Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Not working for the test data #12

Open
xtmgah opened this issue Jan 9, 2023 · 21 comments
Open

Not working for the test data #12

xtmgah opened this issue Jan 9, 2023 · 21 comments

Comments

@xtmgah
Copy link

xtmgah commented Jan 9, 2023

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-DRB1*15:01', '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 apply_hex
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
Copy link
Author

xtmgah commented Jan 12, 2023

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

@priesgo
Copy link
Member

priesgo commented Jan 16, 2023

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
Copy link
Author

xtmgah commented Jan 17, 2023

@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
Copy link
Member

priesgo commented Jan 19, 2023

@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
Copy link
Member

priesgo commented Jan 19, 2023

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

@xtmgah
Copy link
Author

xtmgah commented Jan 19, 2023 via email

@priesgo
Copy link
Member

priesgo commented Jan 19, 2023

@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
Copy link
Author

xtmgah commented Jan 19, 2023

@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
Copy link
Author

xtmgah commented Jan 20, 2023

@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
Copy link
Member

priesgo commented Jan 20, 2023

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

@priesgo
Copy link
Member

priesgo commented Jan 20, 2023

@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
Copy link
Author

xtmgah commented Jan 20, 2023

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

@priesgo
Copy link
Member

priesgo commented Jan 20, 2023

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
Copy link
Author

xtmgah commented Jan 20, 2023

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
Copy link
Author

xtmgah commented Jan 20, 2023 •
edited
Loading

@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
Copy link
Member

priesgo commented Jan 24, 2023

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

channels:
  - conda-forge
  - bioconda
  - defaults

@xtmgah
Copy link
Author

xtmgah commented Jan 24, 2023

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

@xtmgah
Copy link
Author

xtmgah commented Jan 24, 2023

@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
Copy link
Author

xtmgah commented Jan 30, 2023

@priesgo Any updates for your codes? thanks.

@priesgo
Copy link
Member

priesgo commented Feb 8, 2023

@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
Copy link
Author

xtmgah commented Feb 17, 2023

@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.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@priesgo @xtmgah