Hi,
I am trying to use Picard - SamToFastq for the cell line dataset for TCGA,
which is ~200G BAM file. However, when I run the command, the fastq.gz
files are created of 14G each after which Picard just stalls. The java
virtual machine goes into a sleep mode, the job is still running/alive but
there is no progress.
I am running this on a 16 core VM with 48G memory and there is nothing else
running on this machine. Is there a way I can run this so that the job
completes?
Thank you,
Stuti Agrawal
This is the command I have used:
*java* -Xms2G -Xmx30G -jar
/home/ubuntu/software/picard-tools-1.124/picard.jar SamToFastq
VALIDATION_STRINGENCY=SILENT MAX_RECORDS_IN_RAM=7500000
INPUT=/mnt/cinder/SCRATCH/data/tcga/dataset/G15511.HCC1143.1.bam
FASTQ=/mnt/cinder/SCRATCH/data/tcga/dataset/ad3d4757-f358-40a3-9d92-742463a95e88_1.fastq.gz
SECOND_END_FASTQ=/mnt/cinder/SCRATCH/data/tcga/dataset/ad3d4757-f358-40a3-9d92-742463a95e88_2.fastq.gz
--
*Stuti Agrawal*
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