{"action":"created","issue":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1197","labels_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1197/labels{/name}","comments_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1197/comments","events_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1197/events","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/1197","id":128056108,"number":1197,"title":"bcbio python complain on non multithreading  samtools","user":{"login":"apastore","id":6528310,"avatar_url":"https://avatars.githubusercontent.com/u/6528310?v=3","gravatar_id":"","url":"https://api.github.com/users/apastore","html_url":"https://github.com/apastore","followers_url":"https://api.github.com/users/apastore/followers","following_url":"https://api.github.com/users/apastore/following{/other_user}","gists_url":"https://api.github.com/users/apastore/gists{/gist_id}","starred_url":"https://api.github.com/users/apastore/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/apastore/subscriptions","organizations_url":"https://api.github.com/users/apastore/orgs","repos_url":"https://api.github.com/users/apastore/repos","events_url":"https://api.github.com/users/apastore/events{/privacy}","received_events_url":"https://api.github.com/users/apastore/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2016-01-22T00:47:41Z","updated_at":"2016-01-22T12:49:06Z","closed_at":null,"body":"Hi Brad, after update bcbio to 0.9.5 I am running in an error every time I try to run bcbio ipython. \r\n\r\nbasically it stop during Testing minimum versions of installed programs. If i run a local multi core run I do not have any problem ...\r\ndo you have a Hint?\r\nThanks!\r\n\r\n2016-01-21 19:42:21.779 [IPClusterStart] {'BcbioTORQUEEngineSetLauncher': {'mem': '8.1', 'tag': '', 'cores': 4, 'resources': 'mem=22G;pmem=22G;pvmem=50G'}, 'IPClusterEngines': {'early_shutdown': 240}, 'Application': {'log_level': 10}, 'ProfileDir': {'location': u'/cbio/cslab/nobackup/pastore/install/bcbio-vm/data/project/Hemepact_PCNSL/Hempact_pair/Hempact_pair/work/log/ipython'}, 'BaseParallelApplication': {'log_to_file': True, 'cluster_id': u'a031e333-245a-4666-8e17-da0f313b61fc'}, 'TORQUELauncher': {'queue': 'batch'}, 'BcbioTORQUEControllerLauncher': {'mem': '', 'tag': '', 'cores': 1, 'resources': 'mem=22G;pmem=22G;pvmem=50G'}, 'IPClusterStart': {'controller_launcher_class': u'cluster_helper.cluster.BcbioTORQUEControllerLauncher', 'engine_launcher_class': u'cluster_helper.cluster.BcbioTORQUEEngineSetLauncher', 'n': 8, 'delay': 10, 'daemonize': True}}\r\n8 Engines running\r\n[2016-01-22T00:43Z] mskcc-ln1.local: Timing: organize samples\r\n[2016-01-22T00:43Z] mskcc-ln1.local: ipython: organize_samples\r\n[2016-01-22T00:43Z] gpu-3-9.local: Using input YAML configuration: /cbio/cslab/nobackup/pastore/install/bcbio-vm/data/project/Hemepact_PCNSL/Hempact_pair/Hempact_pair/config/Hempact_pair.yaml\r\n[2016-01-22T00:43Z] gpu-3-9.local: Checking sample YAML configuration: /cbio/cslab/nobackup/pastore/install/bcbio-vm/data/project/Hemepact_PCNSL/Hempact_pair/Hempact_pair/config/Hempact_pair.yaml\r\n[2016-01-22T00:43Z] gpu-3-9.local: Testing minimum versions of installed programs\r\n[2016-01-22T00:43Z] gpu-3-9.local: Unexpected error\r\nTraceback (most recent call last):\r\n  File \"/cbio/cslab/home/pastore/nobackup/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipythontasks.py\", line 45, in _setup_logging\r\n    yield config\r\n  File \"/cbio/cslab/nobackup/pastore/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipythontasks.py\", line 402, in organize_samples\r\n    return ipython.zip_args(apply(run_info.organize, *args))\r\n  File \"/cbio/cslab/home/pastore/nobackup/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/run_info.py\", line 69, in organize\r\n    out = _add_provenance(out, dirs, config, add_provenance)\r\n  File \"/cbio/cslab/home/pastore/nobackup/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/run_info.py\", line 81, in _add_provenance\r\n    versioncheck.testall(items)\r\n  File \"/cbio/cslab/home/pastore/nobackup/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/versioncheck.py\", line 66, in testall\r\n    \"\\n\".join(msgs))\r\nOSError: Program problems found. You can upgrade dependencies with:\r\nbcbio_nextgen.py upgrade -u skip --tooldir=/usr/local\r\n\r\nInstalled version of samtools sort does not have support for multithreading (-@ option) required to support bwa piped alignment and BAM merging. Please upgrade to the latest version from http://samtools.sourceforge.net/\r\nSending a shutdown signal to the controller and engines.\r\n2016-01-21 19:44:05.438 [IPClusterStop] Using existing profile dir: u'/cbio/cslab/nobackup/pastore/install/bcbio-vm/data/project/Hemepact_PCNSL/Hempact_pair/Hempact_pair/work/log/ipython'\r\n2016-01-21 19:44:05.506 [IPClusterStop] Stopping cluster [pid=38495] with [signal=2]\r\n2016-01-21 19:44:07.247 [IPClusterStop] Using existing profile dir: u'/cbio/cslab/nobackup/pastore/install/bcbio-vm/data/project/Hemepact_PCNSL/Hempact_pair/Hempact_pair/work/log/ipython'\r\n2016-01-21 19:44:07.258 [IPClusterStop] Stopping cluster [pid=38495] with [signal=2]\r\nTraceback (most recent call last):\r\n  File \"/cbio/cslab/home/pastore/nobackup/bcbio/anaconda/bin/bcbio_nextgen.py\", line 4, in <module>\r\n    __import__('pkg_resources').run_script('bcbio-nextgen==0.9.6a0', 'bcbio_nextgen.py')\r\n  File \"/cbio/cslab/home/pastore/nobackup/bcbio/anaconda/lib/python2.7/site-packages/setuptools-19.4-py2.7.egg/pkg_resources/__init__.py\", line 726, in run_script\r\n    \r\n  File \"/cbio/cslab/home/pastore/nobackup/bcbio/anaconda/lib/python2.7/site-packages/setuptools-19.4-py2.7.egg/pkg_resources/__init__.py\", line 1651, in run_script\r\n    \r\n  File \"/cbio/cslab/nobackup/pastore/bcbio/anaconda/lib/python2.7/site-packages/bcbio_nextgen-0.9.6a0-py2.7.egg-info/scripts/bcbio_nextgen.py\", line 226, in <module>\r\n    main(**kwargs)\r\n  File \"/cbio/cslab/nobackup/pastore/bcbio/anaconda/lib/python2.7/site-packages/bcbio_nextgen-0.9.6a0-py2.7.egg-info/scripts/bcbio_nextgen.py\", line 43, in main\r\n    run_main(**kwargs)\r\n  File \"/cbio/cslab/nobackup/pastore/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py\", line 47, in run_main\r\n    fc_dir, run_info_yaml)\r\n  File \"/cbio/cslab/nobackup/pastore/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py\", line 82, in _run_toplevel\r\n    for xs in pipeline(config, run_info_yaml, parallel, dirs, samples):\r\n  File \"/cbio/cslab/nobackup/pastore/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py\", line 115, in variant2pipeline\r\n    [x[0][\"description\"] for x in samples]]])\r\n  File \"/cbio/cslab/nobackup/pastore/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipython.py\", line 135, in run\r\n    for data in view.map_sync(fn, items, track=False):\r\n  File \"/cbio/cslab/nobackup/pastore/bcbio/anaconda/lib/python2.7/site-packages/ipyparallel/client/view.py\", line 353, in map_sync\r\n    return self.map(f,*sequences,**kwargs)\r\n  File \"<decorator-gen-140>\", line 2, in map\r\n  File \"/cbio/cslab/nobackup/pastore/bcbio/anaconda/lib/python2.7/site-packages/ipyparallel/client/view.py\", line 54, in sync_results\r\n    ret = f(self, *args, **kwargs)\r\n  File \"<decorator-gen-139>\", line 2, in map\r\n  File \"/cbio/cslab/nobackup/pastore/bcbio/anaconda/lib/python2.7/site-packages/ipyparallel/client/view.py\", line 39, in save_ids\r\n    ret = f(self, *args, **kwargs)\r\n  File \"/cbio/cslab/nobackup/pastore/bcbio/anaconda/lib/python2.7/site-packages/ipyparallel/client/view.py\", line 1119, in map\r\n    return pf.map(*sequences)\r\n  File \"/cbio/cslab/nobackup/pastore/bcbio/anaconda/lib/python2.7/site-packages/ipyparallel/client/remotefunction.py\", line 268, in map\r\n    ret = self(*sequences)\r\n  File \"<decorator-gen-119>\", line 2, in __call__\r\n  File \"/cbio/cslab/nobackup/pastore/bcbio/anaconda/lib/python2.7/site-packages/ipyparallel/client/remotefunction.py\", line 75, in sync_view_results\r\n    return f(self, *args, **kwargs)\r\n  File \"/cbio/cslab/nobackup/pastore/bcbio/anaconda/lib/python2.7/site-packages/ipyparallel/client/remotefunction.py\", line 251, in __call__\r\n    return r.get()\r\n  File \"/cbio/cslab/nobackup/pastore/bcbio/anaconda/lib/python2.7/site-packages/ipyparallel/client/asyncresult.py\", line 104, in get\r\n    raise self._exception\r\nipyparallel.error.CompositeError: one or more exceptions from call to method: organize_samples\r\n[5:apply]: OSError: Program problems found. You can upgrade dependencies with:\r\nbcbio_nextgen.py upgrade -u skip --tooldir=/usr/local\r\n\r\nInstalled version of samtools sort does not have support for multithreading (-@ option) required to support bwa piped alignment and BAM merging. Please upgrade to the latest version from http://samtools.sourceforge.net/"},"comment":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/comments/173911381","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/1197#issuecomment-173911381","issue_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1197","id":173911381,"user":{"login":"apastore","id":6528310,"avatar_url":"https://avatars.githubusercontent.com/u/6528310?v=3","gravatar_id":"","url":"https://api.github.com/users/apastore","html_url":"https://github.com/apastore","followers_url":"https://api.github.com/users/apastore/followers","following_url":"https://api.github.com/users/apastore/following{/other_user}","gists_url":"https://api.github.com/users/apastore/gists{/gist_id}","starred_url":"https://api.github.com/users/apastore/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/apastore/subscriptions","organizations_url":"https://api.github.com/users/apastore/orgs","repos_url":"https://api.github.com/users/apastore/repos","events_url":"https://api.github.com/users/apastore/events{/privacy}","received_events_url":"https://api.github.com/users/apastore/received_events","type":"User","site_admin":false},"created_at":"2016-01-22T12:49:06Z","updated_at":"2016-01-22T12:49:06Z","body":"Thanks! \nSent from my iPhone\n\n> On Jan 21, 2016, at 8:47 PM, Lorena Pantano <notifications@github.com> wrote:\n> \n> Hi @apastore,\n> \n> sorry about that. It is because of the new version of samtools and how it output the usage. @roryk fixed this here 81ca387. It worked for one of the cluster we used. I think you will need to update to development version since this happened after 0.9.5 stable release.\n> \n> hope this help.\n> \n> —\n> Reply to this email directly or view it on GitHub.\n> \n"}}