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Old 05-28-2013, 05:11 AM   #1
lre1234
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Location: US

Join Date: Aug 2011
Posts: 106
Default GATK - PrintReads

Hi all,
I am trying to use the GATK PrintReads function following the BaseQualityRecalibrator using the following command:

Code:
java -jar GenomeAnalysisTK.jar -T PrintReads -R Homo_sapiens.fa -I WGS.sorted.IndelRealigned.fixedbam -BQSR recal_data.grp -o output.file.bam -nct 32
The sample is a whole genome ~35X coverage. After starting, it tells me that it will take about 40 hours to complete, is that a correct estimate?
Then after about 12 hours in, the program crashes with an error that says: "There is no space left on the device, so writing failed". We do have plenty of free space available, so I am not really sure what the problem is. Would anyone have any advice for me on this
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Old 05-28-2013, 07:10 AM   #2
bruce01
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Default

My general advice about GATK issues is to try the GATK forum which I have found to be most useful in diagnosing and solving errors.

Specifically this might be an issue with allocating memory, try using the -Xmx[n] for n space allocated to the process?
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Old 06-19-2013, 08:25 PM   #3
SWP
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Location: Salt Lake City, UT

Join Date: Nov 2010
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Default

Quote:
Originally Posted by lre1234 View Post
Hi all,
I am trying to use the GATK PrintReads function following the BaseQualityRecalibrator using the following command:

Code:
java -jar GenomeAnalysisTK.jar -T PrintReads -R Homo_sapiens.fa -I WGS.sorted.IndelRealigned.fixedbam -BQSR recal_data.grp -o output.file.bam -nct 32
The sample is a whole genome ~35X coverage. After starting, it tells me that it will take about 40 hours to complete, is that a correct estimate?
Then after about 12 hours in, the program crashes with an error that says: "There is no space left on the device, so writing failed". We do have plenty of free space available, so I am not really sure what the problem is. Would anyone have any advice for me on this
PrintReads uses many, many intermediate files. You're likely filling up your temp directory with intermediate files, so redirect the temp files to a location with more space.
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Old 10-02-2013, 06:02 AM   #4
vishnuamaram
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Hey Ire1234,

May be that will be using the space of tmp directory while running this command.

first create a mimic tmp directory in the hard disk and
try to include java -Djava.io.tmpdir=/data/tmp/ -jar

command. That works.
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