{"action":"opened","issue":{"url":"https://api.github.com/repos/marbl/metAMOS/issues/189","labels_url":"https://api.github.com/repos/marbl/metAMOS/issues/189/labels{/name}","comments_url":"https://api.github.com/repos/marbl/metAMOS/issues/189/comments","events_url":"https://api.github.com/repos/marbl/metAMOS/issues/189/events","html_url":"https://github.com/marbl/metAMOS/issues/189","id":62112223,"number":189,"title":"Error during validation","user":{"login":"Biomicrogen","id":10353433,"avatar_url":"https://avatars.githubusercontent.com/u/10353433?v=3","gravatar_id":"","url":"https://api.github.com/users/Biomicrogen","html_url":"https://github.com/Biomicrogen","followers_url":"https://api.github.com/users/Biomicrogen/followers","following_url":"https://api.github.com/users/Biomicrogen/following{/other_user}","gists_url":"https://api.github.com/users/Biomicrogen/gists{/gist_id}","starred_url":"https://api.github.com/users/Biomicrogen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Biomicrogen/subscriptions","organizations_url":"https://api.github.com/users/Biomicrogen/orgs","repos_url":"https://api.github.com/users/Biomicrogen/repos","events_url":"https://api.github.com/users/Biomicrogen/events{/privacy}","received_events_url":"https://api.github.com/users/Biomicrogen/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2015-03-16T15:18:27Z","updated_at":"2015-03-16T15:18:27Z","closed_at":null,"body":"Greetings All,\r\n\r\nI have been using imetamos to optimize an assembly of two librarys obtained from the same culture.  The culture contains 2 or 3 organisms (basically a contaminated culture).  One library is a 150X2 MiSEQ run and the other is a 300X2 MiSEQ run.  I know that my organism of interest is a low GC cyanobacterium (35-45GC%) and at least one of the contaminates is a high GC (55-65%GC) bacterium, so I filtered on GC% then trimmed and combined them into one library and split into F and R files for input into iMetamos using the following commands:\r\n\r\nsudo ./initPipeline -q -1 Low-GC-All-1.fastq -2 Low-GC-All-2.fastq -d /media/biomicrogen/runs/LowGC -i 150:550\r\n\r\nthen\r\nsudo ./runPipeline -d /media/biomicrogen/runs/LowGC -p 8\r\n I got the following Error:\r\n*****************************************************************\r\n*************************ERROR***********************************\r\nDuring findorfs, the following command failed with return code 2:\r\n>> /media/biomicrogen/UBDISK/biomicrogen/metamos/Utilities/cpp/Linux-x86_64/prokka/bin/prokka  --outdir /media/biomicrogen/UBDISK/biomicrogen/runs/LowGC/FindORFS/out/proba.prokka --prefix proba --force /media/biomicrogen/UBDISK/biomicrogen/runs/LowGC/FindORFS/in/proba.asm.contig\r\n\r\n*************************DETAILS***********************************\r\nLast 10 commands run before the error (/media/biomicrogen/UBDISK/biomicrogen/runs/LowGC/Logs/COMMANDS.log)\r\n|2015-03-16 08:14:09| unlink /media/biomicrogen/UBDISK/biomicrogen/runs/LowGC/Assemble/out/proba.contig.cnt\r\n|2015-03-16 08:14:09| ln /media/biomicrogen/UBDISK/biomicrogen/runs/LowGC/Assemble/out/.contig.cnt /media/biomicrogen/UBDISK/biomicrogen/runs/LowGC/Assemble/out/proba.contig.cnt\r\n|2015-03-16 08:14:09| unlink /media/biomicrogen/UBDISK/biomicrogen/runs/LowGC/Assemble/out/proba.contig.cvg\r\n|2015-03-16 08:14:09| ln /media/biomicrogen/UBDISK/biomicrogen/runs/LowGC/Assemble/out/.contig.cvg /media/biomicrogen/UBDISK/biomicrogen/runs/LowGC/Assemble/out/proba.contig.cvg\r\n|2015-03-16 08:14:09| unlink /media/biomicrogen/UBDISK/biomicrogen/runs/LowGC/Assemble/out/proba.afg\r\n|2015-03-16 08:14:09| rm /media/biomicrogen/UBDISK/biomicrogen/runs/LowGC/Logs/findorfs.ok\r\n|2015-03-16 08:14:09|# [FINDORFS]\r\n|2015-03-16 08:14:09| unlink /media/biomicrogen/UBDISK/biomicrogen/runs/LowGC/FindORFS/in/proba.asm.contig\r\n|2015-03-16 08:14:09| ln /media/biomicrogen/UBDISK/biomicrogen/runs/LowGC/Assemble/out/proba.asm.contig /media/biomicrogen/UBDISK/biomicrogen/runs/LowGC/FindORFS/in/proba.asm.contig\r\n|2015-03-16 08:14:09| /media/biomicrogen/UBDISK/biomicrogen/metamos/Utilities/cpp/Linux-x86_64/prokka/bin/prokka  --outdir /media/biomicrogen/UBDISK/biomicrogen/runs/LowGC/FindORFS/out/proba.prokka --prefix proba --force /media/biomicrogen/UBDISK/biomicrogen/runs/LowGC/FindORFS/in/proba.asm.contig\r\n\r\nLast 10 lines of output (/media/biomicrogen/UBDISK/biomicrogen/runs/LowGC/Logs/FINDORFS.log)\r\n[08:14:09] Determined makeblastdb version is 2.2\r\n[08:14:09] Looking for 'parallel' - found /media/biomicrogen/UBDISK/biomicrogen/metamos/Utilities/cpp/Linux-x86_64/prokka/bin/../binaries/linux/parallel\r\n[08:14:09] Determined parallel version is 20130822\r\n[08:14:09] Looking for 'prodigal' - found /media/biomicrogen/UBDISK/biomicrogen/metamos/Utilities/cpp/Linux-x86_64/prokka/bin/../binaries/linux/prodigal\r\n[08:14:09] Determined prodigal version is 2.60\r\n[08:14:09] Looking for 'sed' - found /bin/sed\r\n[08:14:09] Looking for 'tbl2asn' - found /media/biomicrogen/UBDISK/biomicrogen/metamos/Utilities/cpp/Linux-x86_64/prokka/bin/../binaries/linux/tbl2asn\r\n[08:14:09] Determined tbl2asn version is 23.9\r\n[08:14:09] Using genetic code table 11.\r\n[08:14:09] '/media/biomicrogen/UBDISK/biomicrogen/runs/LowGC/FindORFS/in/proba.asm.contig' is not a readable non-empty FASTA file\r\n\r\nPlease veryify input data and restart MetAMOS. If the problem persists please contact the MetAMOS development team.\r\n*************************ERROR***********************************\r\n*****************************************************************\r\nrm: cannot remove ‘/media/biomicrogen/UBDISK/biomicrogen/runs/LowGC/Logs/findorfs.ok’: No such file or directory\r\nOops, MetAMOS finished with errors! see text in red above for details.\r\n\r\nAlso, I have tried installing ReapR a few times, both through the Metamos install script and manually and I cannot get it to work.  Any tips would be appreciated.\r\n\r\nThanks!\r\n\r\n"}}