metAMOS
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marbl
A metagenomic and isolate assembly and analysis pipeline built with AMOS
Hi~, when I test the pipeline on my dataset, it failed at the scaffold step: is there something wrong with my installation ? or ? ************************_ERROR**_******************************** During scaffold, the following...
Dear Dr. Sergey, As you suggested in 197th issue, I replaced -f with -q. I executed the below shell script in my workstation. Scaffold step was running for a long...
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...
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)....
Just installed metamos on a new system - and the test suite is failing with an error in matplotlib . note: I recently removed the latest version of matplotlib and...
Hi again, I'm trying to run the iMetAMOS workflow with the following commands: ``` initPipeline -f -1 ../../reads/120920-bin57_120920_R1.fasta -2 ../../reads/120920-bin57_120920_R2.fasta -d 120920_57 -W iMetAMOS -i 0:800 runPipeline -d 120920_57 -p...
Hello, I've been doing some test with 454 data. I'm running metAMOS with metavelvet and fraggenescan, and stop at the FindORFS step. I initially wanted to use MetaGeneMark but it's...
Allow generic tools to request trimmed or untrimmed datatypes. Currently, this must be turned on or off for the full metAMOS run.
Some advanced users may already have required programs installed (either in their path or non-standard location). INSTALL should check for these or allow the user to specify where the programs...