{"action":"created","issue":{"url":"https://api.github.com/repos/MikeAxtell/ShortStack/issues/42","repository_url":"https://api.github.com/repos/MikeAxtell/ShortStack","labels_url":"https://api.github.com/repos/MikeAxtell/ShortStack/issues/42/labels{/name}","comments_url":"https://api.github.com/repos/MikeAxtell/ShortStack/issues/42/comments","events_url":"https://api.github.com/repos/MikeAxtell/ShortStack/issues/42/events","html_url":"https://github.com/MikeAxtell/ShortStack/issues/42","id":172725672,"number":42,"title":"A bug when parsing file names?","user":{"login":"naumenko-sa","id":13981803,"avatar_url":"https://avatars.githubusercontent.com/u/13981803?v=3","gravatar_id":"","url":"https://api.github.com/users/naumenko-sa","html_url":"https://github.com/naumenko-sa","followers_url":"https://api.github.com/users/naumenko-sa/followers","following_url":"https://api.github.com/users/naumenko-sa/following{/other_user}","gists_url":"https://api.github.com/users/naumenko-sa/gists{/gist_id}","starred_url":"https://api.github.com/users/naumenko-sa/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/naumenko-sa/subscriptions","organizations_url":"https://api.github.com/users/naumenko-sa/orgs","repos_url":"https://api.github.com/users/naumenko-sa/repos","events_url":"https://api.github.com/users/naumenko-sa/events{/privacy}","received_events_url":"https://api.github.com/users/naumenko-sa/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/MikeAxtell/ShortStack/labels/bug","name":"bug","color":"fc2929"}],"state":"closed","locked":false,"assignee":{"login":"MikeAxtell","id":6854537,"avatar_url":"https://avatars.githubusercontent.com/u/6854537?v=3","gravatar_id":"","url":"https://api.github.com/users/MikeAxtell","html_url":"https://github.com/MikeAxtell","followers_url":"https://api.github.com/users/MikeAxtell/followers","following_url":"https://api.github.com/users/MikeAxtell/following{/other_user}","gists_url":"https://api.github.com/users/MikeAxtell/gists{/gist_id}","starred_url":"https://api.github.com/users/MikeAxtell/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/MikeAxtell/subscriptions","organizations_url":"https://api.github.com/users/MikeAxtell/orgs","repos_url":"https://api.github.com/users/MikeAxtell/repos","events_url":"https://api.github.com/users/MikeAxtell/events{/privacy}","received_events_url":"https://api.github.com/users/MikeAxtell/received_events","type":"User","site_admin":false},"assignees":[{"login":"MikeAxtell","id":6854537,"avatar_url":"https://avatars.githubusercontent.com/u/6854537?v=3","gravatar_id":"","url":"https://api.github.com/users/MikeAxtell","html_url":"https://github.com/MikeAxtell","followers_url":"https://api.github.com/users/MikeAxtell/followers","following_url":"https://api.github.com/users/MikeAxtell/following{/other_user}","gists_url":"https://api.github.com/users/MikeAxtell/gists{/gist_id}","starred_url":"https://api.github.com/users/MikeAxtell/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/MikeAxtell/subscriptions","organizations_url":"https://api.github.com/users/MikeAxtell/orgs","repos_url":"https://api.github.com/users/MikeAxtell/repos","events_url":"https://api.github.com/users/MikeAxtell/events{/privacy}","received_events_url":"https://api.github.com/users/MikeAxtell/received_events","type":"User","site_admin":false}],"milestone":null,"comments":5,"created_at":"2016-08-23T15:10:03Z","updated_at":"2016-10-14T16:16:46Z","closed_at":"2016-10-14T16:16:46Z","body":"Hi Mike,\r\nthank you for the excellent tool!\r\n\r\nI'm running it with \r\n```\r\n~/tools/ShortStack/ShortStack --readfile R4215_R1.fastq.gz \\\r\n                              --genome /home/naumenko/work/tools/bcbio/genomes/stuberosum/soltub3/seq/soltub3.fa \\\r\n                              --adapter=TGGAATTCTCGGGTGC \\\r\n                              --bowtie_cores 20 \\\r\n                              --outdir R4215_R1.fastq.gz_output \\\r\n                              --sort_mem 10G\r\n```\r\nIt seems that there is a problem parsing the file name R4215_R1.fastq.gz,\r\nit stops on the mapping step.\r\n\r\nFrom the ErrorLogs.txt I see \r\n```\r\nWrote 194428459 bytes to primary EBWT file: R4215_R1.fastq.gz_output/soltub3_stitched.rev.1.ebwt\r\nWrote 82911232 bytes to secondary EBWT file: R4215_R1.fastq.gz_output/soltub3_stitched.rev.2.ebwt\r\n...\r\nCould not locate a Bowtie index corresponding to basename \"R4215_R1stq.gz_output/soltub3_stitched\"\r\nCommand: bowtie --wrapper basic-0 -q -v 1 -p 20 -S -a -m 50 --best --strata --sam-RG ID:R4215_R1_trimmed R4215_R1stq.gz_output/soltub3_stitched -\r\n```\r\n\r\nIt creates indices with filename R4215_R1.fastq.gz_output/soltub3_stitched.rev.1.ebwt,\r\nand then tries to map with R4215_R1stq.gz_output/soltub3_stitched.\r\n\r\nIn the result the mappings are empty.\r\n\r\nCould you please fix it?\r\nThanks.\r\nSN\r\n\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/MikeAxtell/ShortStack/issues/comments/253848843","html_url":"https://github.com/MikeAxtell/ShortStack/issues/42#issuecomment-253848843","issue_url":"https://api.github.com/repos/MikeAxtell/ShortStack/issues/42","id":253848843,"user":{"login":"MikeAxtell","id":6854537,"avatar_url":"https://avatars.githubusercontent.com/u/6854537?v=3","gravatar_id":"","url":"https://api.github.com/users/MikeAxtell","html_url":"https://github.com/MikeAxtell","followers_url":"https://api.github.com/users/MikeAxtell/followers","following_url":"https://api.github.com/users/MikeAxtell/following{/other_user}","gists_url":"https://api.github.com/users/MikeAxtell/gists{/gist_id}","starred_url":"https://api.github.com/users/MikeAxtell/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/MikeAxtell/subscriptions","organizations_url":"https://api.github.com/users/MikeAxtell/orgs","repos_url":"https://api.github.com/users/MikeAxtell/repos","events_url":"https://api.github.com/users/MikeAxtell/events{/privacy}","received_events_url":"https://api.github.com/users/MikeAxtell/received_events","type":"User","site_admin":false},"created_at":"2016-10-14T16:16:46Z","updated_at":"2016-10-14T16:16:46Z","body":"Thanks again for pointing this out. Version 3.5 fixes this issue."}}
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