{"action":"created","issue":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/2140","repository_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen","labels_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/2140/labels{/name}","comments_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/2140/comments","events_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/2140/events","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/2140","id":271584936,"number":2140,"title":"Cufflinks transcript assembly post-STAR","user":{"login":"aadamk","id":20973091,"avatar_url":"https://avatars3.githubusercontent.com/u/20973091?v=4","gravatar_id":"","url":"https://api.github.com/users/aadamk","html_url":"https://github.com/aadamk","followers_url":"https://api.github.com/users/aadamk/followers","following_url":"https://api.github.com/users/aadamk/following{/other_user}","gists_url":"https://api.github.com/users/aadamk/gists{/gist_id}","starred_url":"https://api.github.com/users/aadamk/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/aadamk/subscriptions","organizations_url":"https://api.github.com/users/aadamk/orgs","repos_url":"https://api.github.com/users/aadamk/repos","events_url":"https://api.github.com/users/aadamk/events{/privacy}","received_events_url":"https://api.github.com/users/aadamk/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":7,"created_at":"2017-11-06T19:04:51Z","updated_at":"2017-11-13T19:38:36Z","closed_at":"2017-11-13T19:38:36Z","author_association":"NONE","body":"I get the following error post-star alignment and during cufflinks transcript assembly:  \r\n...\r\n196662 genes finished\r\nTraceback (most recent call last):\r\n  File \"/home/aadam/local/bin/bcbio_nextgen.py\", line 234, in <module>\r\n    main(**kwargs)\r\n  File \"/home/aadam/local/bin/bcbio_nextgen.py\", line 43, in main\r\n    run_main(**kwargs)\r\n  File \"/home/aadam/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py\", line 42, in run_main\r\n    fc_dir, run_info_yaml)\r\n  File \"/home/aadam/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py\", line 86, in _run_toplevel\r\n    for xs in pipeline(config, run_info_yaml, parallel, dirs, samples):\r\n  File \"/home/aadam/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py\", line 243, in rnaseqpipeline\r\n    samples = rnaseq.assemble_transcripts(run_parallel, samples)\r\n  File \"/home/aadam/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/rnaseq.py\", line 285, in assemble_transcripts\r\n    samples = run_parallel(\"cufflinks_merge\", [samples])\r\n  File \"/home/aadam/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py\", line 28, in run_parallel\r\n    return run_multicore(fn, items, config, parallel=parallel)\r\n  File \"/home/aadam/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py\", line 86, in run_multicore\r\n    for data in joblib.Parallel(parallel[\"num_jobs\"], batch_size=1)(joblib.delayed(fn)(x) for x in items):\r\n  File \"/home/aadam/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 804, in __call__\r\n    while self.dispatch_one_batch(iterator):\r\n  File \"/home/aadam/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 662, in dispatch_one_batch\r\n    self._dispatch(tasks)\r\n  File \"/home/aadam/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 570, in _dispatch\r\n    job = ImmediateComputeBatch(batch)\r\n  File \"/home/aadam/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 183, in __init__\r\n    self.results = batch()\r\n  File \"/home/aadam/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 72, in __call__\r\n    return [func(*args, **kwargs) for func, args, kwargs in self.items]\r\n  File \"/home/aadam/bcbio/anaconda/lib/python2.7/site-packages/bcbio/utils.py\", line 50, in wrapper\r\n    return apply(f, *args, **kwargs)\r\n  File \"/home/aadam/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multitasks.py\", line 387, in cufflinks_merge\r\n    return rnaseq.cufflinks_merge(*args)\r\n  File \"/home/aadam/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/rnaseq.py\", line 246, in cufflinks_merge\r\n    samples[0][0])\r\n  File \"/home/aadam/bcbio/anaconda/lib/python2.7/site-packages/bcbio/rnaseq/cufflinks.py\", line 259, in merge\r\n    filtered = annotate_gtf.cleanup_transcripts(classified, gtf_file, ref_file)\r\n  File \"/home/aadam/bcbio/anaconda/lib/python2.7/site-packages/bcbio/rnaseq/annotate_gtf.py\", line 52, in cleanup_transcripts\r\n    assembled_db = gtf.get_gtf_db(assembled_gtf)\r\n  File \"/home/aadam/bcbio/anaconda/lib/python2.7/site-packages/bcbio/rnaseq/gtf.py\", line 43, in get_gtf_db\r\n    return gffutils.FeatureDB(db_file)\r\n  File \"/home/aadam/bcbio/anaconda/lib/python2.7/site-packages/gffutils/interface.py\", line 131, in __init__\r\n    version, dialect = c.fetchone()\r\nTypeError: 'NoneType' object is not iterable\r\n\r\nNot sure why there is an empty object - after completing the processing of ~19000 loci, the following warning appears in the middle of my log file: \r\n[2017-11-06T16:04Z] multiprocessing: cufflinks_merge\r\n/home/aadam/bcbio/anaconda/lib/python2.7/site-packages/gffutils/create.py:85: UserWarning: 'infer_gene_extent' will be deprecated. For now, the following equivalent values were automatically set: 'disable_infer_genes=True', 'disable_infer_transcripts=True'. Please use these instead in the future.\r\n  warnings.warn(\"'infer_gene_extent' will be deprecated. For now, \"  \r\n\r\nAfter this, there are numerous messages stating 'x # of genes finished' after conversion of the .gtf to fasta format, then this error occurs.  Not sure I understand it.\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/comments/344033368","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/2140#issuecomment-344033368","issue_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/2140","id":344033368,"user":{"login":"aadamk","id":20973091,"avatar_url":"https://avatars3.githubusercontent.com/u/20973091?v=4","gravatar_id":"","url":"https://api.github.com/users/aadamk","html_url":"https://github.com/aadamk","followers_url":"https://api.github.com/users/aadamk/followers","following_url":"https://api.github.com/users/aadamk/following{/other_user}","gists_url":"https://api.github.com/users/aadamk/gists{/gist_id}","starred_url":"https://api.github.com/users/aadamk/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/aadamk/subscriptions","organizations_url":"https://api.github.com/users/aadamk/orgs","repos_url":"https://api.github.com/users/aadamk/repos","events_url":"https://api.github.com/users/aadamk/events{/privacy}","received_events_url":"https://api.github.com/users/aadamk/received_events","type":"User","site_admin":false},"created_at":"2017-11-13T19:38:36Z","updated_at":"2017-11-13T19:38:36Z","author_association":"NONE","body":"Got it, thank you."}}
{"actor":{"display_login":"aadamk"}}