{"action":"created","issue":{"url":"https://api.github.com/repos/bioinform/metasv/issues/108","repository_url":"https://api.github.com/repos/bioinform/metasv","labels_url":"https://api.github.com/repos/bioinform/metasv/issues/108/labels{/name}","comments_url":"https://api.github.com/repos/bioinform/metasv/issues/108/comments","events_url":"https://api.github.com/repos/bioinform/metasv/issues/108/events","html_url":"https://github.com/bioinform/metasv/issues/108","id":146553288,"number":108,"title":"Permissions errors during run_spades_single in run_spades.py ","user":{"login":"aktilot","id":17905622,"avatar_url":"https://avatars.githubusercontent.com/u/17905622?v=3","gravatar_id":"","url":"https://api.github.com/users/aktilot","html_url":"https://github.com/aktilot","followers_url":"https://api.github.com/users/aktilot/followers","following_url":"https://api.github.com/users/aktilot/following{/other_user}","gists_url":"https://api.github.com/users/aktilot/gists{/gist_id}","starred_url":"https://api.github.com/users/aktilot/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/aktilot/subscriptions","organizations_url":"https://api.github.com/users/aktilot/orgs","repos_url":"https://api.github.com/users/aktilot/repos","events_url":"https://api.github.com/users/aktilot/events{/privacy}","received_events_url":"https://api.github.com/users/aktilot/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/bioinform/metasv/labels/bug","name":"bug","color":"fc2929"}],"state":"open","locked":false,"assignee":{"login":"marghoob","id":885355,"avatar_url":"https://avatars.githubusercontent.com/u/885355?v=3","gravatar_id":"","url":"https://api.github.com/users/marghoob","html_url":"https://github.com/marghoob","followers_url":"https://api.github.com/users/marghoob/followers","following_url":"https://api.github.com/users/marghoob/following{/other_user}","gists_url":"https://api.github.com/users/marghoob/gists{/gist_id}","starred_url":"https://api.github.com/users/marghoob/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/marghoob/subscriptions","organizations_url":"https://api.github.com/users/marghoob/orgs","repos_url":"https://api.github.com/users/marghoob/repos","events_url":"https://api.github.com/users/marghoob/events{/privacy}","received_events_url":"https://api.github.com/users/marghoob/received_events","type":"User","site_admin":false},"milestone":null,"comments":4,"created_at":"2016-04-07T09:02:36Z","updated_at":"2016-04-29T16:44:32Z","closed_at":null,"body":"Hi and thanks in advance for your help!\r\n\r\nWhile running MetaSV, it got stuck while running spades. There are a few 'OSError: [Errno 13] Permission denied' errors during the run_spades_single process, and then it seems to hang while merging the contigs. The merged.fa and spades.log files are both empty. Running MetaSV on the same sample with --disable_assembly went fine with no errors. The error messages are below, please let me know if there is anything I should try or additional information that would be helpful. \r\n\r\nThanks!\r\n\r\nAmanda\r\n\r\nErrors: \r\nINFO 2016-04-06 14:10:19,200 extract_read_pairs-<Process(PoolWorker-7, started daemon)> Examined 256 pairs in 11.3396 seconds\r\nINFO 2016-04-06 14:10:19,200 extract_read_pairs-<Process(PoolWorker-7, started daemon)> Extraction counts [('all_pair_hq', 256), ('non_perfect_hq', 107)]\r\nINFO 2016-04-06 14:10:19,202 run_spades_single-<Process(PoolWorker-7, started daemon)> Running /HOME/BIOINFORMATICS/SOFTWARE/SPADES-3.7.1-LINUX/BIN/ with arguments ['-1', 'work/spades/2/_all_pair_hq_1.fq', '-2', 'work/spades/2/_all_pair_hq_2.fq', '-o', 'work/spades/2/spades_all_pair_hq/', '-m', '4', '-t', '1', '--phred-offset', '33']\r\nERROR 2016-04-06 14:10:19,950 run_spades_single-<Process(PoolWorker-7, started daemon)> Caught exception in worker thread\r\nTraceback (most recent call last):\r\n  File \"/home/.local/lib/python2.7/site-packages/metasv/run_spades.py\", line 75, in run_spades_single\r\n    retcode = cmd.run(cmd_log_fd_out=spades_log_fd, timeout=timeout)\r\n  File \"/home/.local/lib/python2.7/site-packages/metasv/external_cmd.py\", line 20, in run\r\n    self.p = subprocess.Popen(self.cmd, stderr=cmd_log_fd_err, stdout=cmd_log_fd_out)\r\n  File \"/usr/local/apps/python-2.7.11/lib/python2.7/subprocess.py\", line 710, in __init__\r\n    errread, errwrite)\r\n  File \"/usr/local/apps/python-2.7.11/lib/python2.7/subprocess.py\", line 1335, in _execute_child\r\n    raise child_exception\r\nOSError: [Errno 13] Permission denied\r\nINFO 2016-04-06 14:10:20,589 metasv.run_spades    Merging the contigs from []\r\n^CTraceback (most recent call last):\r\n  File \"/home/Bioinformatics/software/metasv/scripts/run_metasv.py\", line 143, in <module>\r\n    sys.exit(run_metasv(args))\r\n  File \"/home/.local/lib/python2.7/site-packages/metasv/main.py\", line 306, in run_metasv\r\n    assembly_max_tools=args.assembly_max_tools)\r\n  File \"/home/.local/lib/python2.7/site-packages/metasv/run_spades.py\", line 214, in run_spades_parallel\r\n    for line in fileinput.input(assembly_fastas):\r\n  File \"/usr/local/apps/python-2.7.11/lib/python2.7/fileinput.py\", line 254, in next\r\n    line = self.readline()\r\n  File \"/usr/local/apps/python-2.7.11/lib/python2.7/fileinput.py\", line 349, in readline\r\n    self._buffer = self._file.readlines(self._bufsize)\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/bioinform/metasv/issues/comments/215801994","html_url":"https://github.com/bioinform/metasv/issues/108#issuecomment-215801994","issue_url":"https://api.github.com/repos/bioinform/metasv/issues/108","id":215801994,"user":{"login":"marghoob","id":885355,"avatar_url":"https://avatars.githubusercontent.com/u/885355?v=3","gravatar_id":"","url":"https://api.github.com/users/marghoob","html_url":"https://github.com/marghoob","followers_url":"https://api.github.com/users/marghoob/followers","following_url":"https://api.github.com/users/marghoob/following{/other_user}","gists_url":"https://api.github.com/users/marghoob/gists{/gist_id}","starred_url":"https://api.github.com/users/marghoob/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/marghoob/subscriptions","organizations_url":"https://api.github.com/users/marghoob/orgs","repos_url":"https://api.github.com/users/marghoob/repos","events_url":"https://api.github.com/users/marghoob/events{/privacy}","received_events_url":"https://api.github.com/users/marghoob/received_events","type":"User","site_admin":false},"created_at":"2016-04-29T16:44:32Z","updated_at":"2016-04-29T16:44:32Z","body":"Thanks, Amanda. Please let me know if the solution worked so that I can fix/close this bug.\r\n\r\nBest\r\nMarghoob"}}