Open Biomicrogen opened 9 years ago
skoren
commented
9 years ago Hi,
Did this run report any other warnings/errors before this error message? It appears the ORF indexed bank did not get properly built during the FindORFS step. Does the /media/biomicrogen/UBDISK/biomicrogen/runs/MiSEQ/FindORFS/out/proba.fna.bnk directory exist? What are it's contents? Is this a new run or a resume of a previous run?
Biomicrogen
commented
9 years ago The FINDorfs/Out directory exists and is populated with assembler files but no proba.fna.bnk director exists. There were no warnings before the run exit other than what I posted. This was a new run. I tried to resume it after I posted but it crashed with the same message.
Brandon
-----Original Message----- From: Sergey Koren notifications@github.com To: marbl/metAMOS metAMOS@noreply.github.com Cc: Biomicrogen biomicrogen@aol.com Sent: Wed, Apr 8, 2015 3:35 pm Subject: Re: [metAMOS] exit on classify (#191)
Hi,
Did this run report any other warnings/errors before this error message? It appears the ORF indexed bank did not get properly built during the FindORFS step. Does the /media/biomicrogen/UBDISK/biomicrogen/runs/MiSEQ/FindORFS/out/proba.fna.bnk directory exist? What are it's contents? Is this a new run or a resume of a previous run?
— Reply to this email directly or view it on GitHub.
Heya guys, I'm getting an error on classify?
Run command: sudo ./runPipeline -d /media/biomicrogen/UBDISK/biomicrogen/runs/MiSEQ -p 8 -f Scaffold -n FindORFS,Abundance -a SOAPdenovo2,MaSuRCA,ABySS,SPAdes -X reapr,lap,quast
[***** ****ERROR****** During classify, the following command failed with return code 1:
****DETAILS****** Last 10 commands run before the error (/media/biomicrogen/UBDISK/biomicrogen/runs/MiSEQ/Logs/COMMANDS.log) |2015-04-06 08:56:19| ln /media/biomicrogen/UBDISK/biomicrogen/runs/MiSEQ/Scaffold/out/proba.linearize.scaffolds.final /media/biomicrogen/UBDISK/biomicrogen/runs/MiSEQ/Scaffold/out/proba.scaffolds.final |2015-04-06 08:56:19| touch /media/biomicrogen/UBDISK/biomicrogen/runs/MiSEQ/Scaffold/out/proba.motifs |2015-04-06 08:56:19| touch /media/biomicrogen/UBDISK/biomicrogen/runs/MiSEQ/Logs/scaffold.skip |2015-04-06 08:56:20|# [FINDSCAFFOLDORFS] |2015-04-06 08:56:20| touch /media/biomicrogen/UBDISK/biomicrogen/runs/MiSEQ/Logs/findscaffoldorfs.skip |2015-04-06 08:56:22|# [CLASSIFY] |2015-04-06 08:56:33| /media/biomicrogen/UBDISK/biomicrogen/metamos/AMOS/Linux-x86_64/bin/shuffleBank -c -e -b /media/biomicrogen/UBDISK/biomicrogen/runs/MiSEQ/Scaffold/in/proba.bnk -p ctg -eid -E /media/biomicrogen/UBDISK/biomicrogen/runs/MiSEQ/Classify/out/contig.fofn |2015-04-06 09:00:26| /media/biomicrogen/UBDISK/biomicrogen/metamos/AMOS/Linux-x86_64/bin/shuffleBank -r -e -b /media/biomicrogen/UBDISK/biomicrogen/runs/MiSEQ/Scaffold/in/proba.bnk -eid -E /media/biomicrogen/UBDISK/biomicrogen/runs/MiSEQ/Classify/out/read.fofn |2015-04-06 09:04:14| /media/biomicrogen/UBDISK/biomicrogen/metamos/AMOS/Linux-x86_64/bin/shuffleBank -r -f -e -b /media/biomicrogen/UBDISK/biomicrogen/runs/MiSEQ/Scaffold/in/proba.bnk -eid -E /media/biomicrogen/UBDISK/biomicrogen/runs/MiSEQ/Classify/out/read.fofn |2015-04-06 09:04:14| /media/biomicrogen/UBDISK/biomicrogen/metamos/AMOS/Linux-x86_64/bin/shuffleBank -r -e -b /media/biomicrogen/UBDISK/biomicrogen/runs/MiSEQ/FindORFS/out/proba.fna.bnk -p fna -eid -E /media/biomicrogen/UBDISK/biomicrogen/runs/MiSEQ/Classify/out/orf.fofn
Last 10 lines of output (/media/biomicrogen/UBDISK/biomicrogen/runs/MiSEQ/Logs/CLASSIFY.log) WARNING: no file defined for prefix WARNING: lib1r18111497/1 it has not been assigned, marking as UNKNOWN! WARNING: no file defined for prefix WARNING: lib1r18111497/2 it has not been assigned, marking as UNKNOWN! WARNING: no file defined for prefix WARNING: lib1r18111498/1 it has not been assigned, marking as UNKNOWN! WARNING: no file defined for prefix WARNING: lib1r18111498/2 it has not been assigned, marking as UNKNOWN! WARNING: no file defined for prefix No account found in bank /media/biomicrogen/UBDISK/biomicrogen/runs/MiSEQ/FindORFS/out/proba.fna.bnk
Please veryify input data and restart MetAMOS. If the problem persists please contact the MetAMOS development team. ****ERROR******