{"action":"created","issue":{"url":"https://api.github.com/repos/Ecogenomics/BamM/issues/27","labels_url":"https://api.github.com/repos/Ecogenomics/BamM/issues/27/labels{/name}","comments_url":"https://api.github.com/repos/Ecogenomics/BamM/issues/27/comments","events_url":"https://api.github.com/repos/Ecogenomics/BamM/issues/27/events","html_url":"https://github.com/Ecogenomics/BamM/issues/27","id":98669477,"number":27,"title":"BamM v1.5.0 - failed nosetests - missing filtered bam files - Also python library bug from 1.5.0 and 1.4.1","user":{"login":"AlexRBaker","id":10200912,"avatar_url":"https://avatars.githubusercontent.com/u/10200912?v=3","gravatar_id":"","url":"https://api.github.com/users/AlexRBaker","html_url":"https://github.com/AlexRBaker","followers_url":"https://api.github.com/users/AlexRBaker/followers","following_url":"https://api.github.com/users/AlexRBaker/following{/other_user}","gists_url":"https://api.github.com/users/AlexRBaker/gists{/gist_id}","starred_url":"https://api.github.com/users/AlexRBaker/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/AlexRBaker/subscriptions","organizations_url":"https://api.github.com/users/AlexRBaker/orgs","repos_url":"https://api.github.com/users/AlexRBaker/repos","events_url":"https://api.github.com/users/AlexRBaker/events{/privacy}","received_events_url":"https://api.github.com/users/AlexRBaker/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":5,"created_at":"2015-08-03T04:36:21Z","updated_at":"2015-08-07T11:25:52Z","closed_at":"2015-08-05T01:36:36Z","body":"Hello, \r\n\r\nI am running ubuntu14.04. After upgrading from v1.4.1 to 1.5.0 I now fail the nosetests. Additionally, in both versions trying to run BP.parseBams(bamnames,doLinks=True,doCovs=True,threads=1) resulted in an indefinite runtime in my python environment. This was after the imports and setup at mentioned in page 12 of the manual.\r\n\r\n\r\n/bin/sh: 1: /home/baker/git/BamM/bin/bamm: not found\r\nFNo file: /home/baker/Packages/BamM/bamm/tests/filter_test_data/1_filtered.bam\r\nNo file: /home/baker/Packages/BamM/bamm/tests/filter_test_data/2_filtered.bam\r\n................................................\r\n======================================================================\r\nFAIL: test_bamFilter.TestBamFilter.testFilter\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n  File \"/usr/local/lib/python2.7/dist-packages/nose/case.py\", line 197, in runTest\r\n    self.test(*self.arg)\r\n  File \"/home/baker/Packages/BamM/bamm/tests/test_bamFilter.py\", line 156, in testFilter\r\n    self.assert_equal_query_sequences(out, test)\r\n  File \"/home/baker/Packages/BamM/bamm/tests/test_bamFilter.py\", line 129, in assert_equal_query_sequences\r\n    raise AssertionError('File of filtered reads \"%s\" exists and is readable.' % out)\r\nAssertionError: File of filtered reads \"/home/baker/Packages/BamM/bamm/tests/filter_test_data/1_filtered.bam\" exists and is readable.\r\n\r\n----------------------------------------------------------------------\r\nRan 49 tests in 4.820s\r\n\r\nFAILED (failures=1)\r\n\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/Ecogenomics/BamM/issues/comments/128678962","html_url":"https://github.com/Ecogenomics/BamM/issues/27#issuecomment-128678962","issue_url":"https://api.github.com/repos/Ecogenomics/BamM/issues/27","id":128678962,"user":{"login":"wwood","id":15348,"avatar_url":"https://avatars.githubusercontent.com/u/15348?v=3","gravatar_id":"","url":"https://api.github.com/users/wwood","html_url":"https://github.com/wwood","followers_url":"https://api.github.com/users/wwood/followers","following_url":"https://api.github.com/users/wwood/following{/other_user}","gists_url":"https://api.github.com/users/wwood/gists{/gist_id}","starred_url":"https://api.github.com/users/wwood/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/wwood/subscriptions","organizations_url":"https://api.github.com/users/wwood/orgs","repos_url":"https://api.github.com/users/wwood/repos","events_url":"https://api.github.com/users/wwood/events{/privacy}","received_events_url":"https://api.github.com/users/wwood/received_events","type":"User","site_admin":false},"created_at":"2015-08-07T11:25:52Z","updated_at":"2015-08-07T11:25:52Z","body":"ok. Hard to know what the problem is without example code, and since \nbamm on the command line uses the API, perhaps you are doing something \nunintended?\n\nOn 07/08/15 20:58, Alexander Baker wrote:\n>\n> I tried using the python library to process a 3megabyte bam file based \n> on mapping reads from a 20kb sequence. Using BamM on the command line \n> processes this in less than a minute. I left it running for \n> 30-60minutes via the python library and it still had not completed.\n>\n> —\n> Reply to this email directly or view it on GitHub \n> <https://github.com/Ecogenomics/BamM/issues/27#issuecomment-128672743>.\n>\n\n"}}