Hi Stuti,
In order to diagnose the problem, try the following:
1. Determine the process ID of the hung job by logging onto the machine
where the job is running and execute 'jps -lv'
2. Get a thread dump of the hung process with 'jstack <process-id>'
If it isn't obvious from looking at the thread dump what the problem is,
then send it to the list and someone should be able to figure it out.
-Alec
On 11/25/14, 12:49 PM, Stuti Agrawal wrote:
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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