bbmap taking large amounts of time // freezing?
BBMap short read aligner, and other bioinformatic tools.
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#52 bbmap taking large amounts of time // freezing?
While bbmap.sh has worked well in the past with other samples/references, the current project I am working on has been experiencing either extremely long runtimes, or the verbose progress indicators freeze.
My sample sequences are extremely similar to one another and our reference is a repetitive non-human reference (which I understand poses some difficulties with some tools). When I run the tool, I see mapping progress being printed, but it stalls after awhile. I have left it on overnight without any results. When I terminate it and check the SAM stats, I see that it says that most of the sequences (~98%) have been aligned, so that is what leads me to believe that this might just be a problem with the verbose printing?
Here is the command I ran last:
java -ea -Xmx40g -cp $HOME/software/bbmap/current/ align2.BBMap5 in=data.fastq.gz ref=reference.fa fast=f out=alignment.sam
I forget to mention: we are trying to have the alignment run as quickly as possible, and we want to feed the alignment file into another function via a pipeline, which is why we need the tool to finish successfully.