skoren
commented
9 years ago Hi,
My guess is this is similar to other errors I've seen recently where SOAPdenovo produces an empty assembly but reports no errors during its run.
You mentioned using iMetAMOS but your init/runPipeline commands don't include the workflow flag (-W imetamos). What is the full output from your iMetAMOS run, specifically, did the run generate multiple assemblies and did the Validate step run? You should have multiple Assemble/out/*.asm.contig files if that was the case. If not, adding the -W imetamos flag to your initPipeline command (on a new empty project directory) should fix this by generating multiple assemblies and selecting one that is non-empty.
Greetings All,
I 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:
sudo ./initPipeline -q -1 Low-GC-All-1.fastq -2 Low-GC-All-2.fastq -d /media/biomicrogen/runs/LowGC -i 150:550
then sudo ./runPipeline -d /media/biomicrogen/runs/LowGC -p 8 I got the following Error:
****ERROR****** During findorfs, the following command failed with return code 2:
****DETAILS****** Last 10 commands run before the error (/media/biomicrogen/UBDISK/biomicrogen/runs/LowGC/Logs/COMMANDS.log) |2015-03-16 08:14:09| unlink /media/biomicrogen/UBDISK/biomicrogen/runs/LowGC/Assemble/out/proba.contig.cnt |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 |2015-03-16 08:14:09| unlink /media/biomicrogen/UBDISK/biomicrogen/runs/LowGC/Assemble/out/proba.contig.cvg |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 |2015-03-16 08:14:09| unlink /media/biomicrogen/UBDISK/biomicrogen/runs/LowGC/Assemble/out/proba.afg |2015-03-16 08:14:09| rm /media/biomicrogen/UBDISK/biomicrogen/runs/LowGC/Logs/findorfs.ok |2015-03-16 08:14:09|# [FINDORFS] |2015-03-16 08:14:09| unlink /media/biomicrogen/UBDISK/biomicrogen/runs/LowGC/FindORFS/in/proba.asm.contig |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 |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
Last 10 lines of output (/media/biomicrogen/UBDISK/biomicrogen/runs/LowGC/Logs/FINDORFS.log) [08:14:09] Determined makeblastdb version is 2.2 [08:14:09] Looking for 'parallel' - found /media/biomicrogen/UBDISK/biomicrogen/metamos/Utilities/cpp/Linux-x86_64/prokka/bin/../binaries/linux/parallel [08:14:09] Determined parallel version is 20130822 [08:14:09] Looking for 'prodigal' - found /media/biomicrogen/UBDISK/biomicrogen/metamos/Utilities/cpp/Linux-x86_64/prokka/bin/../binaries/linux/prodigal [08:14:09] Determined prodigal version is 2.60 [08:14:09] Looking for 'sed' - found /bin/sed [08:14:09] Looking for 'tbl2asn' - found /media/biomicrogen/UBDISK/biomicrogen/metamos/Utilities/cpp/Linux-x86_64/prokka/bin/../binaries/linux/tbl2asn [08:14:09] Determined tbl2asn version is 23.9 [08:14:09] Using genetic code table 11. [08:14:09] '/media/biomicrogen/UBDISK/biomicrogen/runs/LowGC/FindORFS/in/proba.asm.contig' is not a readable non-empty FASTA file
Please veryify input data and restart MetAMOS. If the problem persists please contact the MetAMOS development team. ****ERROR******
rm: cannot remove ‘/media/biomicrogen/UBDISK/biomicrogen/runs/LowGC/Logs/findorfs.ok’: No such file or directory Oops, MetAMOS finished with errors! see text in red above for details.
Also, 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.
Thanks!