{"action":"created","issue":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/435","labels_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/435/labels{/name}","comments_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/435/comments","events_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/435/events","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/435","id":34706337,"number":435,"title":"problem with run_tests speed=2","user":{"login":"bosmont","id":7282525,"avatar_url":"https://avatars.githubusercontent.com/u/7282525?v=3","gravatar_id":"","url":"https://api.github.com/users/bosmont","html_url":"https://github.com/bosmont","followers_url":"https://api.github.com/users/bosmont/followers","following_url":"https://api.github.com/users/bosmont/following{/other_user}","gists_url":"https://api.github.com/users/bosmont/gists{/gist_id}","starred_url":"https://api.github.com/users/bosmont/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bosmont/subscriptions","organizations_url":"https://api.github.com/users/bosmont/orgs","repos_url":"https://api.github.com/users/bosmont/repos","events_url":"https://api.github.com/users/bosmont/events{/privacy}","received_events_url":"https://api.github.com/users/bosmont/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":13,"created_at":"2014-05-31T13:27:55Z","updated_at":"2015-07-13T06:40:22Z","closed_at":"2014-06-01T02:55:41Z","body":"I installed gemini by doing:\r\nbcbio_nextgen.py upgrade --tools --toolplus data\r\n\r\n\r\n\r\nbut when running ./run_test2 speed=2, I got the following error:\r\n\r\n[2014-05-31 09:13] Gemini cannot open this annotation file: /usr/local/share/bcbio-nextgen/gemini_data/hg19.gwas.bed.gz.\r\n[2014-05-31 09:13] Have you installed the annotation files?  If so, have they been moved or deleted? Exiting...\r\n[2014-05-31 09:13] \r\n[2014-05-31 09:13] For more details:\r\n[2014-05-31 09:13] \thttp://gemini.readthedocs.org/en/latest/content/#installation.html\\#installing-annotation-files\r\n[2014-05-31 09:13] \r\n[2014-05-31 09:13] Uncaught exception occurred\r\n"},"comment":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/comments/120829651","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/435#issuecomment-120829651","issue_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/435","id":120829651,"user":{"login":"YiChingTang","id":10681937,"avatar_url":"https://avatars.githubusercontent.com/u/10681937?v=3","gravatar_id":"","url":"https://api.github.com/users/YiChingTang","html_url":"https://github.com/YiChingTang","followers_url":"https://api.github.com/users/YiChingTang/followers","following_url":"https://api.github.com/users/YiChingTang/following{/other_user}","gists_url":"https://api.github.com/users/YiChingTang/gists{/gist_id}","starred_url":"https://api.github.com/users/YiChingTang/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/YiChingTang/subscriptions","organizations_url":"https://api.github.com/users/YiChingTang/orgs","repos_url":"https://api.github.com/users/YiChingTang/repos","events_url":"https://api.github.com/users/YiChingTang/events{/privacy}","received_events_url":"https://api.github.com/users/YiChingTang/received_events","type":"User","site_admin":false},"created_at":"2015-07-13T06:40:22Z","updated_at":"2015-07-13T06:40:22Z","body":"thanks again!\r\nI try the gemini update --devel and re-download the bcbio-nextgen test suite. There only 1 failure remained. Oh, btw, the \"dir\" ERROR appears again.\r\n\r\nbelow are the msg return from ./run_test.sh seed=2 (only paste the problematic ones)\r\n\r\n[2015-07-13T06:42Z] Resource requests: sambamba, samtools; memory: 2.00, 2.00; cores: 16, 16\r\n[2015-07-13T06:42Z] Configuring 1 jobs to run, using 1 cores each with 2.00g of memory reserved for each job\r\n[2015-07-13T06:42Z] Timing: organize samples\r\n[2015-07-13T06:42Z] multiprocessing: organize_samples\r\n[2015-07-13T06:42Z] Using input YAML configuration: /opt/bcbio/bcbio-nextgen/tests/data/automated/run_info-bamclean.yaml\r\nTraceback (most recent call last):\r\n  File \"/opt/bcbio/tools/bin/bcbio_nextgen.py\", line 226, in <module>\r\n    main(**kwargs)\r\n  File \"/opt/bcbio/tools/bin/bcbio_nextgen.py\", line 43, in main\r\n    run_main(**kwargs)\r\n  File \"/opt/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py\", line 37, in run_main\r\n    fc_dir, run_info_yaml)\r\n  File \"/opt/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py\", line 80, in _run_toplevel\r\n    for xs in pipeline.run(config, run_info_yaml, parallel, dirs, samples):\r\n  File \"/opt/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py\", line 139, in run\r\n    [x[0][\"description\"] for x in samples]]])\r\n  File \"/opt/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 \"/opt/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\"])(joblib.delayed(fn)(x) for x in items):\r\n  File \"/opt/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 657, in __call__\r\n    self.dispatch(function, args, kwargs)\r\n  File \"/opt/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 404, in dispatch\r\n    job = ImmediateApply(func, args, kwargs)\r\n  File \"/opt/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 142, in __init__\r\n    self.results = func(*args, **kwargs)\r\n  File \"/opt/bcbio/anaconda/lib/python2.7/site-packages/bcbio/utils.py\", line 49, in wrapper\r\n    return apply(f, *args, **kwargs)\r\n  File \"/opt/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multitasks.py\", line 199, in organize_samples\r\n    return run_info.organize(*args)\r\n  File \"/opt/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/run_info.py\", line 40, in organize\r\n    run_details = _run_info_from_yaml(dirs, run_info_yaml, config, sample_names)\r\n  File \"/opt/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/run_info.py\", line 537, in _run_info_from_yaml\r\n    upload[\"dir\"] = _file_to_abs(upload[\"dir\"], [dirs.get(\"work\")], makedir=True)\r\nKeyError: 'dir'\r\nERROR\r\nTest paired tumor-normal calling using multiple calling approaches: MuTect, VarScan, FreeBayes. ... [2015-07-13T06:42Z] Resource requests: bwa, sambamba, samtools; memory: 2.00, 2.00; cores: 16, 16, 16\r\n\r\n======================================================================\r\nERROR: Clean problem BAM input files that do not require alignment.\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n  File \"/opt/bcbio/bcbio-nextgen/tests/test_automated_analysis.py\", line 287, in test_6_bamclean\r\n    subprocess.check_call(cl)\r\n  File \"/opt/bcbio/anaconda/lib/python2.7/subprocess.py\", line 540, in check_call\r\n    raise CalledProcessError(retcode, cmd)\r\nCalledProcessError: Command '['bcbio_nextgen.py', '/opt/bcbio/bcbio-nextgen/tests/test_automated_output/bcbio_system.yaml', '/opt/bcbio/bcbio-nextgen/tests/data/automated/../100326_FC6107FAAXX', '/opt/bcbio/bcbio-nextgen/tests/data/automated/run_info-bamclean.yaml']' returned non-zero exit status 1\r\n\r\n----------------------------------------------------------------------\r\nRan 2 tests in 295.586s\r\n\r\nFAILED (errors=1)\r\n\r\n\r\n "}}