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Question: STAR in multiple threads faces issues in opening genome file
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gravatar for arax.martirosyan
20 months ago by
arax.martirosyan • 0
arax.martirosyan • 0 wrote:

Hi,

I'm running STAR with multiple threads in multiple cores and for some samples I get an error message:

EXITING because of FATAL ERROR: could not open genome file

It seems multithreading causes issues, files open in one thread (like genome indexes, fasta or gtf files) may become unaccessible for other STAR-jobs. Is there a way to fix this issues?

Thank you,

Araks
threads star • 1.1k views
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modified 20 months ago by y.hoogstrate • 460 • written 20 months ago by arax.martirosyan • 0
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gravatar for y.hoogstrate
20 months ago by
y.hoogstrate • 460
Netherlands
y.hoogstrate • 460 wrote:

Do you use references genomes from history or from Galaxy's cache and are you running STAR on identical or Different references?
ADD COMMENT • link written 20 months ago by y.hoogstrate • 460
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gravatar for arax.martirosyan
20 months ago by
arax.martirosyan • 0
arax.martirosyan • 0 wrote:

I'm running star on identical references and using reference genome files located in my local computer. I've downloaded them from genecode.
ADD COMMENT • link written 20 months ago by arax.martirosyan • 0
1

maybe you hit the limit for the number of open files per user in your system? we were running into this problem independent of galaxy with STAR using multiple threads.

Hans-Rudolf

ADD REPLY • link written 20 months ago by Hotz, Hans-Rudolf • 1.8k
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gravatar for y.hoogstrate
20 months ago by
y.hoogstrate • 460
Netherlands
y.hoogstrate • 460 wrote:

how much memory do you have in that machine?

The Galaxy wrapper has set --genomeLoad NoSharedMemory (default STAR option). The consequence is that running two jobs in parallel, makes two copies of the reference genome (~30gb) in the RAM. Could this have anything to do with it?
ADD COMMENT • link written 20 months ago by y.hoogstrate • 460
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