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blahah / transrate

Understand your transcriptome assembly
http://hibberdlab.com/transrate
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snap-aligner running single-threaded instead of multi-threaded #174

Closed KhudyakovLab closed 8 years ago

KhudyakovLab commented 8 years ago

I'm trying to run Transrate with read mapping option. I ran transrate-1.0.1-linux-x86_64/transrate --assembly /mnt/transrate/Trinity.blubber.fixed.fa \ --left /100G/assembly/left.fq \ --right /100G/assembly/right.fq \ --threads 8

However, the snap-aligner has been running single-threaded for over 2 days. Is this normal?

blahah commented 8 years ago

This is not normal! Possibly a bug in SNAP - there have been a few more bugfix releases since the last transrate release.

Some SNAP bugs are non-deterministic, so if you kill the process, delete any .bam files that have been created, and then re-run the transrate command, it may work fine. If not...

We'll push out a new transrate release very soon (tomorrow I hope) that will include the newest SNAP, and this might solve your problem. If not...

Let me know and we'll see what we need to do to debug.

blahah commented 8 years ago

Our latest release is v1.0.3 - it includes a new version of SNAP and Salmon. Hopefully it fixes this, but if you still see it please re-open the issue.