{"action":"created","issue":{"url":"https://api.github.com/repos/ruping/TRUP/issues/3","labels_url":"https://api.github.com/repos/ruping/TRUP/issues/3/labels{/name}","comments_url":"https://api.github.com/repos/ruping/TRUP/issues/3/comments","events_url":"https://api.github.com/repos/ruping/TRUP/issues/3/events","html_url":"https://github.com/ruping/TRUP/issues/3","id":97545221,"number":3,"title":"Issue with fusion detection","user":{"login":"chetanya","id":4974563,"avatar_url":"https://avatars.githubusercontent.com/u/4974563?v=3","gravatar_id":"","url":"https://api.github.com/users/chetanya","html_url":"https://github.com/chetanya","followers_url":"https://api.github.com/users/chetanya/followers","following_url":"https://api.github.com/users/chetanya/following{/other_user}","gists_url":"https://api.github.com/users/chetanya/gists{/gist_id}","starred_url":"https://api.github.com/users/chetanya/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/chetanya/subscriptions","organizations_url":"https://api.github.com/users/chetanya/orgs","repos_url":"https://api.github.com/users/chetanya/repos","events_url":"https://api.github.com/users/chetanya/events{/privacy}","received_events_url":"https://api.github.com/users/chetanya/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":4,"created_at":"2015-07-27T20:12:39Z","updated_at":"2015-08-03T14:35:09Z","closed_at":null,"body":"Hi,\r\n\r\nI would like to use TRUP to detect chimeric fusions in my RNA-Seq datasets. Unfortunately, I keep running into the following issue:\r\n\r\n\r\n# RTrace.pl --runlevel 4 --sampleName sample --seqType p --readpool /sc/orga/scratch/pandyc01/TRUP/Data --root /sc/orga/scratch/pandyc01/TRUP --threads 4 --anno /sc/orga/projects/PBG/REFERENCES/hg19/TRUP/hg19\r\n\r\n[2015/6/26 11:1:13]\t####### lane name is set to sample #######\r\n\r\nlanefile:\t/sc/orga/scratch/pandyc01/TRUP/Data/sample_R1.fq.gz\r\nlanefile:\t/sc/orga/scratch/pandyc01/TRUP/Data/sample_R2.fq.gz\r\n\r\n[2015/6/26 11:1:13]\t####### preparing directories #######\r\n\r\nread length and trimed length are not set, will take the original read length (100 bp) for both (no trimming).\r\n\r\n[2015/6/26 11:1:13]\t####### insert mean and sd calculation #######\r\n\r\nqual_min: 2; qual_max: 41; qual_zero: 35; qual_shift: -2.\r\nError in setwd(path) : cannot change working directory\r\nExecution halted\r\nUse of uninitialized value $number in int at /hpc/packages/minerva-common/trup/0.1/TRUP/bin/RTrace.pl line 2064.\r\nUse of uninitialized value $number in numeric ge (>=) at /hpc/packages/minerva-common/trup/0.1/TRUP/bin/RTrace.pl line 2065.\r\nUse of uninitialized value $insert_sd in substitution (s///) at /hpc/packages/minerva-common/trup/0.1/TRUP/bin/RTrace.pl line 525.\r\nUse of uninitialized value $number in int at /hpc/packages/minerva-common/trup/0.1/TRUP/bin/RTrace.pl line 2064.\r\nUse of uninitialized value $number in numeric ge (>=) at /hpc/packages/minerva-common/trup/0.1/TRUP/bin/RTrace.pl line 2065.\r\ninsert mean: -200\tinsert_sd: 0\r\ntwo mates is overlapping too much, please trim more. "},"comment":{"url":"https://api.github.com/repos/ruping/TRUP/issues/comments/127262763","html_url":"https://github.com/ruping/TRUP/issues/3#issuecomment-127262763","issue_url":"https://api.github.com/repos/ruping/TRUP/issues/3","id":127262763,"user":{"login":"chetanya","id":4974563,"avatar_url":"https://avatars.githubusercontent.com/u/4974563?v=3","gravatar_id":"","url":"https://api.github.com/users/chetanya","html_url":"https://github.com/chetanya","followers_url":"https://api.github.com/users/chetanya/followers","following_url":"https://api.github.com/users/chetanya/following{/other_user}","gists_url":"https://api.github.com/users/chetanya/gists{/gist_id}","starred_url":"https://api.github.com/users/chetanya/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/chetanya/subscriptions","organizations_url":"https://api.github.com/users/chetanya/orgs","repos_url":"https://api.github.com/users/chetanya/repos","events_url":"https://api.github.com/users/chetanya/events{/privacy}","received_events_url":"https://api.github.com/users/chetanya/received_events","type":"User","site_admin":false},"created_at":"2015-08-03T14:35:09Z","updated_at":"2015-08-03T14:35:09Z","body":"Hi Ruping,\r\n\r\nYou can access the files here:\r\nhttps://drive.google.com/file/d/0B8cD1iIefQ6Bc2V1SVJkbjhrOTA/view?usp=sharing\r\nhttps://drive.google.com/file/d/0B8cD1iIefQ6BenE0Y084VVBXRVU/view?usp=sharing\r\n\r\nThe commands I'm running:\r\ncd /sc/orga/scratch/pandyc01/TRUP\r\n\r\nRTrace.pl --runlevel 1 --sampleName sample --seqType p --readpool /sc/orga/scratch/pandyc01/TRUP/Data --root /sc/orga/scratch/pandyc01/TRUP --threads 4 --anno /sc/orga/projects/PBG/REFERENCES/hg19/TRUP/hg19 --QC\r\n\r\nRTrace.pl --runlevel 4 --sampleName sample --seqType p --readpool /sc/orga/scratch/pandyc01/TRUP/Data --root /sc/orga/scratch/pandyc01/TRUP --threads 4 --anno /sc/orga/projects/PBG/REFERENCES/hg19/TRUP/hg19 --RA 1\r\n\r\nLook forward to hearing from you.\r\n\r\nBest,\r\nChetanya\r\n\r\n"}}