Question: Memory Problems Running Gatk Printreads
2
gravatar for ajc8
7.3 years ago by
ajc8120
University of Iowa
ajc8120 wrote:

Hi everyone,

I have been unable to run GATK Printreads as a part of my normal pipeline - I keep getting an error message stating that the startup disk has run out of memory. There is plenty of room on my Mac hard drive (~250 Gig), and I tried specifying a temp directory in the java command line, but that doesn't seem to help.

I have never had this problem before - I am doing one thing differently - running bwa mem instead of bwa aln and sampe. The raw data is illumina paired-end, exome. The fastq files are 7.3 GB each, which isn't any larger than files I have run in the past.

I am running the Printreads command after the BaseRecalibrator. And I'm specifying 8G RAM in the java command. My computer is a Macbook Pro i7 with 16G RAM. I haven't been using multiple cores.

Does bwa mem introduce a bug that isn't compatable with GATK Printreads?

Thanks for your help. Allison

Hi - this is the command line: java -Xmx8g -Djava.io.tmpdir=/Volumes/Passport/temp -jar GenomeAnalysisTK.jar -T PrintReads -R /Volumes/Passport/ref_genome/human_g1k_v37.fasta -I /Volumes/Passport/epilepsy_data/family2/Epi_362.realigned.fixed.dedup.bam -BQSR /Volumes/Passport/epilepsy_data/family2/Epi_362.recal_data.grp -o /Volumes/Passport/epilepsy_data/family2/Epi_362.realigned.fixed.dedup.recal.bam

The error message is from my Mac, saying there is no memory remaining to run any applications and then I have to force quit everything - I'm not able to copy and paste the message.

memory • 2.8k views
ADD COMMENTlink modified 7.3 years ago • written 7.3 years ago by ajc8120

Allison -- could you include the command line and the error message? That would make it easier to offer suggestions about the potential problem.

ADD REPLYlink written 7.3 years ago by Brad Chapman9.5k

Thanks for posting the command line. It's a good idea to post this as an edit to your original post, instead of as an answer to the question. Biostars is a bit different from standard forum sites since it separates question and answers; your information isn't an answer but rather an addition to the initial question. In terms of the actual problem, two suggestions:

  • Try also setting the initial memory size (-Xms4g) in addition to your -Xmx8g option to java. Without this, programs can sometimes eat up lots of stack and cause memory issues.
  • Are other processes running using significant memory? Using top in a console should let you monitor memory usage and identify what is using up your memory.

Hope this helps

ADD REPLYlink modified 7.3 years ago • written 7.3 years ago by Brad Chapman9.5k

Thank you - it is running right now - we'll see what happens. I ran top and it says that java is using ~95% CPU and terminal is using around 85%. I don't usually see terminal taking up that much memory. Does that ring a bell?

and top is using up ~17% which is much higher than usual (~3%).

ADD REPLYlink modified 7.3 years ago • written 7.3 years ago by ajc8120

You should focus on monitoring memory usage since that's related to the error you're seeing. CPU usage won't help much with diagnosing the problem.

ADD REPLYlink written 7.3 years ago by Brad Chapman9.5k

Hi Allison, I just moved your error message post to your original question because this showed the question as "answered" which might cause people to think your problem was solved.

ADD REPLYlink modified 7.3 years ago • written 7.3 years ago by Josh Herr5.7k

thank you! I'm new at this

ADD REPLYlink written 7.3 years ago by ajc8120
0
gravatar for ajc8
7.3 years ago by
ajc8120
University of Iowa
ajc8120 wrote:

Hi everyone, Thanks for all of your help.
It turns out it was an '\n' before the -o in my command that caused the problem - it must have snuck into the script somehow. So the PrintReads was printing everything to screen and overloading my computer. It is running just fine now. Allison

ADD COMMENTlink written 7.3 years ago by ajc8120
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