{"action":"created","issue":{"url":"https://api.github.com/repos/griffithlab/pVACtools/issues/109","repository_url":"https://api.github.com/repos/griffithlab/pVACtools","labels_url":"https://api.github.com/repos/griffithlab/pVACtools/issues/109/labels{/name}","comments_url":"https://api.github.com/repos/griffithlab/pVACtools/issues/109/comments","events_url":"https://api.github.com/repos/griffithlab/pVACtools/issues/109/events","html_url":"https://github.com/griffithlab/pVACtools/issues/109","id":313178662,"number":109,"title":"pvacseq run MHCII break off with KeyError: 'seq_num'","user":{"login":"huangxiaogua","id":37363950,"avatar_url":"https://avatars1.githubusercontent.com/u/37363950?v=4","gravatar_id":"","url":"https://api.github.com/users/huangxiaogua","html_url":"https://github.com/huangxiaogua","followers_url":"https://api.github.com/users/huangxiaogua/followers","following_url":"https://api.github.com/users/huangxiaogua/following{/other_user}","gists_url":"https://api.github.com/users/huangxiaogua/gists{/gist_id}","starred_url":"https://api.github.com/users/huangxiaogua/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/huangxiaogua/subscriptions","organizations_url":"https://api.github.com/users/huangxiaogua/orgs","repos_url":"https://api.github.com/users/huangxiaogua/repos","events_url":"https://api.github.com/users/huangxiaogua/events{/privacy}","received_events_url":"https://api.github.com/users/huangxiaogua/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2018-04-11T05:29:17Z","updated_at":"2018-04-13T05:09:13Z","closed_at":null,"author_association":"NONE","body":"hello,\r\nWhen I used pvacseq 4.0.9 to run mouse MHCII prediction,the program broke off while Running IEDB.Here is my input command\r\n\r\n`pvacseq run /home/jm/DATA/vepout_files/mC0001-3vepout.vcf mc0001 H2-IAb NNalign /home/jm/DATA/mc0001_mhcII2 --tdna-vaf 20 --net-chop-method cterm --netmhc-stab --top-score-metric=lowest -d full --keep-tmp-files`\r\nfollowing are the output of my terminal\r\n`Executing MHC Class II predictions\r\nConverting VCF to TSV\r\nCompleted\r\nSplitting TSV into smaller chunks\r\nSplitting TSV into smaller chunks - Entries 1-100\r\nSplitting TSV into smaller chunks - Entries 101-200\r\nSplitting TSV into smaller chunks - Entries 201-300\r\nSplitting TSV into smaller chunks - Entries 301-400\r\nSplitting TSV into smaller chunks - Entries 401-500\r\nSplitting TSV into smaller chunks - Entries 501-600\r\nSplitting TSV into smaller chunks - Entries 601-700\r\nSplitting TSV into smaller chunks - Entries 701-800\r\nSplitting TSV into smaller chunks - Entries 801-900\r\nSplitting TSV into smaller chunks - Entries 901-1000\r\nSplitting TSV into smaller chunks - Entries 1001-1100\r\nSplitting TSV into smaller chunks - Entries 1101-1200\r\nSplitting TSV into smaller chunks - Entries 1201-1300\r\nSplitting TSV into smaller chunks - Entries 1301-1400\r\n...........\r\n\r\nCompleted\r\nProcessing entries for Allele H2-IAb - Entries 5601-5800\r\nRunning IEDB on Allele H2-IAb with Method NNalign - Entries 5601-5800\r\nCompleted\r\nParsing IEDB Output for Allele H2-IAb - Entries 5601-5800\r\nTraceback (most recent call last):\r\n  File \"/home/jm/miniconda2/envs/env_name/bin/pvacseq\", line 6, in <module>\r\n    sys.exit(pvacseq.pvacseq.main())\r\n  File \"/home/jm/miniconda2/envs/env_name/lib/python3.6/site-packages/pvacseq/pvacseq.py\", line 84, in main\r\n    args[0].func.main(args[1])\r\n  File \"/home/jm/miniconda2/envs/env_name/lib/python3.6/site-packages/pvacseq/lib/main.py\", line 313, in main\r\n    pipeline.execute()\r\n  File \"/home/jm/miniconda2/envs/env_name/lib/python3.6/site-packages/pvacseq/lib/pipeline.py\", line 300, in execute\r\n    split_parsed_output_files = self.call_iedb_and_parse_outputs(chunks)\r\n  File \"/home/jm/miniconda2/envs/env_name/lib/python3.6/site-packages/pvacseq/lib/pipeline.py\", line 548, in call_iedb_and_parse_outputs\r\n    lib.parse_output.main(params)\r\n  File \"/home/jm/miniconda2/envs/env_name/lib/python3.6/site-packages/pvacseq/lib/parse_output.py\", line 461, in main\r\n    iedb_results = process_input_iedb_file(args.input_iedb_files, tsv_entries, args.key_file, args.top_result_per_mutation, args.top_score_metric)\r\n  File \"/home/jm/miniconda2/envs/env_name/lib/python3.6/site-packages/pvacseq/lib/parse_output.py\", line 370, in process_input_iedb_file\r\n    iedb_results              = parse_iedb_file(input_iedb_files, tsv_entries, key_file)\r\n  File \"/home/jm/miniconda2/envs/env_name/lib/python3.6/site-packages/pvacseq/lib/parse_output.py\", line 258, in parse_iedb_file\r\n    protein_label  = int(line['seq_num'])\r\nKeyError: 'seq_num'`\r\n\r\nCan you find the  wrong point? Thank you."},"comment":{"url":"https://api.github.com/repos/griffithlab/pVACtools/issues/comments/381025354","html_url":"https://github.com/griffithlab/pVACtools/issues/109#issuecomment-381025354","issue_url":"https://api.github.com/repos/griffithlab/pVACtools/issues/109","id":381025354,"user":{"login":"huangxiaogua","id":37363950,"avatar_url":"https://avatars1.githubusercontent.com/u/37363950?v=4","gravatar_id":"","url":"https://api.github.com/users/huangxiaogua","html_url":"https://github.com/huangxiaogua","followers_url":"https://api.github.com/users/huangxiaogua/followers","following_url":"https://api.github.com/users/huangxiaogua/following{/other_user}","gists_url":"https://api.github.com/users/huangxiaogua/gists{/gist_id}","starred_url":"https://api.github.com/users/huangxiaogua/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/huangxiaogua/subscriptions","organizations_url":"https://api.github.com/users/huangxiaogua/orgs","repos_url":"https://api.github.com/users/huangxiaogua/repos","events_url":"https://api.github.com/users/huangxiaogua/events{/privacy}","received_events_url":"https://api.github.com/users/huangxiaogua/received_events","type":"User","site_admin":false},"created_at":"2018-04-13T05:09:13Z","updated_at":"2018-04-13T05:09:13Z","author_association":"NONE","body":"I followed your advice that installed pvactools, it can be run normally. Thank you very much!"}}
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