the website is "--candidate-file". So, Can you also explain the difference here?

priesgo commented 1 year ago

@xtmgah so far I can inform you that the --candidate-file in the docs is a typo, this changed some time ago but we failed to update this part of the docs. The right parameter is --input-file

priesgo commented 1 year ago

@xtmgah also --with-table and --with-json do not exist anymore

xtmgah commented 1 year ago

Thanks. Do you have chance to fix the HEX config?

Get Outlook for iOShttps://aka.ms/o0ukef

From: Pablo Riesgo-Ferreiro @.> Sent: Thursday, January 19, 2023 8:30:50 AM To: TRON-Bioinformatics/neofox @.> Cc: xtmgah @.>; Mention @.> Subject: Re: [TRON-Bioinformatics/neofox] Not working for the test data (Issue #12)

@xtmgahhttps://github.com/xtmgah also --with-table and --with-json do not exist anymore

— Reply to this email directly, view it on GitHubhttps://github.com/TRON-Bioinformatics/neofox/issues/12#issuecomment-1396979156, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABAKG5GVI6EN4CVO7WTH3UDWTE6YVANCNFSM6AAAAAATVXVTO4. You are receiving this because you were mentioned.Message ID: @.***>

priesgo commented 1 year ago

@xtmgah I just tested the test data on a local installation and it worked. From your error message it seems like your hex command has troubles, but it is difficult to know why without knowing how you built the singularity image.

xtmgah commented 1 year ago

@priesgo Thanks for you help here. Here is the detailed information on how we build this image. Let me know if there is something wrong here. Thanks.

git clone https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FTRON-Bioinformatics%2Fneofox.git&data=05%7C01%7Ctongwu.zhang%40nih.gov%7C22b21a44237542b91fc408daee8d53a5%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638084587997933687%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Lrp%2BGZGtM8b6WMvUTemKeWhvdbfakmCMMS%2FmcTgr%2FBs%3D&reserved=0 cd neofix

Register and get download links, they will have a long series of

letters/numbers in place of DOWNLOAD_UUID wget https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fservices.healthtech.dtu.dk%2Fdownload%2FDOWNLOAD_UUID%2FnetMHCpan-4.1b.Linux.tar.gz&data=05%7C01%7Ctongwu.zhang%40nih.gov%7C22b21a44237542b91fc408daee8d53a5%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638084587997933687%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=O4v3XDM%2FAEVJWm8ydu1gbDOOOHZcwR5MwDjBsB7CKbo%3D&reserved=0 wget https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fservices.healthtech.dtu.dk%2Fdownload%2FDOWNLOAD_UUID%2FnetMHCIIpan-4.0.Linux.tar.gz&data=05%7C01%7Ctongwu.zhang%40nih.gov%7C22b21a44237542b91fc408daee8d53a5%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638084587997933687%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Zk%2FR0fg5dFlOG840VXznb95YivdJrmbPS%2B%2Bol3fACVo%3D&reserved=0

docker build --platform linux/amd64 --tag neofox-docker . # build the Docker and tag

singularity build neofox.sif docker-daemon://neofox-docker:latest # build the Singularity image and save to a single file

xtmgah commented 1 year ago

@priesgo I just reinstall everything again using the conda pip and install/configure as your suggestion in the document. However, i have different issue in this version. Can you help to check? The neofox --help looks fine. But the example testing have the issue related to python panda. Any suggestions will be appreciated. thanks.

zhangt8@cn4285:/data/zhangt8/Ref/Neoantigen/neofox/test$ neofox --input-file test_data.tsv --patient-data test_patients.tsv --output-folder ./output --output-prefix test [E 230119 19:49:40 command_line:192] Error tokenizing data. C error: Expected 1 fields in line 28, saw 367 Traceback (most recent call last): File "/data/zhangt8/conda/envs/neofox/lib/python3.7/site-packages/neofox/command_line.py", line 171, in neofox_cli reference_folder.get_mhc_database()) File "/data/zhangt8/conda/envs/neofox/lib/python3.7/site-packages/neofox/references/references.py", line 310, in get_mhc_database self.__mhc_database = HlaDatabase(self.mhc_database_filename) File "/data/zhangt8/conda/envs/neofox/lib/python3.7/site-packages/neofox/references/references.py", line 170, in init self.alleles = self._load_alleles(database_filename) File "/data/zhangt8/conda/envs/neofox/lib/python3.7/site-packages/neofox/references/references.py", line 196, in _load_alleles hla_database = pd.read_csv(hla_database_filename, comment="#") File "/data/zhangt8/conda/envs/neofox/lib/python3.7/site-packages/pandas/util/_decorators.py", line 311, in wrapper return func(*args, **kwargs) File "/data/zhangt8/conda/envs/neofox/lib/python3.7/site-packages/pandas/io/parsers/readers.py", line 586, in read_csv return _read(filepath_or_buffer, kwds) File "/data/zhangt8/conda/envs/neofox/lib/python3.7/site-packages/pandas/io/parsers/readers.py", line 488, in _read return parser.read(nrows) File "/data/zhangt8/conda/envs/neofox/lib/python3.7/site-packages/pandas/io/parsers/readers.py", line 1047, in read index, columns, col_dict = self._engine.read(nrows) File "/data/zhangt8/conda/envs/neofox/lib/python3.7/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 224, in read chunks = self._reader.read_low_memory(nrows) File "pandas/_libs/parsers.pyx", line 801, in pandas._libs.parsers.TextReader.read_low_memory File "pandas/_libs/parsers.pyx", line 857, in pandas._libs.parsers.TextReader._read_rows File "pandas/_libs/parsers.pyx", line 843, in pandas._libs.parsers.TextReader._tokenize_rows File "pandas/_libs/parsers.pyx", line 1925, in pandas._libs.parsers.raise_parser_error pandas.errors.ParserError: Error tokenizing data. C error: Expected 1 fields in line 28, saw 367

Traceback (most recent call last): File "/data/zhangt8/conda/envs/neofox/bin/neofox", line 10, in sys.exit(neofox_cli()) File "/data/zhangt8/conda/envs/neofox/lib/python3.7/site-packages/neofox/command_line.py", line 193, in neofox_cli raise e File "/data/zhangt8/conda/envs/neofox/lib/python3.7/site-packages/neofox/command_line.py", line 171, in neofox_cli reference_folder.get_mhc_database()) File "/data/zhangt8/conda/envs/neofox/lib/python3.7/site-packages/neofox/references/references.py", line 310, in get_mhc_database self.__mhc_database = HlaDatabase(self.mhc_database_filename) File "/data/zhangt8/conda/envs/neofox/lib/python3.7/site-packages/neofox/references/references.py", line 170, in init self.alleles = self._load_alleles(database_filename) File "/data/zhangt8/conda/envs/neofox/lib/python3.7/site-packages/neofox/references/references.py", line 196, in _load_alleles hla_database = pd.read_csv(hla_database_filename, comment="#") File "/data/zhangt8/conda/envs/neofox/lib/python3.7/site-packages/pandas/util/_decorators.py", line 311, in wrapper return func(*args, **kwargs) File "/data/zhangt8/conda/envs/neofox/lib/python3.7/site-packages/pandas/io/parsers/readers.py", line 586, in read_csv return _read(filepath_or_buffer, kwds) File "/data/zhangt8/conda/envs/neofox/lib/python3.7/site-packages/pandas/io/parsers/readers.py", line 488, in _read return parser.read(nrows) File "/data/zhangt8/conda/envs/neofox/lib/python3.7/site-packages/pandas/io/parsers/readers.py", line 1047, in read index, columns, col_dict = self._engine.read(nrows) File "/data/zhangt8/conda/envs/neofox/lib/python3.7/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 224, in read chunks = self._reader.read_low_memory(nrows) File "pandas/_libs/parsers.pyx", line 801, in pandas._libs.parsers.TextReader.read_low_memory File "pandas/_libs/parsers.pyx", line 857, in pandas._libs.parsers.TextReader._read_rows File "pandas/_libs/parsers.pyx", line 843, in pandas._libs.parsers.TextReader._tokenize_rows File "pandas/_libs/parsers.pyx", line 1925, in pandas._libs.parsers.raise_parser_error pandas.errors.ParserError: Error tokenizing data. C error: Expected 1 fields in line 28, saw 367

priesgo commented 1 year ago

@xtmgah brief update: I was able to replicate your exact error using Docker, hence this is not a singularity thing.

priesgo commented 1 year ago

@priesgo I just reinstall everything again using the conda pip and install/configure as your suggestion in the document. However, i have different issue in this version. Can you help to check? The neofox --help looks fine. But the example testing have the issue related to python panda. Any suggestions will be appreciated. thanks.

zhangt8@cn4285:/data/zhangt8/Ref/Neoantigen/neofox/test$ neofox --input-file test_data.tsv --patient-data test_patients.tsv --output-folder ./output --output-prefix test [E 230119 19:49:40 command_line:192] Error tokenizing data. C error: Expected 1 fields in line 28, saw 367 Traceback (most recent call last): File "/data/zhangt8/conda/envs/neofox/lib/python3.7/site-packages/neofox/command_line.py", line 171, in neofox_cli reference_folder.get_mhc_database()) File "/data/zhangt8/conda/envs/neofox/lib/python3.7/site-packages/neofox/references/references.py", line 310, in get_mhc_database self.__mhc_database = HlaDatabase(self.mhc_database_filename) File "/data/zhangt8/conda/envs/neofox/lib/python3.7/site-packages/neofox/references/references.py", line 170, in init self.alleles = self._load_alleles(database_filename) File "/data/zhangt8/conda/envs/neofox/lib/python3.7/site-packages/neofox/references/references.py", line 196, in _load_alleles hla_database = pd.read_csv(hla_database_filename, comment="#") File "/data/zhangt8/conda/envs/neofox/lib/python3.7/site-packages/pandas/util/_decorators.py", line 311, in wrapper return func(*args, **kwargs) File "/data/zhangt8/conda/envs/neofox/lib/python3.7/site-packages/pandas/io/parsers/readers.py", line 586, in read_csv return _read(filepath_or_buffer, kwds) File "/data/zhangt8/conda/envs/neofox/lib/python3.7/site-packages/pandas/io/parsers/readers.py", line 488, in _read return parser.read(nrows) File "/data/zhangt8/conda/envs/neofox/lib/python3.7/site-packages/pandas/io/parsers/readers.py", line 1047, in read index, columns, col_dict = self._engine.read(nrows) File "/data/zhangt8/conda/envs/neofox/lib/python3.7/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 224, in read chunks = self._reader.read_low_memory(nrows) File "pandas/_libs/parsers.pyx", line 801, in pandas._libs.parsers.TextReader.read_low_memory File "pandas/_libs/parsers.pyx", line 857, in pandas._libs.parsers.TextReader._read_rows File "pandas/_libs/parsers.pyx", line 843, in pandas._libs.parsers.TextReader._tokenize_rows File "pandas/_libs/parsers.pyx", line 1925, in pandas._libs.parsers.raise_parser_error pandas.errors.ParserError: Error tokenizing data. C error: Expected 1 fields in line 28, saw 367

Traceback (most recent call last): File "/data/zhangt8/conda/envs/neofox/bin/neofox", line 10, in sys.exit(neofox_cli()) File "/data/zhangt8/conda/envs/neofox/lib/python3.7/site-packages/neofox/command_line.py", line 193, in neofox_cli raise e File "/data/zhangt8/conda/envs/neofox/lib/python3.7/site-packages/neofox/command_line.py", line 171, in neofox_cli reference_folder.get_mhc_database()) File "/data/zhangt8/conda/envs/neofox/lib/python3.7/site-packages/neofox/references/references.py", line 310, in get_mhc_database self.__mhc_database = HlaDatabase(self.mhc_database_filename) File "/data/zhangt8/conda/envs/neofox/lib/python3.7/site-packages/neofox/references/references.py", line 170, in init self.alleles = self._load_alleles(database_filename) File "/data/zhangt8/conda/envs/neofox/lib/python3.7/site-packages/neofox/references/references.py", line 196, in _load_alleles hla_database = pd.read_csv(hla_database_filename, comment="#") File "/data/zhangt8/conda/envs/neofox/lib/python3.7/site-packages/pandas/util/_decorators.py", line 311, in wrapper return func(*args, **kwargs) File "/data/zhangt8/conda/envs/neofox/lib/python3.7/site-packages/pandas/io/parsers/readers.py", line 586, in read_csv return _read(filepath_or_buffer, kwds) File "/data/zhangt8/conda/envs/neofox/lib/python3.7/site-packages/pandas/io/parsers/readers.py", line 488, in _read return parser.read(nrows) File "/data/zhangt8/conda/envs/neofox/lib/python3.7/site-packages/pandas/io/parsers/readers.py", line 1047, in read index, columns, col_dict = self._engine.read(nrows) File "/data/zhangt8/conda/envs/neofox/lib/python3.7/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 224, in read chunks = self._reader.read_low_memory(nrows) File "pandas/_libs/parsers.pyx", line 801, in pandas._libs.parsers.TextReader.read_low_memory File "pandas/_libs/parsers.pyx", line 857, in pandas._libs.parsers.TextReader._read_rows File "pandas/_libs/parsers.pyx", line 843, in pandas._libs.parsers.TextReader._tokenize_rows File "pandas/_libs/parsers.pyx", line 1925, in pandas._libs.parsers.raise_parser_error pandas.errors.ParserError: Error tokenizing data. C error: Expected 1 fields in line 28, saw 367

There is an issue with python 3.8, try with python 3.7. I actually have a fix for this, will be released soon.

xtmgah commented 1 year ago

@priesgo I did use the Python 3.7.12; Can you let me know how to fix this issue before your release? thanks.

priesgo commented 1 year ago

Wait I was too fast, this is something else. Your input file seems to have a problem. Have you modified it in any way? Can you confirm your line endings are not Windows ones?

xtmgah commented 1 year ago

I used the file from the GitHub folder: /neofox/docs/testfiles/; Or can you let me know what the best the example files to test in linux?

xtmgah commented 1 year ago

@priesgo I don't think it is windows ones. I did not see the '^M' at the end of lines and it show file in unix format when i check with vim. BTW, i also test the python=3.7.9 and it has the same issue here.

priesgo commented 1 year ago

@xtmgah have you tried setting up the order of the conda channels as described below?

channels:
  - conda-forge
  - bioconda
  - defaults
xtmgah commented 1 year ago

No. I did not set up like this. I just follow what you have in the documents.

xtmgah commented 1 year ago

@priesgo Just let you know that i reinstall the neofox as your suggested by setting up the conda channels. But the issue is still there. I don't think that is related to that. Any other suggestion?

xtmgah commented 1 year ago

@priesgo Any updates for your codes? thanks.

priesgo commented 1 year ago

@xtmgah apologies for the long wait, we have been investigating several things. We just made a beta release that deals with several things. Among other things, this reimplements the hex scoring in Python and hopefully this fixes your docker. Would you try this now, please?

https://github.com/TRON-Bioinformatics/neofox/releases/tag/v1.1.0b1

xtmgah commented 1 year ago

@priesgo Thanks for your help . I just reinstall your new version, the hex issue have been fixed, but looks like there are some other issues, see the detail log bellow:

more output/test.log [E 230217 11:21:50 command_line:192] Error tokenizing data. C error: Expected 1 fields in line 28, saw 367 Traceback (most recent call last): File "/data/zhangt8/conda/envs/neofox/lib/python3.7/site-packages/neofox/command_line.py", line 171, in neofox_cli reference_folder.get_mhc_database()) File "/data/zhangt8/conda/envs/neofox/lib/python3.7/site-packages/neofox/references/references.py", line 310, in get_mhc_database self.__mhc_database = HlaDatabase(self.mhc_database_filename) File "/data/zhangt8/conda/envs/neofox/lib/python3.7/site-packages/neofox/references/references.py", line 170, in init self.alleles = self._load_alleles(database_filename) File "/data/zhangt8/conda/envs/neofox/lib/python3.7/site-packages/neofox/references/references.py", line 196, in _load_alleles hla_database = pd.read_csv(hla_database_filename, comment="#") File "/data/zhangt8/conda/envs/neofox/lib/python3.7/site-packages/pandas/util/_decorators.py", line 311, in wrapper return func(*args, **kwargs) File "/data/zhangt8/conda/envs/neofox/lib/python3.7/site-packages/pandas/io/parsers/readers.py", line 586, in read_csv return _read(filepath_or_buffer, kwds) File "/data/zhangt8/conda/envs/neofox/lib/python3.7/site-packages/pandas/io/parsers/readers.py", line 488, in _read return parser.read(nrows) File "/data/zhangt8/conda/envs/neofox/lib/python3.7/site-packages/pandas/io/parsers/readers.py", line 1047, in read index, columns, col_dict = self._engine.read(nrows) File "/data/zhangt8/conda/envs/neofox/lib/python3.7/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 224, in read chunks = self._reader.read_low_memory(nrows) File "pandas/_libs/parsers.pyx", line 801, in pandas._libs.parsers.TextReader.read_low_memory File "pandas/_libs/parsers.pyx", line 857, in pandas._libs.parsers.TextReader._read_rows File "pandas/_libs/parsers.pyx", line 843, in pandas._libs.parsers.TextReader._tokenize_rows File "pandas/_libs/parsers.pyx", line 1925, in pandas._libs.parsers.raise_parser_error pandas.errors.ParserError: Error tokenizing data. C error: Expected 1 fields in line 28, saw 367

[E 230217 11:24:23 command_line:192] Error tokenizing data. C error: Expected 1 fields in line 28, saw 367 Traceback (most recent call last): File "/data/zhangt8/conda/envs/neofox/lib/python3.7/site-packages/neofox/command_line.py", line 171, in neofox_cli reference_folder.get_mhc_database()) File "/data/zhangt8/conda/envs/neofox/lib/python3.7/site-packages/neofox/references/references.py", line 310, in get_mhc_database self.__mhc_database = HlaDatabase(self.mhc_database_filename) File "/data/zhangt8/conda/envs/neofox/lib/python3.7/site-packages/neofox/references/references.py", line 170, in init self.alleles = self._load_alleles(database_filename) File "/data/zhangt8/conda/envs/neofox/lib/python3.7/site-packages/neofox/references/references.py", line 196, in _load_alleles hla_database = pd.read_csv(hla_database_filename, comment="#") File "/data/zhangt8/conda/envs/neofox/lib/python3.7/site-packages/pandas/util/_decorators.py", line 311, in wrapper return func(*args, **kwargs) File "/data/zhangt8/conda/envs/neofox/lib/python3.7/site-packages/pandas/io/parsers/readers.py", line 586, in read_csv return _read(filepath_or_buffer, kwds) File "/data/zhangt8/conda/envs/neofox/lib/python3.7/site-packages/pandas/io/parsers/readers.py", line 488, in _read return parser.read(nrows) File "/data/zhangt8/conda/envs/neofox/lib/python3.7/site-packages/pandas/io/parsers/readers.py", line 1047, in read index, columns, col_dict = self._engine.read(nrows) File "/data/zhangt8/conda/envs/neofox/lib/python3.7/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 224, in read chunks = self._reader.read_low_memory(nrows) File "pandas/_libs/parsers.pyx", line 801, in pandas._libs.parsers.TextReader.read_low_memory File "pandas/_libs/parsers.pyx", line 857, in pandas._libs.parsers.TextReader._read_rows File "pandas/_libs/parsers.pyx", line 843, in pandas._libs.parsers.TextReader._tokenize_rows File "pandas/_libs/parsers.pyx", line 1925, in pandas._libs.parsers.raise_parser_error pandas.errors.ParserError: Error tokenizing data. C error: Expected 1 fields in line 28, saw 367

Any suggestion? Thansk.