{"action":"closed","issue":{"url":"https://api.github.com/repos/wwood/singlem/issues/11","repository_url":"https://api.github.com/repos/wwood/singlem","labels_url":"https://api.github.com/repos/wwood/singlem/issues/11/labels{/name}","comments_url":"https://api.github.com/repos/wwood/singlem/issues/11/comments","events_url":"https://api.github.com/repos/wwood/singlem/issues/11/events","html_url":"https://github.com/wwood/singlem/issues/11","id":161814505,"number":11,"title":"AttributeError: 'module' object has no attribute 'run_many'","user":{"login":"xvazquezc","id":14157565,"avatar_url":"https://avatars.githubusercontent.com/u/14157565?v=3","gravatar_id":"","url":"https://api.github.com/users/xvazquezc","html_url":"https://github.com/xvazquezc","followers_url":"https://api.github.com/users/xvazquezc/followers","following_url":"https://api.github.com/users/xvazquezc/following{/other_user}","gists_url":"https://api.github.com/users/xvazquezc/gists{/gist_id}","starred_url":"https://api.github.com/users/xvazquezc/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/xvazquezc/subscriptions","organizations_url":"https://api.github.com/users/xvazquezc/orgs","repos_url":"https://api.github.com/users/xvazquezc/repos","events_url":"https://api.github.com/users/xvazquezc/events{/privacy}","received_events_url":"https://api.github.com/users/xvazquezc/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":16,"created_at":"2016-06-23T00:14:04Z","updated_at":"2016-06-29T07:53:05Z","closed_at":"2016-06-29T07:53:05Z","body":"Tried with v 0.6.0 and 0.6.1. Memory allocated 20GB, used <2GB\r\n\r\nCommand:\r\n```\r\nsinglem pipe --sequences 028-LFA*R1*.fastq.gz --otu_table 028-LFA_otu_table.csv --threads 12\r\n```\r\nLog:\r\n```\r\n06/23/2016 10:00:26 AM INFO: Using as input 4 different sequence files e.g. 028-LFA_S1_L001_R1_001.fastq.gz\r\n06/23/2016 10:00:26 AM INFO: Searching for reads matching 30 different protein HMMs\r\n06/23/2016 10:09:29 AM INFO: Finished search phase\r\n06/23/2016 10:09:29 AM INFO: Running separate alignments in GraftM..\r\nTraceback (most recent call last):\r\n  File \"/home/z3382651/bin/singlem/bin/singlem\", line 327, in <module>\r\n    known_sequence_taxonomy = args.known_sequence_taxonomy)\r\n  File \"/home/z3382651/bin/singlem/bin/../singlem/pipe.py\", line 118, in run\r\n    align_result = self._align(search_result)\r\n  File \"/home/z3382651/bin/singlem/bin/../singlem/pipe.py\", line 564, in _align\r\n    extern.run_many(commands, num_threads=self._num_threads)\r\nAttributeError: 'module' object has no attribute 'run_many'\r\n```\r\n\r\nAny idea what can be wrong?"}}
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