Question: STAR in multiple threads faces issues in opening genome file
0
gravatar for arax.martirosyan
5 weeks ago by
arax.martirosyan0 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 • 92 views
ADD COMMENTlink modified 5 weeks ago by y.hoogstrate400 • written 5 weeks ago by arax.martirosyan0
1
gravatar for y.hoogstrate
5 weeks ago by
y.hoogstrate400
Netherlands
y.hoogstrate400 wrote:

Do you use references genomes from history or from Galaxy's cache and are you running STAR on identical or Different references?

ADD COMMENTlink written 5 weeks ago by y.hoogstrate400
0
gravatar for arax.martirosyan
5 weeks ago by
arax.martirosyan0 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 COMMENTlink written 5 weeks ago by arax.martirosyan0
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 REPLYlink written 5 weeks ago by Hotz, Hans-Rudolf1.5k
0
gravatar for y.hoogstrate
5 weeks ago by
y.hoogstrate400
Netherlands
y.hoogstrate400 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 COMMENTlink written 5 weeks ago by y.hoogstrate400
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