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alexdobin / STAR

RNA-seq aligner
MIT License
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Abort trap when using --genomeLoad LoadAndExit #138

Closed roro883 closed 8 years ago

roro883 commented 8 years ago

Hi,

I'm trying to load the genome using the "shared memory" mode to save memory before analyzing several FASTQ files, but an error occur immediately when launching the command : STAR --genomeLoad LoadAndExit --genomeDir myGenomeDirectory/ Here's the output : 

Apr 26 13:35:05 ..... Started STAR run
Apr 26 13:35:05 ..... Loading genome
Abort trap: 6

Log.out.zip note: same issue with LoadAndKeep when launching a reads alignment.

However when I launch a reads alignement with the following command line, everything works fine : STAR --runThreadN 8 --genomeDir myGenomeDirectory/ --readFilesIn $fastq --outFileNamePrefix $outdir --readFilesCommand gunzip -c --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts

For information, I'm on Mac OS X 10.11 (El Capitan) with 32GB RAM.

Can you please help me troubleshoot?

Many thanks in advance Regards

alexdobin commented 8 years ago

Hi @graurelien

this could be a problem with max shared RAM allowed for your Linux. Please check this link for more details on configuring shared RAM fo Mac OS X: http://www.spy-hill.com/~myers/help/apple/SharedMemory.html

What is the output of $ grep shm /etc/sysctl.conf

The two important parameters you would nee to set by editing /etc/sysctl.conf kern.sysv.shmmax: 32000000000 kern.sysv.shmall: 7812500

Then you will need to reboot, or you can also try sysctl -p (this work on Linux, not sure about OS X).

Please let me know if this solves the problem..

Cheers Alex

roro883 commented 8 years ago

Hi Alex,

Thanks a lot, this solves my problem of shared memory. Just for information, the file /etc/sysctl.conf didn't exist on my system, so I created it with the following lines and reboot : 

kern.sysv.shmmax=32000000000
kern.sysv.shmmin=1
kern.sysv.shmmni=128
kern.sysv.shmseg=32
kern.sysv.shmall=7812500

Note that the command LoadAndExit works, but I still get the same error Abort trap: 6 when I use Remove. However, the genome is removed from the memory anyway, so it's not a big deal...

alexdobin commented 8 years ago

Hi @graurelien

sounds good! Since the "Remove" error does not interfere with operations seriously, let's consider it solved for the moment.

Cheers Alex