{"action":"closed","issue":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/867","labels_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/867/labels{/name}","comments_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/867/comments","events_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/867/events","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/867","id":81851049,"number":867,"title":"RNAseq pipeline with tophat2 on test data fails in alignment step ","user":{"login":"kajetanb","id":11680358,"avatar_url":"https://avatars.githubusercontent.com/u/11680358?v=3","gravatar_id":"","url":"https://api.github.com/users/kajetanb","html_url":"https://github.com/kajetanb","followers_url":"https://api.github.com/users/kajetanb/followers","following_url":"https://api.github.com/users/kajetanb/following{/other_user}","gists_url":"https://api.github.com/users/kajetanb/gists{/gist_id}","starred_url":"https://api.github.com/users/kajetanb/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/kajetanb/subscriptions","organizations_url":"https://api.github.com/users/kajetanb/orgs","repos_url":"https://api.github.com/users/kajetanb/repos","events_url":"https://api.github.com/users/kajetanb/events{/privacy}","received_events_url":"https://api.github.com/users/kajetanb/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2015-05-28T09:45:13Z","updated_at":"2015-05-28T15:24:18Z","closed_at":"2015-05-28T15:24:18Z","body":"Hi, \r\nI downloaded test data for the RNASeq-pipeline as described in the\r\nbcbio docs\r\n(<https://bcbio-nextgen.readthedocs.org/en/latest/contents/testing.html#rnaseq-example>)\r\nand then ran\r\n\r\n    bcbio_nextgen.py -w template rnaseq-seqc.yaml input/seqc.csv input\r\n    cd seqc/work\r\n    nohup bcbio_nextgen.py ../config/seqc.yaml > bcbio_nextgen.log 2> bcbio_nextgen.err &\r\n\r\ntrimming workded, but the alignment steps failed from the very beginning on:\r\n\r\n    [2015-05-28T04:49Z] Resource requests: picard, tophat2; memory: 3.50, 24.00; cores: 1, 6\r\n    [2015-05-28T04:49Z] Configuring 1 jobs to run, using 1 cores each with 24.00g of memory reserved for each job\r\n    [2015-05-28T04:49Z] Timing: alignment\r\n    [2015-05-28T04:49Z] multiprocessing: disambiguate_split\r\n    [2015-05-28T04:49Z] multiprocessing: process_alignment\r\n    [2015-05-28T04:49Z] Aligning lane 1_2015-05-27_seqc with tophat2 aligner\r\n    Traceback (most recent call last):\r\n      File \"/extra/kbentele/bcbio/bin/bcbio_nextgen.py\", line 220, in <module>\r\n        main(**kwargs)\r\n      File \"/extra/kbentele/bcbio/bin/bcbio_nextgen.py\", line 43, in main\r\n        run_main(**kwargs)\r\n      File \"/extra/kbentele/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py\", line 36, in run_main\r\n        fc_dir, run_info_yaml)\r\n      File \"/extra/kbentele/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py\", line 79, in _run_toplevel\r\n        for xs in pipeline.run(config, run_info_yaml, parallel, dirs, samples):\r\n      File \"/extra/kbentele/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py\", line 291, in run\r\n        samples = run_parallel(\"process_alignment\", samples)\r\n      File \"/extra/kbentele/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 \"/extra/kbentele/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py\", line 84, in run_multicore\r\n        for data in joblib.Parallel(parallel[\"num_jobs\"])(joblib.delayed(fn)(x) for x in items):\r\n      File \"/extra/kbentele/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 657, in __call__\r\n        self.dispatch(function, args, kwargs)\r\n      File \"/extra/kbentele/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 404, in dispatch\r\n        job = ImmediateApply(func, args, kwargs)\r\n      File \"/extra/kbentele/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 142, in __init__\r\n        self.results = func(*args, **kwargs)\r\n      File \"/extra/kbentele/bcbio/anaconda/lib/python2.7/site-packages/bcbio/utils.py\", line 49, in wrapper\r\n        return apply(f, *args, **kwargs)\r\n      File \"/extra/kbentele/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multitasks.py\", line 31, in process_alignment\r\n        return sample.process_alignment(*args)\r\n      File \"/extra/kbentele/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/sample.py\", line 100, in process_alignment\r\n        data = align_to_sort_bam(fastq1, fastq2, aligner, data)\r\n      File \"/extra/kbentele/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.py\", line 64, in align_to_sort_bam\r\n        names, align_dir, data)\r\n      File \"/extra/kbentele/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.py\", line 99, in _align_from_fastq\r\n        out = align_fn(fastq1, fastq2, align_ref, names, align_dir, data)\r\n      File \"/extra/kbentele/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/tophat.py\", line 260, in align\r\n        align_dir, data, names)\r\n      File \"/extra/kbentele/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/tophat.py\", line 98, in tophat_align\r\n        options = _set_quality_flag(options, config)\r\n      File \"/extra/kbentele/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/tophat.py\", line 35, in _set_quality_flag\r\n        if qual_format.lower() == \"illumina\":\r\n    AttributeError: 'NoneType' object has no attribute 'lower'\r\n\r\nThanks for any help!"}}