{"action":"created","issue":{"url":"https://api.github.com/repos/genouest/biomaj/issues/13","repository_url":"https://api.github.com/repos/genouest/biomaj","labels_url":"https://api.github.com/repos/genouest/biomaj/issues/13/labels{/name}","comments_url":"https://api.github.com/repos/genouest/biomaj/issues/13/comments","events_url":"https://api.github.com/repos/genouest/biomaj/issues/13/events","html_url":"https://github.com/genouest/biomaj/issues/13","id":106766439,"number":13,"title":"gunzip command returned non-zero exit status 1","user":{"login":"pfem-bioinfo","id":14312712,"avatar_url":"https://avatars.githubusercontent.com/u/14312712?v=3","gravatar_id":"","url":"https://api.github.com/users/pfem-bioinfo","html_url":"https://github.com/pfem-bioinfo","followers_url":"https://api.github.com/users/pfem-bioinfo/followers","following_url":"https://api.github.com/users/pfem-bioinfo/following{/other_user}","gists_url":"https://api.github.com/users/pfem-bioinfo/gists{/gist_id}","starred_url":"https://api.github.com/users/pfem-bioinfo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pfem-bioinfo/subscriptions","organizations_url":"https://api.github.com/users/pfem-bioinfo/orgs","repos_url":"https://api.github.com/users/pfem-bioinfo/repos","events_url":"https://api.github.com/users/pfem-bioinfo/events{/privacy}","received_events_url":"https://api.github.com/users/pfem-bioinfo/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/genouest/biomaj/labels/bug","name":"bug","color":"fc2929"}],"state":"closed","locked":false,"assignee":{"login":"osallou","id":1024098,"avatar_url":"https://avatars.githubusercontent.com/u/1024098?v=3","gravatar_id":"","url":"https://api.github.com/users/osallou","html_url":"https://github.com/osallou","followers_url":"https://api.github.com/users/osallou/followers","following_url":"https://api.github.com/users/osallou/following{/other_user}","gists_url":"https://api.github.com/users/osallou/gists{/gist_id}","starred_url":"https://api.github.com/users/osallou/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/osallou/subscriptions","organizations_url":"https://api.github.com/users/osallou/orgs","repos_url":"https://api.github.com/users/osallou/repos","events_url":"https://api.github.com/users/osallou/events{/privacy}","received_events_url":"https://api.github.com/users/osallou/received_events","type":"User","site_admin":false},"milestone":{"url":"https://api.github.com/repos/genouest/biomaj/milestones/2","html_url":"https://github.com/genouest/biomaj/milestones/3.0.8","labels_url":"https://api.github.com/repos/genouest/biomaj/milestones/2/labels","id":1308667,"number":2,"title":"3.0.8","description":null,"creator":{"login":"osallou","id":1024098,"avatar_url":"https://avatars.githubusercontent.com/u/1024098?v=3","gravatar_id":"","url":"https://api.github.com/users/osallou","html_url":"https://github.com/osallou","followers_url":"https://api.github.com/users/osallou/followers","following_url":"https://api.github.com/users/osallou/following{/other_user}","gists_url":"https://api.github.com/users/osallou/gists{/gist_id}","starred_url":"https://api.github.com/users/osallou/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/osallou/subscriptions","organizations_url":"https://api.github.com/users/osallou/orgs","repos_url":"https://api.github.com/users/osallou/repos","events_url":"https://api.github.com/users/osallou/events{/privacy}","received_events_url":"https://api.github.com/users/osallou/received_events","type":"User","site_admin":false},"open_issues":0,"closed_issues":1,"state":"open","created_at":"2015-09-16T15:06:19Z","updated_at":"2015-09-18T07:28:24Z","due_on":null,"closed_at":null},"comments":15,"created_at":"2015-09-16T12:46:56Z","updated_at":"2016-05-03T05:52:05Z","closed_at":"2015-09-18T07:28:24Z","body":"Dears all,\r\n\r\nAfter a clean install of biomaj and biomajwtacher on a CentOS server, I starting to configure some proteic banks. Today, I manage a pool of 19 banks with 17 of them working well. For two banks (large ones), I got the following message during an update step in log : \r\n\r\nFTP:Download:Progress:1/1 downloading file uniprotkb_bacteria.gz\r\n2015-09-04 14:11:44,240 DEBUG [root][Thread-88] FT\r\n\r\nP:Download:Progress:1/1 save as uniprotkb_bacteria.gz\r\n2015-09-04 14:28:24,240 DEBUG [root][MainThread] Workflow:wf_download:Download:Threads:[None]\r\n2015-09-04 14:28:24,240 DEBUG [root][MainThread] Workflow:wf_download:Download:Threads:[]\r\n2015-09-04 14:28:24,241 INFO  [root][MainThread] Workflow:wf_download:Download:Threads:Over\r\n2015-09-04 14:28:24,241 INFO  [root][MainThread] Workflow:wf_uncompress\r\n2015-09-04 14:29:23,235 ERROR [root][MainThread] Workflow:download subtask: wf_uncompress:Exception:Command 'gunzip -f /banks/offline/ebi-uniprot-ref_bacteria/uniprotkb_bacteria.gz' returned non-zero exit status 1\r\n2015-09-04 14:29:23,235 DEBUG [root][MainThread] Traceback (most recent call last):\r\n  File \"/opt/biomaj3/lib/python2.7/site-packages/biomaj-3.0.7-py2.7.egg/biomaj/workflow.py\", line 140, in start\r\n    res = getattr(self, 'wf_'+step)()\r\n  File \"/opt/biomaj3/lib/python2.7/site-packages/biomaj-3.0.7-py2.7.egg/biomaj/workflow.py\", line 781, in wf_uncompress\r\n    Utils.uncompress(self.session.get_offline_directory() + '/' + file['save_as'])\r\n  File \"/opt/biomaj3/lib/python2.7/site-packages/biomaj-3.0.7-py2.7.egg/biomaj/utils.py\", line 231, in uncompress\r\n    proc = subprocess.check_call(\"gunzip -f \"+archivefile, shell=True)\r\n  File \"/usr/lib64/python2.7/subprocess.py\", line 542, in check_call\r\n    raise CalledProcessError(retcode, cmd)\r\nCalledProcessError: Command 'gunzip -f /banks/offline/ebi-uniprot-ref_bacteria/uniprotkb_bacteria.gz' returned non-zero exit status 1\r\n\r\nThank you for your help.\r\nRegards \r\nFranck Giacomoni - INRA Clermont-Ferrand \r\n\r\nPlease find my ebi-uniprot-ref_bacteria.properties\r\n\r\n    ## ##\r\n    [GENERAL]\r\n    protocol = ftp\r\n    db.name = ebi-uniprot-ref_bacteria\r\n    db.type = proteic\r\n    offline.dir.name = offline/ebi-uniprot-ref_bacteria\r\n    server = ftp.ebi.ac.uk\r\n    remote.files = ^uniprotkb_bacteria\\.gz$\r\n    db.fullname = Proteomes Datasets UniProt Knowledgebase Bacteria on EBI\r\n    local.files = ^uniprotkb_bacteria\r\n    remote.dir = /pub/databases/fastafiles/uniprot/\r\n    dir.version = auto/ebi-uniprot-ref_bacteria\r\n    keep.old.version = 1\r\n    \r\n    BLOCKS=BLOCK1\r\n    BLOCK1.db.post.process=META0\r\n    META0=PROC0\r\n    PROC0.name=test0\r\n    PROC0.desc=sample test\r\n    PROC0.type=test\r\n    # Command to execute, in process.dir or path\r\n    PROC0.exe=scp_bank.sh\r\n    # Arguments\r\n    PROC0.args=ebi-uniprot-ref_bacteria uniprotkb_bacteria ebi-uniprot-ref_bacteria.fasta\r\n    # Expand shell variables (default true)\r\n    PROC0.expand=true\r\n"},"comment":{"url":"https://api.github.com/repos/genouest/biomaj/issues/comments/216444197","html_url":"https://github.com/genouest/biomaj/issues/13#issuecomment-216444197","issue_url":"https://api.github.com/repos/genouest/biomaj/issues/13","id":216444197,"user":{"login":"Public-Health-Bioinformatics","id":10779910,"avatar_url":"https://avatars.githubusercontent.com/u/10779910?v=3","gravatar_id":"","url":"https://api.github.com/users/Public-Health-Bioinformatics","html_url":"https://github.com/Public-Health-Bioinformatics","followers_url":"https://api.github.com/users/Public-Health-Bioinformatics/followers","following_url":"https://api.github.com/users/Public-Health-Bioinformatics/following{/other_user}","gists_url":"https://api.github.com/users/Public-Health-Bioinformatics/gists{/gist_id}","starred_url":"https://api.github.com/users/Public-Health-Bioinformatics/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Public-Health-Bioinformatics/subscriptions","organizations_url":"https://api.github.com/users/Public-Health-Bioinformatics/orgs","repos_url":"https://api.github.com/users/Public-Health-Bioinformatics/repos","events_url":"https://api.github.com/users/Public-Health-Bioinformatics/events{/privacy}","received_events_url":"https://api.github.com/users/Public-Health-Bioinformatics/received_events","type":"User","site_admin":false},"created_at":"2016-05-03T05:52:05Z","updated_at":"2016-05-03T05:52:05Z","body":"Ok, thanks, or, in my very rusty French, \"merci pour travailler dans la problème\".  Yes download was empty.\r\n\r\nCiao,\r\n\r\nDamion\r\n\r\n\r\n\r\n\r\n\r\nFrom: Olivier Sallou <notifications@github.com<mailto:notifications@github.com>>\r\nReply-To: genouest/biomaj <reply@reply.github.com<mailto:reply@reply.github.com>>\r\nDate: Monday, May 2, 2016 at 10:36 PM\r\nTo: genouest/biomaj <biomaj@noreply.github.com<mailto:biomaj@noreply.github.com>>\r\nCc: Damion Dooley <damion.dooley@bccdc.ca<mailto:damion.dooley@bccdc.ca>>, Comment <comment@noreply.github.com<mailto:comment@noreply.github.com>>\r\nSubject: Re: [genouest/biomaj] gunzip command returned non-zero exit status 1 (#13)\r\n\r\nok, looks like a bug in directhttp and uncompress, I gonna test and check.\r\n\r\nIs download empty?\r\nAs you specified target.name=current_Bacteria_unaligned.fa.gz, file is\r\nsaved in \"root\" directory, not under download, so it is fine for download\r\nstep. I think we may omit to \"save\" the final name/path in directhttp and\r\nuncompress think we keep the original path. We let you know.\r\n\r\nOlivier\r\n"}}