{"action":"created","issue":{"url":"https://api.github.com/repos/snayfach/MIDAS/issues/73","repository_url":"https://api.github.com/repos/snayfach/MIDAS","labels_url":"https://api.github.com/repos/snayfach/MIDAS/issues/73/labels{/name}","comments_url":"https://api.github.com/repos/snayfach/MIDAS/issues/73/comments","events_url":"https://api.github.com/repos/snayfach/MIDAS/issues/73/events","html_url":"https://github.com/snayfach/MIDAS/issues/73","id":273599488,"number":73,"title":"Help with genes error: libchtslib ","user":{"login":"elhwashington","id":33432917,"avatar_url":"https://avatars1.githubusercontent.com/u/33432917?v=4","gravatar_id":"","url":"https://api.github.com/users/elhwashington","html_url":"https://github.com/elhwashington","followers_url":"https://api.github.com/users/elhwashington/followers","following_url":"https://api.github.com/users/elhwashington/following{/other_user}","gists_url":"https://api.github.com/users/elhwashington/gists{/gist_id}","starred_url":"https://api.github.com/users/elhwashington/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/elhwashington/subscriptions","organizations_url":"https://api.github.com/users/elhwashington/orgs","repos_url":"https://api.github.com/users/elhwashington/repos","events_url":"https://api.github.com/users/elhwashington/events{/privacy}","received_events_url":"https://api.github.com/users/elhwashington/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2017-11-13T22:22:53Z","updated_at":"2017-11-28T17:21:35Z","closed_at":"2017-11-28T17:21:35Z","author_association":"NONE","body":"Hello,\r\n   I have been trying to get MIDAS, installed by a former lab member, to run. So far I think that I have run_midas.py species running but when I then try run_midas.py genes on the samples I just ran through species I receive the following error\r\nTraceback (most recent call last):\r\n  File \"/Users/mcleanlab/Tools/MIDAS/scripts/run_midas.py\", line 757, in <module>\r\n    run_program(program, args)\r\n  File \"/Users/mcleanlab/Tools/MIDAS/scripts/run_midas.py\", line 79, in run_program\r\n    genes.run_pipeline(args)\r\n  File \"/Users/mcleanlab/Tools/MIDAS/midas/run/genes.py\", line 286, in run_pipeline\r\n    pangenome_coverage(args, species, genes)\r\n  File \"/Users/mcleanlab/Tools/MIDAS/midas/run/genes.py\", line 149, in pangenome_coverage\r\n    count_mapped_bp(args, species, genes)\r\n  File \"/Users/mcleanlab/Tools/MIDAS/midas/run/genes.py\", line 173, in count_mapped_bp\r\n    import pysam\r\n  File \"/Users/mcleanlab/Downloads/pysam-master/pysam/__init__.py\", line 5, in <module>\r\n    from pysam.libchtslib import *\r\nImportError: No module named libchtslib\r\nI have looked for libchtslib and found libchtslib.pxd, libchstlib.c and libchtslib.o deep inside the pysam-master folder.  However, even adding the corresponding folders to the python path did not correct the issue. \r\nI  am looking for help.  Hopefully I'm just confused and the answer is simple.\r\n\r\nthank you for your time\r\nErik Hendrickson"},"comment":{"url":"https://api.github.com/repos/snayfach/MIDAS/issues/comments/347597353","html_url":"https://github.com/snayfach/MIDAS/issues/73#issuecomment-347597353","issue_url":"https://api.github.com/repos/snayfach/MIDAS/issues/73","id":347597353,"user":{"login":"snayfach","id":2104237,"avatar_url":"https://avatars1.githubusercontent.com/u/2104237?v=4","gravatar_id":"","url":"https://api.github.com/users/snayfach","html_url":"https://github.com/snayfach","followers_url":"https://api.github.com/users/snayfach/followers","following_url":"https://api.github.com/users/snayfach/following{/other_user}","gists_url":"https://api.github.com/users/snayfach/gists{/gist_id}","starred_url":"https://api.github.com/users/snayfach/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/snayfach/subscriptions","organizations_url":"https://api.github.com/users/snayfach/orgs","repos_url":"https://api.github.com/users/snayfach/repos","events_url":"https://api.github.com/users/snayfach/events{/privacy}","received_events_url":"https://api.github.com/users/snayfach/received_events","type":"User","site_admin":false},"created_at":"2017-11-28T17:21:35Z","updated_at":"2017-11-28T17:21:35Z","author_association":"OWNER","body":"In that case I'm closing this issue, but feel free to reopen as necessary.\r\n\r\nThanks,\r\nStephen"}}
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