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marbl / metAMOS

A metagenomic and isolate assembly and analysis pipeline built with AMOS
http://marbl.github.io/metAMOS
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idba-ud assembly error file missing #146

Closed jffkm closed 10 years ago

jffkm commented 10 years ago

Ran into an issue where idba-ud output files cannot be found. The error message I get is as follows:

"Completed Task = preprocess.Preprocess Starting Task = assemble.ASSEMBLE Job = [preprocess.success -> .run] completed Completed Task = assemble.SplitAssemblers Job = [idba-ud.31.run -> idba-ud.31.asm.contig] completed Completed Task = assemble.Assemble ** MetAMOS Warning: idba-ud assembler did not run successfully! \ MetAMOS Error: no selected assembler ran successfully! Please check the logs in /data/bug/Log/ASSEMBLE.log for details. Oops, MetAMOS finished with errors! see text in red above for details."

The Log states the following: "number of threads 32 unlink: cannot unlink ‘/data/bug/Assemble/out/idba-ud.31.asm.contig’: No such file or directory ln: failed to access ‘/data/bug/Assemble/out/idba-ud.31.asm/contig.fa’: No such file or directory"

The pipeline was run as su and previous steps did not have issues with read write so I don't think that's the issue. Any ideas? Thanks

skoren commented 10 years ago

The Logs/ASSEMBLE.LOG should have the output from IDBA-UD, my guess is the assembler crashed for whatever reason. Some datasets can cause issues for some assemblers (such as out of memory or other errors) which is why we support multiple assemblers in iMetAMOS. In your run's case it looks like you only specified IDBA-UD so when it failed, metAMOS had to stop: * MetAMOS Warning: idba-ud assembler did not run successfully! * MetAMOS Error: no selected assembler ran successfully! Please check the logs in /data/bug/Log/ASSEMBLE.log for details.

If you specify more than a single assembler you should be able to proceed as long as one of them runs successfully. I'd recommend -a spades,idba,soap2,masurca

jffkm commented 10 years ago

Thanks Sergey, I proceeded to trying some alternatives in the interest of time restraints and it's humming along with spades.

The ASSEMBLE.log just has a few lines and states that it cannot find the output despite successfully writing those files in the preceeding step. Looks like the following:

""number of threads 32 unlink: cannot unlink ‘/data/bug/Assemble/out/idba-ud.31.asm.contig’: No such file or directory ln: failed to access ‘/data/bug/Assemble/out/idba-ud.31.asm/contig.fa’: No such file or directory""

I'll dig into more detail later to see if there is a piping issue in the code. Thanks again for all of your help. - J