{"action":"created","issue":{"url":"https://api.github.com/repos/fenderglass/ABruijn/issues/3","repository_url":"https://api.github.com/repos/fenderglass/ABruijn","labels_url":"https://api.github.com/repos/fenderglass/ABruijn/issues/3/labels{/name}","comments_url":"https://api.github.com/repos/fenderglass/ABruijn/issues/3/comments","events_url":"https://api.github.com/repos/fenderglass/ABruijn/issues/3/events","html_url":"https://github.com/fenderglass/ABruijn/issues/3","id":168443133,"number":3,"title":"BLASR error","user":{"login":"StefanoLonardi","id":18489339,"avatar_url":"https://avatars.githubusercontent.com/u/18489339?v=3","gravatar_id":"","url":"https://api.github.com/users/StefanoLonardi","html_url":"https://github.com/StefanoLonardi","followers_url":"https://api.github.com/users/StefanoLonardi/followers","following_url":"https://api.github.com/users/StefanoLonardi/following{/other_user}","gists_url":"https://api.github.com/users/StefanoLonardi/gists{/gist_id}","starred_url":"https://api.github.com/users/StefanoLonardi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/StefanoLonardi/subscriptions","organizations_url":"https://api.github.com/users/StefanoLonardi/orgs","repos_url":"https://api.github.com/users/StefanoLonardi/repos","events_url":"https://api.github.com/users/StefanoLonardi/events{/privacy}","received_events_url":"https://api.github.com/users/StefanoLonardi/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2016-07-30T02:02:40Z","updated_at":"2016-07-30T03:33:42Z","closed_at":null,"body":"I have been trying to run ABruijn but I get an error related to BLASR.\r\n\r\n```\r\n(myenv) stelo@H4:~/ABruijn$ ./abruijn.py reads.fa out_dir 50\r\n[17:57:56] INFO: Running ABruijn\r\n[17:57:56] INFO: Assembling reads\r\n[17:58:13] INFO: Counting kmers (1/2):\r\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%\r\n[17:58:27] INFO: Counting kmers (2/2):\r\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%\r\n[17:59:04] INFO: Building kmer index\r\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%\r\n[18:00:09] INFO: Finding overlaps:\r\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%\r\n[18:04:25] INFO: Extending reads\r\n[18:04:26] INFO: Assembled 1 contigs\r\n[18:04:26] INFO: Generating contig sequences\r\n[18:07:59] INFO: Polishing genome (1/2)\r\n[18:07:59] INFO: Running BLASR\r\n   Options for blasr\r\n   Basic usage: 'blasr reads.{bam|fasta|bax.h5|fofn} genome.fasta [-options]\r\n option\tDescription (default_value).\r\n[... LISTS OF ALL BLASR PARAMETERS ...]\r\nIn release v5.1 of BLASR, command-line options will use the\r\nsingle dash/double dash convention:\r\nCharacter options are preceded by a single dash. (Example: -v)\r\nWord options are preceded by a double dash. (Example: --verbose)\r\nPlease modify your scripts accordingly when BLASR v5.1 is released.\r\n\r\nTo cite BLASR, please use: Chaisson M.J., and Tesler G., Mapping\r\nsingle molecule sequencing reads using Basic Local Alignment with\r\nSuccessive Refinement (BLASR): Theory and Application, BMC\r\nBioinformatics 2012, 13:238.\r\nPlease report any bugs to 'https://github.com/PacificBiosciences/blasr/issues'.\r\n\r\nERROR: -bestn is not a valid option.\r\n[18:07:59] ERROR: While running blasr: Command '['blasr', 'reads.fa', '/24-2/home/stelo/ABruijn/out_dir/blasr_ref_1.fasta', '-bestn', '1', '-minMatch', '15', '-maxMatch', '25', '-m', '5', '-nproc', '1', '-out', '/24-2/home/stelo/ABruijn/out_dir/blasr_1.m5']' returned non-zero exit status 1\r\n[18:07:59] ERROR: Error: Error in alignment module, exiting\r\n```\r\n\r\nIt seems that options now need the double dash.\r\n\r\n My version of BLASR is\r\n\r\n```\r\n(myenv) stelo@H4:~/ABruijn$ blasr --version\r\nblasr\t5.2.def62de\r\n```\r\n"},"comment":{"url":"https://api.github.com/repos/fenderglass/ABruijn/issues/comments/236338341","html_url":"https://github.com/fenderglass/ABruijn/issues/3#issuecomment-236338341","issue_url":"https://api.github.com/repos/fenderglass/ABruijn/issues/3","id":236338341,"user":{"login":"fenderglass","id":2475380,"avatar_url":"https://avatars.githubusercontent.com/u/2475380?v=3","gravatar_id":"","url":"https://api.github.com/users/fenderglass","html_url":"https://github.com/fenderglass","followers_url":"https://api.github.com/users/fenderglass/followers","following_url":"https://api.github.com/users/fenderglass/following{/other_user}","gists_url":"https://api.github.com/users/fenderglass/gists{/gist_id}","starred_url":"https://api.github.com/users/fenderglass/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/fenderglass/subscriptions","organizations_url":"https://api.github.com/users/fenderglass/orgs","repos_url":"https://api.github.com/users/fenderglass/repos","events_url":"https://api.github.com/users/fenderglass/events{/privacy}","received_events_url":"https://api.github.com/users/fenderglass/received_events","type":"User","site_admin":false},"created_at":"2016-07-30T03:33:42Z","updated_at":"2016-07-30T03:33:42Z","body":"It should be fixed now, please try the latest master branch."}}
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