{"action":"created","issue":{"url":"https://api.github.com/repos/institut-de-genomique/NaS/issues/3","repository_url":"https://api.github.com/repos/institut-de-genomique/NaS","labels_url":"https://api.github.com/repos/institut-de-genomique/NaS/issues/3/labels{/name}","comments_url":"https://api.github.com/repos/institut-de-genomique/NaS/issues/3/comments","events_url":"https://api.github.com/repos/institut-de-genomique/NaS/issues/3/events","html_url":"https://github.com/institut-de-genomique/NaS/issues/3","id":139214240,"number":3,"title":"fatal division by zero error","user":{"login":"PhilipStev","id":15832525,"avatar_url":"https://avatars.githubusercontent.com/u/15832525?v=3","gravatar_id":"","url":"https://api.github.com/users/PhilipStev","html_url":"https://github.com/PhilipStev","followers_url":"https://api.github.com/users/PhilipStev/followers","following_url":"https://api.github.com/users/PhilipStev/following{/other_user}","gists_url":"https://api.github.com/users/PhilipStev/gists{/gist_id}","starred_url":"https://api.github.com/users/PhilipStev/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/PhilipStev/subscriptions","organizations_url":"https://api.github.com/users/PhilipStev/orgs","repos_url":"https://api.github.com/users/PhilipStev/repos","events_url":"https://api.github.com/users/PhilipStev/events{/privacy}","received_events_url":"https://api.github.com/users/PhilipStev/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":16,"created_at":"2016-03-08T08:45:39Z","updated_at":"2016-03-29T08:09:25Z","closed_at":null,"body":"Hi,\r\n\r\nI am trying to use NaS to correct nanopore reads. However, after some runtime (~5 days) it ends/crashes with some error warnings:\r\n\r\n```\r\n[Tue Mar  1 10:15:33 CET 2016] Create output directory : /OxNano_Sequencing_ProjectsSX2_Neo5/SX2_2D_NaS_corrected\r\n[Tue Mar  1 10:15:33 CET 2016] Create fasta file from fastq...\r\n[Tue Mar  1 10:18:09 CET 2016] Alignement step in sensitive mode...\r\n[Tue Mar  1 11:28:24 CET 2016] Convert maf file to psl file...\r\n[Tue Mar  1 13:51:32 CET 2016] Select reads...\r\n[Tue Mar  1 16:23:54 CET 2016] Retrieve similar reads...\r\n[Sun Mar  6 15:44:38 CET 2016] Generate NaS reads...\r\n[Sun Mar  6 15:44:40 CET 2016] Untangle complex NaS reads...\r\ncat: OxNano_Sequencing_Projects/SX2_Neo5/SX2_2D_NaS_corrected/assemblies/*/NaS_hqctg_reads_final.fa: No such file or directory\r\n[Sun Mar  6 15:44:40 CET 2016] Generate statistics...\r\ncat: write error: Input/output error\r\nrm: write error: Input/output error\r\nawk: cmd. line:1: (FILENAME=- FNR=1) fatal: division by zero attempted\r\nawk: cmd. line:1: fatal: division by zero attempted\r\ngawk: cmd. line:1: fatal: division by zero attempted\r\nNbReads=    CumulativeSize=    N50size=    minSize=    maxSize=    avgSize=    =>  /OxNano_Sequencing_Projects/SX2_Neo5/SX2_2D_NaS_corrected/NANO_reads.stats\r\nNbReads=    CumulativeSize=    N50size=    minSize=    maxSize=    avgSize=    =>  /OxNano_Sequencing_Projects/CNAPS_SX2_Neo5/SX2_2D_NaS_corrected/NaS_hqctg_reads.stats\r\n[Sun Mar  6 15:44:41 CET 2016] Temporary files are not deleted because errors occurs...\r\n[Sun Mar  6 15:44:41 CET 2016] Total execution time with 8 core(s) : [05:29:08]\r\n\r\n```\r\nIs it the case that if this happens NaS is not able to actually perfrom an assembly of the nanopore reads and therefore can not correct them properly? \r\n\r\nThe OS is Fedora 22.\r\n\r\nThanks,\r\n\r\nPhil\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/institut-de-genomique/NaS/issues/comments/202772006","html_url":"https://github.com/institut-de-genomique/NaS/issues/3#issuecomment-202772006","issue_url":"https://api.github.com/repos/institut-de-genomique/NaS/issues/3","id":202772006,"user":{"login":"PhilipStev","id":15832525,"avatar_url":"https://avatars.githubusercontent.com/u/15832525?v=3","gravatar_id":"","url":"https://api.github.com/users/PhilipStev","html_url":"https://github.com/PhilipStev","followers_url":"https://api.github.com/users/PhilipStev/followers","following_url":"https://api.github.com/users/PhilipStev/following{/other_user}","gists_url":"https://api.github.com/users/PhilipStev/gists{/gist_id}","starred_url":"https://api.github.com/users/PhilipStev/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/PhilipStev/subscriptions","organizations_url":"https://api.github.com/users/PhilipStev/orgs","repos_url":"https://api.github.com/users/PhilipStev/repos","events_url":"https://api.github.com/users/PhilipStev/events{/privacy}","received_events_url":"https://api.github.com/users/PhilipStev/received_events","type":"User","site_admin":false},"created_at":"2016-03-29T08:09:25Z","updated_at":"2016-03-29T08:09:25Z","body":"Hi,\r\n\r\nafter updating my version of NaS and running the following command:\r\n\r\n`NaS --fq1 kamo_65_R1_AQ20_NaS_compatible.fastq --fq2 kamo_65_R2_AQ20_NaS_compatible.fastq --nano ./F1_d21_2DMetrichor_2DComplete.fasta --ilmn_size 150 --mode sensitive --nb_proc 10 --out ./NaS_corrected --t 2 --k 30`\r\n\r\nNaS run smoothly up to the stage of \"retrieving similar reads\" it stuck there for a good week. Filled up quite some HDD storage (10s to 20s of TB) and then failed cause of the disk going down.\r\n\r\nAny idea why it would fill up so much space??\r\n\r\nThanks!"}}