{"action":"opened","issue":{"url":"https://api.github.com/repos/morispi/HG-CoLoR/issues/7","repository_url":"https://api.github.com/repos/morispi/HG-CoLoR","labels_url":"https://api.github.com/repos/morispi/HG-CoLoR/issues/7/labels{/name}","comments_url":"https://api.github.com/repos/morispi/HG-CoLoR/issues/7/comments","events_url":"https://api.github.com/repos/morispi/HG-CoLoR/issues/7/events","html_url":"https://github.com/morispi/HG-CoLoR/issues/7","id":381896837,"node_id":"MDU6SXNzdWUzODE4OTY4Mzc=","number":7,"title":"Error","user":{"login":"pjmaughan43","id":18358997,"node_id":"MDQ6VXNlcjE4MzU4OTk3","avatar_url":"https://avatars0.githubusercontent.com/u/18358997?v=4","gravatar_id":"","url":"https://api.github.com/users/pjmaughan43","html_url":"https://github.com/pjmaughan43","followers_url":"https://api.github.com/users/pjmaughan43/followers","following_url":"https://api.github.com/users/pjmaughan43/following{/other_user}","gists_url":"https://api.github.com/users/pjmaughan43/gists{/gist_id}","starred_url":"https://api.github.com/users/pjmaughan43/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pjmaughan43/subscriptions","organizations_url":"https://api.github.com/users/pjmaughan43/orgs","repos_url":"https://api.github.com/users/pjmaughan43/repos","events_url":"https://api.github.com/users/pjmaughan43/events{/privacy}","received_events_url":"https://api.github.com/users/pjmaughan43/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-11-17T20:10:30Z","updated_at":"2018-11-17T20:10:30Z","closed_at":null,"author_association":"NONE","body":"I'm using the anaconda installation of HG-CoLoR, but running into the following error and hoping you point me in the right direction. \r\n\r\nHere's the slurm output:\r\n[Fri Nov 16 15:45:54 MST 2018] Correcting the short reads\r\n[Fri Nov 16 18:28:37 MST 2018] Removing short reads containing weak k-mers\r\n[Fri Nov 16 20:52:45 MST 2018] Building the graph\r\n[Fri Nov 16 23:12:53 MST 2018] Aligning the short reads on the long reads\r\n[Fri Nov 16 23:18:18 MST 2018] Removing short alignments\r\nTraceback (most recent call last):\r\n  File \"/fslgroup/fslg_pws_module/compute/software/.conda/envs/hg-color_v1.0.0/bin/filterOutShortAlignments.py\", line 36, in <module>\r\n    out.write(finalString)\r\nNameError: name 'out' is not defined\r\n[Fri Nov 16 23:18:18 MST 2018] Generating the corrected long reads\r\n[Fri Nov 16 23:18:19 MST 2018] Removing temporary files\r\n[Fri Nov 16 23:19:11 MST 2018] Exiting\r\n\r\nHere is the HG-CoLoR.stdout:\r\n\r\n----- QuorUM -----\r\n----- revseq -----\r\n----- KMC -----\r\n1st stage: 174.623s\r\n2nd stage: 942.759s\r\nTotal    : 1117.38s\r\nTmp size : 81150MB\r\n\r\nStats:\r\n   No. of k-mers below min. threshold :    635141104\r\n   No. of k-mers above max. threshold :            0\r\n   No. of unique k-mers               :   2185558665\r\n   No. of unique counted k-mers       :   1550417561\r\n   Total no. of k-mers                :  87948736520\r\n   Total no. of reads                 :    542495294\r\n   Total no. of super-k-mers          :   3458687932\r\n----- KMC_tools -----\r\n----- KMC_dump -----\r\n----- PgSAgen_hgcolor -----\r\nReading reads set\r\nreads count: 1452761050\r\nall reads length: 92976707200\r\nreads length is constant\r\nmaxReadLength: 64\r\nsymbolsCount: 4\r\nsymbols: ACGT\r\n\r\nFound 0 duplicates.\r\nStart overlapping.\r\n6820830 reads left after 63 overlap\r\n6080059 reads left after 62 overlap\r\n5530567 reads left after 61 overlap\r\n5111566 reads left after 60 overlap\r\n4764051 reads left after 59 overlap\r\n4458165 reads left after 58 overlap\r\n4199852 reads left after 57 overlap\r\n3972326 reads left after 56 overlap\r\n3763990 reads left after 55 overlap\r\n3584244 reads left after 54 overlap\r\n3420892 reads left after 53 overlap\r\n3267275 reads left after 52 overlap\r\n3131134 reads left after 51 overlap\r\n3004685 reads left after 50 overlap\r\n2884016 reads left after 49 overlap\r\n2775758 reads left after 48 overlap\r\n2672523 reads left after 47 overlap\r\n2574105 reads left after 46 overlap\r\n2482159 reads left after 45 overlap\r\n2396981 reads left after 44 overlap\r\n2313961 reads left after 43 overlap\r\n2236406 reads left after 42 overlap\r\n2163594 reads left after 41 overlap\r\n2090936 reads left after 40 overlap\r\n2024386 reads left after 39 overlap\r\n1961520 reads left after 38 overlap\r\n1899004 reads left after 37 overlap\r\n1840888 reads left after 36 overlap\r\n1786350 reads left after 35 overlap\r\n1731747 reads left after 34 overlap\r\n1680180 reads left after 33 overlap\r\n1631172 reads left after 32 overlap\r\n1582092 reads left after 31 overlap\r\n1535704 reads left after 30 overlap\r\n1490125 reads left after 29 overlap\r\n1445786 reads left after 28 overlap\r\n1403406 reads left after 27 overlap\r\n1361982 reads left after 26 overlap\r\n1321812 reads left after 25 overlap\r\n1281887 reads left after 24 overlap\r\n1242301 reads left after 23 overlap\r\n1205276 reads left after 22 overlap\r\n1170604 reads left after 21 overlap\r\n1136651 reads left after 20 overlap\r\n1103473 reads left after 19 overlap\r\n1071540 reads left after 18 overlap\r\n1040447 reads left after 17 overlap\r\n1008606 reads left after 16 overlap\r\n975248 reads left after 15 overlap\r\n937730 reads left after 14 overlap\r\n889391 reads left after 13 overlap\r\n816493 reads left after 12 overlap\r\n701226 reads left after 11 overlap\r\n538223 reads left after 10 overlap\r\n372007 reads left after 9 overlap\r\n244437 reads left after 8 overlap\r\n159908 reads left after 7 overlap\r\n103350 reads left after 6 overlap\r\n66897 reads left after 5 overlap\r\n41576 reads left after 4 overlap\r\n28021 reads left after 3 overlap\r\n18225 reads left after 2 overlap\r\n14822 reads left after 1 overlap\r\n14822 pseudo-genome components\r\nOverlapping done in 954060 msec\r\n\r\n1579325618 bytes after overlapping\r\n14822 pseudo-genome components\r\n0 single reads\r\nPseudogenome assembled in 1193560 msec\r\n\r\nFound 62521749 reads containing duplicate 11-mers in 16510 msec!\r\nSA creation start.\r\nWritten 2147483644 bytes\r\nWritten 2147483644 bytes\r\nWritten 2022335952 bytes\r\nSAIS generation time 615460 msec!\r\nSA generation time 1112850 msec!\r\n4194305 elements in SA lookup\r\nSA LUT generation time 23110 msec!\r\nWritten 1579325682 bytes\r\nWritten 13074849459 bytes\r\nWritten 7896628100 bytes\r\nWritten 16777220 bytes\r\n\r\nThanks in advance.\r\n\r\n\r\n\r\n\r\n\r\n"}}
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