{"action":"created","issue":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/846","labels_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/846/labels{/name}","comments_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/846/comments","events_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/846/events","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/846","id":74407204,"number":846,"title":"vep genome reference error on upgrade","user":{"login":"dwaggott","id":3149944,"avatar_url":"https://avatars.githubusercontent.com/u/3149944?v=3","gravatar_id":"","url":"https://api.github.com/users/dwaggott","html_url":"https://github.com/dwaggott","followers_url":"https://api.github.com/users/dwaggott/followers","following_url":"https://api.github.com/users/dwaggott/following{/other_user}","gists_url":"https://api.github.com/users/dwaggott/gists{/gist_id}","starred_url":"https://api.github.com/users/dwaggott/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dwaggott/subscriptions","organizations_url":"https://api.github.com/users/dwaggott/orgs","repos_url":"https://api.github.com/users/dwaggott/repos","events_url":"https://api.github.com/users/dwaggott/events{/privacy}","received_events_url":"https://api.github.com/users/dwaggott/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-05-08T15:47:57Z","updated_at":"2015-05-08T16:13:35Z","closed_at":"2015-05-08T16:11:38Z","body":"Sorry no gist, does the upgrade produce a log if you don't send to stdout/stderr?\r\n\r\n```\r\nbcbio_nextgen.py upgrade -u development --tools --data\r\n...\r\nINFO: Now, testing connection to host...\r\nINFO: Connection to host appears to work!\r\nINFO: Connection to host appears to work!\r\nDBG [utils.py]: Expand paths\r\nDBG [utils.py]: Expand paths\r\nINFO: List of genomes to get (from the config file at '{'install_liftover': False, 'genome_indexes': ['bwa', 'bowtie2', 'novoalign', 'seq', 'ucsc'], 'genomes': [{'rnaseq': True, 'dbsnp': True, 'name': 'Hu\r\nman (GRCh37)', 'dbkey': 'GRCh37'}], 'install_uniref': False}'): Human (GRCh37)\r\nINFO: List of genomes to get (from the config file at '{'install_liftover': False, 'genome_indexes': ['bwa', 'bowtie2', 'novoalign', 'seq', 'ucsc'], 'genomes': [{'rnaseq': True, 'dbsnp': True, 'name': 'Hu\r\nman (GRCh37)', 'dbkey': 'GRCh37'}], 'install_uniref': False}'): Human (GRCh37)\r\nUpdating GRCh37 genome resources configuration\r\n[2015-05-08 15:16:30.973633] DEBUG: bcbio-nextgen: Prepare VEP directory for homo_sapiens_vep_79_GRCh37\r\n[2015-05-08 15:16:30.974149] DEBUG: bcbio-nextgen-commands: vep_install.pl -a c -s homo_sapiens_vep_79_GRCh37 -c /share/PI/euan/apps/bcbio/genomes/Hsapiens/GRCh37/vep\r\n[2015-05-08 15:16:31.468923] DEBUG: bcbio-nextgen: Getting list of available cache files\r\n[2015-05-08 15:16:35.755355] DEBUG: bcbio-nextgen:  - downloading ftp://ftp.ensembl.org/pub/release-79/variation/VEP/homo_sapiens_vep_79_GRCh37.tar.gz\r\n\r\n[2015-05-08 15:33:55.330290] DEBUG: bcbio-nextgen:  - unpacking homo_sapiens_vep_79_GRCh37.tar.gz\r\n[2015-05-08 15:40:33.606993] DEBUG: bcbio-nextgen: \r\n[2015-05-08 15:40:33.607171] DEBUG: bcbio-nextgen: All done\r\n[2015-05-08 15:40:33.613603] DEBUG: bcbio-nextgen: Convert VEP cache to tabix homo_sapiens_vep_79_GRCh37\r\n[2015-05-08 15:40:33.613708] DEBUG: bcbio-nextgen-commands: vep_convert_cache.pl -species homo_sapiens_vep_79_GRCh37 -version 79 -d /share/PI/euan/apps/bcbio/genomes/Hsapiens/GRCh37/vep\r\n[2015-05-08 15:40:34.239214] DEBUG: bcbio-nextgen: ERROR: Species homo_sapiens_vep_79_GRCh37 not found\r\n[2015-05-08 15:40:34.247410] ERROR: bcbio-nextgen: Uncaught exception occurred\r\nTraceback (most recent call last):\r\n  File \"/share/PI/euan/apps/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py\", line 21, in run\r\n    _do_run(cmd, checks, log_stdout)\r\n  File \"/share/PI/euan/apps/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py\", line 95, in _do_run\r\n    raise subprocess.CalledProcessError(exitcode, error_msg)\r\nCalledProcessError: Command 'vep_convert_cache.pl -species homo_sapiens_vep_79_GRCh37 -version 79 -d /share/PI/euan/apps/bcbio/genomes/Hsapiens/GRCh37/vep\r\nERROR: Species homo_sapiens_vep_79_GRCh37 not found\r\n' returned non-zero exit status 255\r\nTraceback (most recent call last):\r\n  File \"/share/PI/euan/apps/bin/bcbio_nextgen.py\", line 199, in <module>\r\n    kwargs = parse_cl_args(sys.argv[1:])\r\n  File \"/share/PI/euan/apps/bcbio/anaconda/lib/python2.7/site-packages/bcbio/install.py\", line 93, in upgrade_bcbio\r\n    upgrade_bcbio_data(args, REMOTES)\r\n  File \"/share/PI/euan/apps/bcbio/anaconda/lib/python2.7/site-packages/bcbio/install.py\", line 245, in upgrade_bcbio_data\r\n    s[\"genomes\"] = _get_biodata(cbl[\"biodata\"], args)\r\n  File \"/share/PI/euan/apps/bcbio/anaconda/lib/python2.7/site-packages/bcbio/install.py\", line 280, in _upgrade_vep_data\r\n    if needs_update:\r\n  File \"/share/PI/euan/apps/bcbio/anaconda/lib/python2.7/site-packages/bcbio/variation/effects.py\", line 105, in prep_vep_cache\r\n    assert in_file.endswith(\".gz\") and out_file.endswith(\".gz\")\r\n  File \"/share/PI/euan/apps/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py\", line 21, in run\r\n    _do_run(cmd, checks, log_stdout)\r\n  File \"/share/PI/euan/apps/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py\", line 95, in _do_run\r\n    raise subprocess.CalledProcessError(exitcode, error_msg)\r\nsubprocess.CalledProcessError: Command 'vep_convert_cache.pl -species homo_sapiens_vep_79_GRCh37 -version 79 -d /share/PI/euan/apps/bcbio/genomes/Hsapiens/GRCh37/vep\r\nERROR: Species homo_sapiens_vep_79_GRCh37 not found\r\n' returned non-zero exit status 255\r\n```"},"comment":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/comments/100283802","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/846#issuecomment-100283802","issue_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/846","id":100283802,"user":{"login":"chapmanb","id":39391,"avatar_url":"https://avatars.githubusercontent.com/u/39391?v=3","gravatar_id":"","url":"https://api.github.com/users/chapmanb","html_url":"https://github.com/chapmanb","followers_url":"https://api.github.com/users/chapmanb/followers","following_url":"https://api.github.com/users/chapmanb/following{/other_user}","gists_url":"https://api.github.com/users/chapmanb/gists{/gist_id}","starred_url":"https://api.github.com/users/chapmanb/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/chapmanb/subscriptions","organizations_url":"https://api.github.com/users/chapmanb/orgs","repos_url":"https://api.github.com/users/chapmanb/repos","events_url":"https://api.github.com/users/chapmanb/events{/privacy}","received_events_url":"https://api.github.com/users/chapmanb/received_events","type":"User","site_admin":false},"created_at":"2015-05-08T16:13:35Z","updated_at":"2015-05-08T16:13:35Z","body":"Daryl;\r\nApologies, this VEP update touches a lot of things. You actually need a two part upgrade, first get the tools and development code (with the fixes for handling the new databases):\r\n```\r\nbcbio_nextgen.py upgrade -u development --tools\r\n```\r\nthen update the data with the fixed installation code:\r\n```\r\nbcbio_nextgen.py upgrade --data\r\n```\r\nYou already got the tools and code so re-running the data command should hopefully work cleanly for you now. Sorry again about the confusion and difficult upgrade process."}}