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.