splitNCigar needs Xmx argument

[tgenahmet]

This pbs script needs to define the Xmx argument. Maybe then it wouldn't need to be on an highmem node....?

" An error occurred because you did not provide enough memory to run this program. You can use the -Xmx argument (before the -jar argument) to adjust the maximum heap size provided to Java. Note that this is a JVM argument, not a GATK argument."

[tgenahmet]

@denriquez what do you think? Do you know how much RAM is available on regular nodes?

[PedalheadPHX]

The standard nodes have 48Gb per 16 core node. @tgenahmet Which script is this exactly

[tgenahmet]

pegasus_splitNCigarReads.pbs would need the Xmx parameter.

[tgenahmet]

Note to self: Testing on old project TGRB_0009_ps201612251310 with job id 3497089. Trying standard node with -Xmx40G. Forgot bai file. Job ID now: 3498973

[tgenahmet]

Unfortunately I have to re-open this issue. Regardless of Xmx parameter some splitNCigar jobs are failing because of not enough memory. I have even tried -maxInMemory 10000. (default is 150K) Still the same outcome.

We can go back to using hmem nodes but this whole thread started because jobs were failing on hmem nodes as well.

@PedalheadPHX @denriquez

[tgenahmet]

Some clues here: http://gatkforums.broadinstitute.org/gatk/discussion/8848/splitncigarreads-endless-memory-hunger

[tgenahmet]

The funny thing is all of our samples also fail at chr12:66million position just like the example above.

[tgenahmet]

I tried excluding this region using the -XL option in GATK. It worked on one of the samples. I'm going to try it on about 8 other samples failing at the exact same spot. I don't know what's the deal with chr12 position 66million...

This is the option I'm using: -XL 12:65000000-67000000

[PedalheadPHX]

Doesn’t look to special for any specific reason. Do samples always fail or is it periodic? - - - Jonathan Keats Director of Bioinformatics & Assistant Professor Translational Genomics Research Institute 445 North Fifth Street, Phoenix, AZ, 85004 p: 602-343-8690 c: 480-543-0634 jkeats@tgen.org | www.keatslab.org | www.tgen.org

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On Mar 30, 2017, at 16:56, tgenahmet ***@***.***> wrote: I tried excluding this region using the -XL option in GATK. It worked on one of the samples. I'm going to try it on about 8 other samples failing at the exact same spot. I don't know what's the deal with chr12 position 66million... This is the option I'm using: -XL 12:65000000-67000000 — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#6 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AL1RHFROK1mQQqdrJzlgID6vMM3n98cXks5rrBbggaJpZM4MGogu>.

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[tgenahmet]

Only some samples fail but always at that spot. Skipping that section of chr12 seems to work so far.