{"action":"created","issue":{"url":"https://api.github.com/repos/fenderglass/ABruijn/issues/2","repository_url":"https://api.github.com/repos/fenderglass/ABruijn","labels_url":"https://api.github.com/repos/fenderglass/ABruijn/issues/2/labels{/name}","comments_url":"https://api.github.com/repos/fenderglass/ABruijn/issues/2/comments","events_url":"https://api.github.com/repos/fenderglass/ABruijn/issues/2/events","html_url":"https://github.com/fenderglass/ABruijn/issues/2","id":159269403,"number":2,"title":"Getting started...","user":{"login":"JohnUrban","id":7783314,"avatar_url":"https://avatars.githubusercontent.com/u/7783314?v=3","gravatar_id":"","url":"https://api.github.com/users/JohnUrban","html_url":"https://github.com/JohnUrban","followers_url":"https://api.github.com/users/JohnUrban/followers","following_url":"https://api.github.com/users/JohnUrban/following{/other_user}","gists_url":"https://api.github.com/users/JohnUrban/gists{/gist_id}","starred_url":"https://api.github.com/users/JohnUrban/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/JohnUrban/subscriptions","organizations_url":"https://api.github.com/users/JohnUrban/orgs","repos_url":"https://api.github.com/users/JohnUrban/repos","events_url":"https://api.github.com/users/JohnUrban/events{/privacy}","received_events_url":"https://api.github.com/users/JohnUrban/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":32,"created_at":"2016-06-08T20:55:39Z","updated_at":"2016-07-05T03:17:48Z","closed_at":null,"body":"Hi,\r\n\r\nThis is an exciting tool - thanks for developing it. I am eager to get it up and running.\r\n\r\nI installed and tried a simple test with 37X coverage of simulated lambda reads. All are 15000 bp long and have no errors. I cannot seem to get abruijn.py to run.\r\n\r\nIf I try:\r\n```\r\nabruijn.py reads.fasta out 37\r\n```\r\nI get:\r\n```\r\n[16:52:16] INFO: Running ABruijn\r\n[16:52:16] INFO: Assembling reads\r\n[16:52:16] INFO: Indexing kmers (1/2):\r\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \r\n[16:52:21] INFO: Indexing kmers (2/2):\r\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \r\n[16:52:23] WARNING: Unable to choose minimum kmer count cutoff. Check if the coverage parameter is correct. Running with default parameter t = 4\r\n[16:52:23] INFO: Building read index\r\n[16:52:23] INFO: Finding overlaps:\r\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \r\n[16:52:41] INFO: Extending reads\r\n[16:52:41] INFO: Assembled 0 contigs\r\n[16:52:41] INFO: Generating contig sequences\r\n[16:52:41] INFO: Running Blasr\r\nERROR, Fail to load FASTA file /gpfs/scratch/jurban/male-ilmn/lambda/abruijn/out/draft_assembly.fasta to virtual memory.\r\n[16:52:41] ERROR: While running blasr: Command '['blasr', 'reads.fasta', '/gpfs/scratch/jurban/male-ilmn/lambda/abruijn/out/draft_assembly.fasta', '-bestn', '1', '-minMatch', '15', '-maxMatch', '25', '-m', '5', '-nproc', '1', '-out', '/gpfs/scratch/jurban/male-ilmn/lambda/abruijn/out/alignment.m5']' returned non-zero exit status 1\r\n[16:52:41] ERROR: Error: Error in alignment module, exiting\r\n```\r\nNote that ```draft_assembly.fasta ``` is an empty file.\r\n\r\nI saw the warning: ``` WARNING: Unable to choose minimum kmer count cutoff. Check if the coverage parameter is correct. Running with default parameter t = 4```\r\n\r\nSo I tried adding in a minimum cutoff instead of default auto, but when I add any arguments it gives another error:\r\n```\r\n$ abruijn.py reads.fasta out 37 -m 10\r\n[16:49:22] INFO: Running ABruijn\r\n[16:49:22] INFO: Assembling reads\r\nTraceback (most recent call last):\r\n  File \"/users/jurban/software/abruijn/ABruijn/abruijn.py\", line 35, in <module>\r\n    sys.exit(main())\r\n  File \"/gpfs_home/jurban/software/abruijn/ABruijn/abruijn/main.py\", line 102, in main\r\n    run(args)\r\n  File \"/gpfs_home/jurban/software/abruijn/ABruijn/abruijn/main.py\", line 41, in run\r\n    args.max_cov, args.coverage, args.debug, log_file)\r\n  File \"/gpfs_home/jurban/software/abruijn/ABruijn/abruijn/assemble.py\", line 48, in assemble\r\n    subprocess.check_call(cmdline)\r\n  File \"/gpfs/runtime/opt/python/2.7.3/lib/python2.7/subprocess.py\", line 506, in check_call\r\n    retcode = call(*popenargs, **kwargs)\r\n  File \"/gpfs/runtime/opt/python/2.7.3/lib/python2.7/subprocess.py\", line 493, in call\r\n    return Popen(*popenargs, **kwargs).wait()\r\n  File \"/gpfs/runtime/opt/python/2.7.3/lib/python2.7/subprocess.py\", line 679, in __init__\r\n    errread, errwrite)\r\n  File \"/gpfs/runtime/opt/python/2.7.3/lib/python2.7/subprocess.py\", line 1249, in _execute_child\r\n    raise child_exception\r\nTypeError: execv() arg 2 must contain only strings\r\n```\r\n\r\nAny advice to help me get up and running would be appreciated. \r\n\r\nbest,\r\n  John\r\n"},"comment":{"url":"https://api.github.com/repos/fenderglass/ABruijn/issues/comments/230379914","html_url":"https://github.com/fenderglass/ABruijn/issues/2#issuecomment-230379914","issue_url":"https://api.github.com/repos/fenderglass/ABruijn/issues/2","id":230379914,"user":{"login":"JohnUrban","id":7783314,"avatar_url":"https://avatars.githubusercontent.com/u/7783314?v=3","gravatar_id":"","url":"https://api.github.com/users/JohnUrban","html_url":"https://github.com/JohnUrban","followers_url":"https://api.github.com/users/JohnUrban/followers","following_url":"https://api.github.com/users/JohnUrban/following{/other_user}","gists_url":"https://api.github.com/users/JohnUrban/gists{/gist_id}","starred_url":"https://api.github.com/users/JohnUrban/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/JohnUrban/subscriptions","organizations_url":"https://api.github.com/users/JohnUrban/orgs","repos_url":"https://api.github.com/users/JohnUrban/repos","events_url":"https://api.github.com/users/JohnUrban/events{/privacy}","received_events_url":"https://api.github.com/users/JohnUrban/received_events","type":"User","site_admin":false},"created_at":"2016-07-05T03:17:48Z","updated_at":"2016-07-05T03:17:48Z","body":"```\r\n[06:49:13] INFO: Running ABruijn\r\n[06:49:13] INFO: Resuming previous run\r\n[06:52:16] INFO: Chosen 'pacbio' polishing profile\r\n[06:52:16] INFO: Separating draft genome into bubbles\r\n[13:34:38] INFO: Correcting bubbles\r\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \r\n[15:37:24] INFO: Done! Your assembly is in file: /gpfs/scratch/jurban/male-ilmn/abruijn/sciara/polished_1.fasta\r\n```\r\nwooooo!\r\n\r\nAmazing. Great program. Can't wait to take a look at the assembly. :)"}}
{"actor":{"display_login":"JohnUrban"}}