{"action":"created","issue":{"url":"https://api.github.com/repos/griffithlab/pVAC-Seq/issues/231","repository_url":"https://api.github.com/repos/griffithlab/pVAC-Seq","labels_url":"https://api.github.com/repos/griffithlab/pVAC-Seq/issues/231/labels{/name}","comments_url":"https://api.github.com/repos/griffithlab/pVAC-Seq/issues/231/comments","events_url":"https://api.github.com/repos/griffithlab/pVAC-Seq/issues/231/events","html_url":"https://github.com/griffithlab/pVAC-Seq/issues/231","id":189721253,"number":231,"title":"Using local copy of IEDB.","user":{"login":"Akado2009","id":10945651,"avatar_url":"https://avatars.githubusercontent.com/u/10945651?v=3","gravatar_id":"","url":"https://api.github.com/users/Akado2009","html_url":"https://github.com/Akado2009","followers_url":"https://api.github.com/users/Akado2009/followers","following_url":"https://api.github.com/users/Akado2009/following{/other_user}","gists_url":"https://api.github.com/users/Akado2009/gists{/gist_id}","starred_url":"https://api.github.com/users/Akado2009/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Akado2009/subscriptions","organizations_url":"https://api.github.com/users/Akado2009/orgs","repos_url":"https://api.github.com/users/Akado2009/repos","events_url":"https://api.github.com/users/Akado2009/events{/privacy}","received_events_url":"https://api.github.com/users/Akado2009/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2016-11-16T14:32:08Z","updated_at":"2016-11-16T14:53:42Z","closed_at":null,"body":"Hello! As it was suggested earlier in 4.0.2 release review, I can now use local copy of IEDB. I downloaded it from [http://tools.iedb.org/mhci/download/](IEDB). And now, when I'm trying to execute pvacseq with --iedb-install-directory parameter, I get errors.\r\n\r\n` pvacseq run -e 8 --iedb-install-directory /home/akado2009/Desktop/IEDB input.vcf Test H-2-Db,H-2-Dd,H-2-Kb,H-2-Kd,H-2-Kk,H-2-Ld NetMHC .` where ` /home/akado2009/Desktop/IEDB` is a directory containing mhc-i folder. I get these errors:\r\n` Executing MHC Class I predictions\r\nConverting VCF to TSV\r\nTSV file already exists. Skipping.\r\nSplitting TSV into smaller chunks\r\nSplitting TSV into smaller chunks - Entries 1-64\r\nSplit TSV file for Entries 1-64 already exists. Skipping.\r\nCompleted\r\nGenerating Variant Peptide FASTA and Key Files\r\nGenerating Variant Peptide FASTA and Key Files - Entries 1-128\r\nCompleted\r\nProcessing entries for Allele H-2-Db and Epitope Length 8 - Entries 1-128\r\nRunning IEDB on Allele H-2-Db and Epitope Length 8 with Method NetMHC - Entries 1-128\r\nTraceback (most recent call last):\r\n  File \"/home/akado2009/Desktop/IEDB/mhc_i/src/predict_binding.py\", line 334, in <module>\r\n    Prediction().main()\r\n  File \"/home/akado2009/Desktop/IEDB/mhc_i/src/predict_binding.py\", line 326, in main\r\n    elif (len(args)  == 4):                            self.commandline_input(args)  # args=[method, mhc, length, fname]\r\n  File \"/home/akado2009/Desktop/IEDB/mhc_i/src/predict_binding.py\", line 67, in commandline_input\r\n    mhc_scores = mhc_predictor.predict(input.input_protein.sequences)\r\n  File \"/home/akado2009/Desktop/IEDB/mhc_i/src/seqpredictor.py\", line 1010, in predict\r\n    scores.append(predictor.predict_sequence(sequence,pred))\r\n  File \"/home/akado2009/Desktop/IEDB/mhc_i/src/seqpredictor.py\", line 251, in predict_sequence\r\n    scores = netmhc_prediction(allele_name, str(self.length), sequence)\r\n  File \"/home/akado2009/Desktop/IEDB/mhc_i/method/netmhc_4_0_executable/__init__.py\", line 33, in predict\r\n    process = Popen(cmd, stdout=PIPE)\r\n  File \"/usr/lib/python2.7/subprocess.py\", line 711, in __init__\r\n    errread, errwrite)\r\n  File \"/usr/lib/python2.7/subprocess.py\", line 1343, in _execute_child\r\n    raise child_exception\r\nOSError: [Errno 2] No such file or directory\r\nCompleted\r\nParsing IEDB Output for Allele H-2-Db and Epitope Length 8 - Entries 1-128\r\nCompleted\r\nProcessing entries for Allele H-2-Dd and Epitope Length 8 - Entries 1-128\r\nRunning IEDB on Allele H-2-Dd and Epitope Length 8 with Method NetMHC - Entries 1-128\r\nTraceback (most recent call last):\r\n  File \"/home/akado2009/Desktop/IEDB/mhc_i/src/predict_binding.py\", line 334, in <module>\r\n    Prediction().main()\r\n  File \"/home/akado2009/Desktop/IEDB/mhc_i/src/predict_binding.py\", line 326, in main\r\n    elif (len(args)  == 4):                            self.commandline_input(args)  # args=[method, mhc, length, fname]\r\n  File \"/home/akado2009/Desktop/IEDB/mhc_i/src/predict_binding.py\", line 67, in commandline_input\r\n    mhc_scores = mhc_predictor.predict(input.input_protein.sequences)\r\n  File \"/home/akado2009/Desktop/IEDB/mhc_i/src/seqpredictor.py\", line 1010, in predict\r\n    scores.append(predictor.predict_sequence(sequence,pred))\r\n  File \"/home/akado2009/Desktop/IEDB/mhc_i/src/seqpredictor.py\", line 251, in predict_sequence\r\n    scores = netmhc_prediction(allele_name, str(self.length), sequence)\r\n  File \"/home/akado2009/Desktop/IEDB/mhc_i/method/netmhc_4_0_executable/__init__.py\", line 33, in predict\r\n    process = Popen(cmd, stdout=PIPE)\r\n  File \"/usr/lib/python2.7/subprocess.py\", line 711, in __init__\r\n    errread, errwrite)\r\n  File \"/usr/lib/python2.7/subprocess.py\", line 1343, in _execute_child\r\n    raise child_exception\r\nOSError: [Errno 2] No such file or directory\r\nCompleted\r\nParsing IEDB Output for Allele H-2-Dd and Epitope Length 8 - Entries 1-128\r\nCompleted\r\nProcessing entries for Allele H-2-Kb and Epitope Length 8 - Entries 1-128\r\nRunning IEDB on Allele H-2-Kb and Epitope Length 8 with Method NetMHC - Entries 1-128\r\nTraceback (most recent call last):\r\n  File \"/home/akado2009/Desktop/IEDB/mhc_i/src/predict_binding.py\", line 334, in <module>\r\n    Prediction().main()\r\n  File \"/home/akado2009/Desktop/IEDB/mhc_i/src/predict_binding.py\", line 326, in main\r\n    elif (len(args)  == 4):                            self.commandline_input(args)  # args=[method, mhc, length, fname]\r\n  File \"/home/akado2009/Desktop/IEDB/mhc_i/src/predict_binding.py\", line 67, in commandline_input\r\n    mhc_scores = mhc_predictor.predict(input.input_protein.sequences)\r\n  File \"/home/akado2009/Desktop/IEDB/mhc_i/src/seqpredictor.py\", line 1010, in predict\r\n    scores.append(predictor.predict_sequence(sequence,pred))\r\n  File \"/home/akado2009/Desktop/IEDB/mhc_i/src/seqpredictor.py\", line 251, in predict_sequence\r\n    scores = netmhc_prediction(allele_name, str(self.length), sequence)\r\n  File \"/home/akado2009/Desktop/IEDB/mhc_i/method/netmhc_4_0_executable/__init__.py\", line 33, in predict\r\n    process = Popen(cmd, stdout=PIPE)\r\n  File \"/usr/lib/python2.7/subprocess.py\", line 711, in __init__\r\n    errread, errwrite)\r\n  File \"/usr/lib/python2.7/subprocess.py\", line 1343, in _execute_child\r\n    raise child_exception\r\nOSError: [Errno 2] No such file or directory\r\nCompleted\r\nParsing IEDB Output for Allele H-2-Kb and Epitope Length 8 - Entries 1-128\r\nCompleted\r\nProcessing entries for Allele H-2-Kd and Epitope Length 8 - Entries 1-128\r\nRunning IEDB on Allele H-2-Kd and Epitope Length 8 with Method NetMHC - Entries 1-128\r\nTraceback (most recent call last):\r\n  File \"/home/akado2009/Desktop/IEDB/mhc_i/src/predict_binding.py\", line 334, in <module>\r\n    Prediction().main()\r\n  File \"/home/akado2009/Desktop/IEDB/mhc_i/src/predict_binding.py\", line 326, in main\r\n    elif (len(args)  == 4):                            self.commandline_input(args)  # args=[method, mhc, length, fname]\r\n  File \"/home/akado2009/Desktop/IEDB/mhc_i/src/predict_binding.py\", line 67, in commandline_input\r\n    mhc_scores = mhc_predictor.predict(input.input_protein.sequences)\r\n  File \"/home/akado2009/Desktop/IEDB/mhc_i/src/seqpredictor.py\", line 1010, in predict\r\n    scores.append(predictor.predict_sequence(sequence,pred))\r\n  File \"/home/akado2009/Desktop/IEDB/mhc_i/src/seqpredictor.py\", line 251, in predict_sequence\r\n    scores = netmhc_prediction(allele_name, str(self.length), sequence)\r\n  File \"/home/akado2009/Desktop/IEDB/mhc_i/method/netmhc_4_0_executable/__init__.py\", line 33, in predict\r\n    process = Popen(cmd, stdout=PIPE)\r\n  File \"/usr/lib/python2.7/subprocess.py\", line 711, in __init__\r\n    errread, errwrite)\r\n  File \"/usr/lib/python2.7/subprocess.py\", line 1343, in _execute_child\r\n    raise child_exception\r\nOSError: [Errno 2] No such file or directory\r\nCompleted\r\nParsing IEDB Output for Allele H-2-Kd and Epitope Length 8 - Entries 1-128\r\nCompleted\r\nProcessing entries for Allele H-2-Kk and Epitope Length 8 - Entries 1-128\r\nRunning IEDB on Allele H-2-Kk and Epitope Length 8 with Method NetMHC - Entries 1-128\r\nTraceback (most recent call last):\r\n  File \"/home/akado2009/Desktop/IEDB/mhc_i/src/predict_binding.py\", line 334, in <module>\r\n    Prediction().main()\r\n  File \"/home/akado2009/Desktop/IEDB/mhc_i/src/predict_binding.py\", line 326, in main\r\n    elif (len(args)  == 4):                            self.commandline_input(args)  # args=[method, mhc, length, fname]\r\n  File \"/home/akado2009/Desktop/IEDB/mhc_i/src/predict_binding.py\", line 67, in commandline_input\r\n    mhc_scores = mhc_predictor.predict(input.input_protein.sequences)\r\n  File \"/home/akado2009/Desktop/IEDB/mhc_i/src/seqpredictor.py\", line 1010, in predict\r\n    scores.append(predictor.predict_sequence(sequence,pred))\r\n  File \"/home/akado2009/Desktop/IEDB/mhc_i/src/seqpredictor.py\", line 251, in predict_sequence\r\n    scores = netmhc_prediction(allele_name, str(self.length), sequence)\r\n  File \"/home/akado2009/Desktop/IEDB/mhc_i/method/netmhc_4_0_executable/__init__.py\", line 33, in predict\r\n    process = Popen(cmd, stdout=PIPE)\r\n  File \"/usr/lib/python2.7/subprocess.py\", line 711, in __init__\r\n    errread, errwrite)\r\n  File \"/usr/lib/python2.7/subprocess.py\", line 1343, in _execute_child\r\n    raise child_exception\r\nOSError: [Errno 2] No such file or directory\r\nCompleted\r\nParsing IEDB Output for Allele H-2-Kk and Epitope Length 8 - Entries 1-128\r\nCompleted\r\nProcessing entries for Allele H-2-Ld and Epitope Length 8 - Entries 1-128\r\nRunning IEDB on Allele H-2-Ld and Epitope Length 8 with Method NetMHC - Entries 1-128\r\nTraceback (most recent call last):\r\n  File \"/home/akado2009/Desktop/IEDB/mhc_i/src/predict_binding.py\", line 334, in <module>\r\n    Prediction().main()\r\n  File \"/home/akado2009/Desktop/IEDB/mhc_i/src/predict_binding.py\", line 326, in main\r\n    elif (len(args)  == 4):                            self.commandline_input(args)  # args=[method, mhc, length, fname]\r\n  File \"/home/akado2009/Desktop/IEDB/mhc_i/src/predict_binding.py\", line 67, in commandline_input\r\n    mhc_scores = mhc_predictor.predict(input.input_protein.sequences)\r\n  File \"/home/akado2009/Desktop/IEDB/mhc_i/src/seqpredictor.py\", line 1010, in predict\r\n    scores.append(predictor.predict_sequence(sequence,pred))\r\n  File \"/home/akado2009/Desktop/IEDB/mhc_i/src/seqpredictor.py\", line 251, in predict_sequence\r\n    scores = netmhc_prediction(allele_name, str(self.length), sequence)\r\n  File \"/home/akado2009/Desktop/IEDB/mhc_i/method/netmhc_4_0_executable/__init__.py\", line 33, in predict\r\n    process = Popen(cmd, stdout=PIPE)\r\n  File \"/usr/lib/python2.7/subprocess.py\", line 711, in __init__\r\n    errread, errwrite)\r\n  File \"/usr/lib/python2.7/subprocess.py\", line 1343, in _execute_child\r\n    raise child_exception\r\nOSError: [Errno 2] No such file or directory\r\nCompleted\r\nParsing IEDB Output for Allele H-2-Ld and Epitope Length 8 - Entries 1-128\r\nCompleted\r\nCombining Parsed IEDB Output Files\r\nCompleted\r\nRunning Binding Filters\r\nCompleted\r\n\r\nDone: pvacseq has completed. File /home/akado2009/Desktop/pvacIedb/pvacseq-bss/tests/input_data/MHC_Class_I/Test.final.tsv contains list of filtered putative neoantigensWe recommend appending coverage information and running `pvacseq coverage_filter` to filter based on sequencing coverage information\r\n`\r\nApparently, output files are empty. \r\nSo, if you know, what can I do? Or there is a problem with IEDB itself?\r\n\r\nKing regards, akado2009.\r\n[input.vcf.gz](https://github.com/griffithlab/pVAC-Seq/files/594862/input.vcf.gz)\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/griffithlab/pVAC-Seq/issues/comments/260966310","html_url":"https://github.com/griffithlab/pVAC-Seq/issues/231#issuecomment-260966310","issue_url":"https://api.github.com/repos/griffithlab/pVAC-Seq/issues/231","id":260966310,"user":{"login":"Akado2009","id":10945651,"avatar_url":"https://avatars.githubusercontent.com/u/10945651?v=3","gravatar_id":"","url":"https://api.github.com/users/Akado2009","html_url":"https://github.com/Akado2009","followers_url":"https://api.github.com/users/Akado2009/followers","following_url":"https://api.github.com/users/Akado2009/following{/other_user}","gists_url":"https://api.github.com/users/Akado2009/gists{/gist_id}","starred_url":"https://api.github.com/users/Akado2009/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Akado2009/subscriptions","organizations_url":"https://api.github.com/users/Akado2009/orgs","repos_url":"https://api.github.com/users/Akado2009/repos","events_url":"https://api.github.com/users/Akado2009/events{/privacy}","received_events_url":"https://api.github.com/users/Akado2009/received_events","type":"User","site_admin":false},"created_at":"2016-11-16T14:53:42Z","updated_at":"2016-11-16T14:53:42Z","body":"Yup, I have `/usr/lib/python2.7`. I have tow separate versions of python (2.7 & 3.5) with separate PYTHONPATH. "}}
{"actor":{"display_login":"Akado2009"}}