{"action":"created","issue":{"url":"https://api.github.com/repos/lpantano/mirdeep2_core/issues/2","repository_url":"https://api.github.com/repos/lpantano/mirdeep2_core","labels_url":"https://api.github.com/repos/lpantano/mirdeep2_core/issues/2/labels{/name}","comments_url":"https://api.github.com/repos/lpantano/mirdeep2_core/issues/2/comments","events_url":"https://api.github.com/repos/lpantano/mirdeep2_core/issues/2/events","html_url":"https://github.com/lpantano/mirdeep2_core/issues/2","id":201460690,"number":2,"title":"mirdeep2 - Unknown option: f","user":{"login":"miasteinberg","id":4191521,"avatar_url":"https://avatars.githubusercontent.com/u/4191521?v=3","gravatar_id":"","url":"https://api.github.com/users/miasteinberg","html_url":"https://github.com/miasteinberg","followers_url":"https://api.github.com/users/miasteinberg/followers","following_url":"https://api.github.com/users/miasteinberg/following{/other_user}","gists_url":"https://api.github.com/users/miasteinberg/gists{/gist_id}","starred_url":"https://api.github.com/users/miasteinberg/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/miasteinberg/subscriptions","organizations_url":"https://api.github.com/users/miasteinberg/orgs","repos_url":"https://api.github.com/users/miasteinberg/repos","events_url":"https://api.github.com/users/miasteinberg/events{/privacy}","received_events_url":"https://api.github.com/users/miasteinberg/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2017-01-18T02:13:52Z","updated_at":"2017-01-18T20:34:34Z","closed_at":"2017-01-18T20:34:34Z","body":"Hello! I installed bcbio and have upgraded with bcbio_nextgen.py upgrade --genomes hg19. Running through the small RNA example pipeline, I am getting an error at the miRDeep2 step:\r\n\r\n```\r\n#Starting miRDeep2\r\n/path/to/bcbio/anaconda/bin/miRDeep2.pl /mnt/nfs/gigantor/ifs/DCEG/path/to/smallrna_test/mirqc_bcbio/work/mirdeep2/file_reads.fa /mnt/nfs/gigantor/ifs/DCEG/path/to/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa /mnt/nfs/gigantor/ifs/DCEG/path/to/smallrna_test/mirqc_bcbio/work/mirdeep2/align.bam /path/to/bcbio/genomes/Hsapiens/hg19/srnaseq/mature.fa\r\n none /path/to/bcbio/genomes/Hsapiens/hg19/srnaseq/hairpin.fa -f /path/to/bcbio/genomes/Hsapiens/hg19/srnaseq/Rfam_for_miRDeep.fa -r simple -c -P -t h\r\nsa -z res\r\n\r\nmiRDeep2 started at 17:27:17\r\n\r\nUnknown option: f\r\nmkdir mirdeep_runs/run_17_01_2017_t_17_27_17\r\n\r\n#Starting miRDeep2\r\nError:   Rfam_for_miRDeep.fa not found in your miRDeep2 scripts directory\r\nPlease copy this file from the miRDeep2 archive to your miRDeep2 directory\r\n\r\n' returned non-zero exit status 2\r\n[2017-01-17T22:27Z] mirdeep2 failed. Please report the error to https://github.com/lpantano/mirdeep2_core/issues.\r\n```\r\n\r\nI noticed that the code in this repo has an -f option added that the original mirdeep does not, so I double checked which version of mirdeep I was using, but it looks correct:\r\n\r\n```\r\n[steinbergmk@node041 work]$ which miRDeep2.pl\r\n/path/to/bcbio/anaconda/bin/miRDeep2.pl\r\n```\r\n\r\nThe code in this repo is mirdeep 2.0.0.7 while the mirdeep packaged with bcbio is 2.0.0.8. Do I need to roll back to 2.0.0.7 somehow?\r\n\r\nThanks much,\r\nMia"},"comment":{"url":"https://api.github.com/repos/lpantano/mirdeep2_core/issues/comments/273593563","html_url":"https://github.com/lpantano/mirdeep2_core/issues/2#issuecomment-273593563","issue_url":"https://api.github.com/repos/lpantano/mirdeep2_core/issues/2","id":273593563,"user":{"login":"miasteinberg","id":4191521,"avatar_url":"https://avatars.githubusercontent.com/u/4191521?v=3","gravatar_id":"","url":"https://api.github.com/users/miasteinberg","html_url":"https://github.com/miasteinberg","followers_url":"https://api.github.com/users/miasteinberg/followers","following_url":"https://api.github.com/users/miasteinberg/following{/other_user}","gists_url":"https://api.github.com/users/miasteinberg/gists{/gist_id}","starred_url":"https://api.github.com/users/miasteinberg/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/miasteinberg/subscriptions","organizations_url":"https://api.github.com/users/miasteinberg/orgs","repos_url":"https://api.github.com/users/miasteinberg/repos","events_url":"https://api.github.com/users/miasteinberg/events{/privacy}","received_events_url":"https://api.github.com/users/miasteinberg/received_events","type":"User","site_admin":false},"created_at":"2017-01-18T20:34:34Z","updated_at":"2017-01-18T20:34:34Z","body":"That fixed the problem, thanks!"}}
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