{"action":"opened","issue":{"url":"https://api.github.com/repos/sreeramkannan/Shannon/issues/5","repository_url":"https://api.github.com/repos/sreeramkannan/Shannon","labels_url":"https://api.github.com/repos/sreeramkannan/Shannon/issues/5/labels{/name}","comments_url":"https://api.github.com/repos/sreeramkannan/Shannon/issues/5/comments","events_url":"https://api.github.com/repos/sreeramkannan/Shannon/issues/5/events","html_url":"https://github.com/sreeramkannan/Shannon/issues/5","id":132945297,"number":5,"title":"Error: sh: 1: -ufactor=1000: not found","user":{"login":"macmanes","id":164752,"avatar_url":"https://avatars.githubusercontent.com/u/164752?v=3","gravatar_id":"","url":"https://api.github.com/users/macmanes","html_url":"https://github.com/macmanes","followers_url":"https://api.github.com/users/macmanes/followers","following_url":"https://api.github.com/users/macmanes/following{/other_user}","gists_url":"https://api.github.com/users/macmanes/gists{/gist_id}","starred_url":"https://api.github.com/users/macmanes/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/macmanes/subscriptions","organizations_url":"https://api.github.com/users/macmanes/orgs","repos_url":"https://api.github.com/users/macmanes/repos","events_url":"https://api.github.com/users/macmanes/events{/privacy}","received_events_url":"https://api.github.com/users/macmanes/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2016-02-11T11:14:18Z","updated_at":"2016-02-11T11:14:18Z","closed_at":null,"body":"Run command:\r\n\r\n```\r\npython /share/shannon/shannon.py -k25 -p 60 \\\r\n-o /mnt/data3/macmanes/error/shannon/shannon20Mk25 \\\r\n--left $RAID/error/rcorr20M/20.subsamp_1.cor.fq \\\r\n--right $RAID/error/rcorr20M/20.subsamp_2.cor.fq\r\n```\r\n\r\nThis is strange, because the 1st `gpmetis` command worked, but not the second.. This package is def. in my $PATH as well:\r\n\r\n```\r\n$which gpmetis\r\n/usr/bin/gpmetis\r\n```\r\n\r\nthe stdout, with error:\r\n\r\n```\r\n--------------------------------------------\r\nShannon: RNA Seq de novo Assembly\r\n--------------------------------------------\r\nChecking the various dependencies\r\n--------------------------------------------\r\nUsing jellyfish in /share/quorum/bin/jellyfish\r\nUsing GPMETIS in /usr/bin/gpmetis\r\n--------------------------------------------\r\nWed Feb 10 09:08:22 2016: Starting Shannon run..\r\nUsing Quorum in /share/quorum/bin/quorum\r\nUsing GNU Parallel in /usr/bin/parallel\r\nWed Feb 10 09:08:22 2016: Running Quorum for read error correction with quality scores..\r\nWed Feb 10 09:31:28 2016: Starting Jellyfish to extract Kmers from Reads..\r\nWed Feb 10 09:32:49 2016: Jellyfish finished..\r\nWed Feb 10 09:32:49 2016: Starting Kmer error correction..\r\nWed Feb 10 09:33:28 2016: Loading, processed 1000000\r\n...\r\nWed Feb 10 11:41:25 2016: Correction, processed 137000000\r\nWed Feb 10 11:42:49 2016: 137863768 K-mers remaining after error correction.\r\nWed Feb 10 12:08:49 2016: Creating Kmers from (K+1)-mers..\r\nWed Feb 10 12:14:49 2016: 137863768 K+1-mers loaded.\r\nWed Feb 10 12:20:27 2016: 137812539 K-mers produced.\r\ngpmetis -ufactor=1000 /mnt/data3/macmanes/error/shannon/shannon20Mk25/component1.txt 100\r\n******************************************************************************\r\nMETIS 5.0 Copyright 1998-13, Regents of the University of Minnesota\r\n (HEAD: , Built on: Jul 20 2013, 23:18:43)\r\n size of idx_t: 32bits, real_t: 32bits, idx_t *: 64bits\r\n\r\nGraph Information -----------------------------------------------------------\r\n Name: /mnt/data3/macmanes/error/shannon/shannon20Mk25/component1.txt, #Vertices: 308394, #Edges: 573390, #Parts: 100\r\n\r\nOptions ---------------------------------------------------------------------\r\n ptype=kway, objtype=cut, ctype=shem, rtype=greedy, iptype=metisrb\r\n dbglvl=0, ufactor=2.000, no2hop=NO, minconn=NO, contig=NO, nooutput=NO\r\n seed=-1, niter=10, ncuts=1\r\n\r\nDirect k-way Partitioning ---------------------------------------------------\r\n - Edgecut: 105916, communication volume: 148626.\r\n\r\n - Balance:\r\n     constraint #0:  2.000 out of 0.000\r\n\r\n - Most overweight partition:\r\n     pid: 17, actual: 6168, desired: 3083, ratio: 2.00.\r\n\r\n - Subdomain connectivity: max: 99, min: 52, avg: 86.80\r\n\r\n - There are 96 non-contiguous partitions.\r\n   Total components after removing the cut edges: 660,\r\n   max components: 30 for pid: 47.\r\n\r\nTiming Information ----------------------------------------------------------\r\n  I/O:                             0.153 sec\r\n  Partitioning:                    1.130 sec   (METIS time)\r\n  Reporting:                       0.083 sec\r\n\r\nMemory Information ----------------------------------------------------------\r\n  Max memory used:                39.662 MB\r\n******************************************************************************\r\nWed Feb 10 12:49:27 2016: gpmetis for partitioning 1 is complete -- Component 0: 100 partitions,\r\nr\r\nWed Feb 10 12:57:41 2016: k1mers2component dictionary created\r\nWed Feb 10 13:31:13 2016: reads partititoned\r\n...\r\nWed Feb 10 14:30:44 2016: k1mer Streaming, processed 137000000\r\nWed Feb 10 14:31:06 2016: k1mers weights stored in dictionary\r\nWed Feb 10 14:36:22 2016: k1mers written to file\r\nWed Feb 10 14:44:35 2016: kmers2component dictionary created\r\nWed Feb 10 14:44:58 2016: kmer Streaming, processed 1000000\r\n...\r\nWed Feb 10 15:38:07 2016: kmer Streaming, processed 137000000\r\nWed Feb 10 15:38:26 2016: kmers weights stored in dictionary\r\nWed Feb 10 15:43:05 2016: kmers written to file\r\n -ufactor=1000 /mnt/data3/macmanes/error/shannon/shannon20Mk25/component1r2.txt 100\r\nsh: 1: -ufactor=1000: not found\r\nWed Feb 10 15:44:22 2016: gpmetis for partitioning 2 is complete -- Component 0: 100 partitions,\r\nTraceback (most recent call last):\r\n  File \"/share/shannon/shannon.py\", line 317, in <module>\r\n    [r2_components_broken, r2_new_components] = kmers_for_component(kmer_directory, reads_files, base_directory_name, r1_contig_file_extension, r2_new_kmer_tag, r2_graph_file_extens\r\nion, get_og_comp_kmers, get_partition_kmers, double_stranded, paired_end, True, partition_size, overload, K)\r\n  File \"/share/shannon/kmers_for_component.py\", line 96, in kmers_for_component\r\n    with open(directory_name+\"/component\" + str(i+1) + graph_file_extension + \".part.\" + str(components_broken[i]) , 'r') as f_component:\r\nIOError: [Errno 2] No such file or directory: '/mnt/data3/macmanes/error/shannon/shannon20Mk25/component1r2.txt.part.100'"}}