{"action":"created","issue":{"url":"https://api.github.com/repos/BioInf-Wuerzburg/proovread/issues/25","labels_url":"https://api.github.com/repos/BioInf-Wuerzburg/proovread/issues/25/labels{/name}","comments_url":"https://api.github.com/repos/BioInf-Wuerzburg/proovread/issues/25/comments","events_url":"https://api.github.com/repos/BioInf-Wuerzburg/proovread/issues/25/events","html_url":"https://github.com/BioInf-Wuerzburg/proovread/issues/25","id":114864350,"number":25,"title":"Incompatibility with new SeqFilter comand line","user":{"login":"marcelauliano","id":4116164,"avatar_url":"https://avatars.githubusercontent.com/u/4116164?v=3","gravatar_id":"","url":"https://api.github.com/users/marcelauliano","html_url":"https://github.com/marcelauliano","followers_url":"https://api.github.com/users/marcelauliano/followers","following_url":"https://api.github.com/users/marcelauliano/following{/other_user}","gists_url":"https://api.github.com/users/marcelauliano/gists{/gist_id}","starred_url":"https://api.github.com/users/marcelauliano/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/marcelauliano/subscriptions","organizations_url":"https://api.github.com/users/marcelauliano/orgs","repos_url":"https://api.github.com/users/marcelauliano/repos","events_url":"https://api.github.com/users/marcelauliano/events{/privacy}","received_events_url":"https://api.github.com/users/marcelauliano/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-11-03T17:14:04Z","updated_at":"2015-11-20T10:43:04Z","closed_at":"2015-11-12T06:58:24Z","body":"Hey guys, I've just downloaded proovread and have installed all the dependencies, but still I'm getting an error message.\r\n\r\ncommand line: ./proovread --sample --pre pr-sample --overwrite --cfg proovread.cfg\r\n\r\nError log:\r\n[Tue Nov  3 17:56:09 2015] Checking short read files\r\n  \r\nF.antasticus_short.fq\r\n  Detected FASTQ format\r\n  Estimated short read length: 100 +-0\r\n  Estimating approximate number of short reads: 50.0k\r\n\r\n[Tue Nov  3 17:56:10 2015] Checking required binaries\r\n\r\n  [ok] samtools-1.2    /data/scratch/muliano/scripts/samtools-1.2\r\n  [ok] bwa-proovread   /data/scratch/muliano/scripts/proovread-master/bin/../ut\\\r\nil/bwa\r\n  [ok] blastn-2.2.29   /usr/bin\r\n\r\n[Tue Nov  3 17:56:10 2015] Running mode: sr\r\n[Tue Nov  3 17:56:10 2015] Preparing long reads\r\n#------------------------------------------------------------------------------#\r\nperl -I/data/scratch/muliano/scripts/proovread-master/bin/../lib/ /data/scratch\\\r\n/muliano/scripts/proovread-master/bin/SeqFilter --fasta --in pr-sample/read-lon\\\r\ng/pr-sample.fq --line-width 80 --lower-case --out pr-sample/read-long/pr-sample\\\r\n.masked.fa --phred-offset 33\r\nUnknown option: in\r\n#------------------------------------------------------------------------------#\r\n[Tue Nov  3 17:56:10 2015] Read IDs don't look like proper PacBio subread IDs.\r\nFalling back to running mode: sr-noccs\r\n\r\n[Tue Nov  3 17:56:10 2015] Running task bwa-sr-1\r\n[Tue Nov  3 17:56:10 2015] Indexing Long reads\r\n#------------------------------------------------------------------------------#\r\n/data/scratch/muliano/scripts/proovread-master/bin/../util/bwa/bwa-proovread in\\\r\ndex pr-sample/read-long/pr-sample.masked.fa pr-sample/read-long/pr-sample.maske\\\r\nd.fa 2>pr-sample/bwa-sr-1/pr-sample_bwa.log\r\n#------------------------------------------------------------------------------#\r\n#------------------------------------------------------------------------------#\r\n  \r\n\tExited at 'main'\r\n\t'./proovread', line 1280\r\n\tLast call 'main::run_bwa'\r\n\t'./proovread', line 856\r\nEND\r\n\r\nI was checking the new SeqFilter and it does not have a parameter --in \r\n\r\nSounds to me the new SeqFilter version is not competible with proovread! Do you advice me on downloading an older one?\r\n\r\nThank you so much!"},"comment":{"url":"https://api.github.com/repos/BioInf-Wuerzburg/proovread/issues/comments/158353898","html_url":"https://github.com/BioInf-Wuerzburg/proovread/issues/25#issuecomment-158353898","issue_url":"https://api.github.com/repos/BioInf-Wuerzburg/proovread/issues/25","id":158353898,"user":{"login":"marcelauliano","id":4116164,"avatar_url":"https://avatars.githubusercontent.com/u/4116164?v=3","gravatar_id":"","url":"https://api.github.com/users/marcelauliano","html_url":"https://github.com/marcelauliano","followers_url":"https://api.github.com/users/marcelauliano/followers","following_url":"https://api.github.com/users/marcelauliano/following{/other_user}","gists_url":"https://api.github.com/users/marcelauliano/gists{/gist_id}","starred_url":"https://api.github.com/users/marcelauliano/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/marcelauliano/subscriptions","organizations_url":"https://api.github.com/users/marcelauliano/orgs","repos_url":"https://api.github.com/users/marcelauliano/repos","events_url":"https://api.github.com/users/marcelauliano/events{/privacy}","received_events_url":"https://api.github.com/users/marcelauliano/received_events","type":"User","site_admin":false},"created_at":"2015-11-20T10:43:04Z","updated_at":"2015-11-20T10:43:04Z","body":"Thanks thackl! I manage to get it working! Sorry for not answering sooner! "}}