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Old 02-12-2012, 01:23 PM   #1
bjchen
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Location: New York

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Default GATK: unable to write data to BAM schedule file

Hi,

I am trying to use UnifiedGenotyper in GATK, but encountered the following error message (below). Does anyone know how to deal with this? I check my quota on the directory of the bam file and I still have enough space.

Thanks!

ps. I do this with multiple jobs on a cluster and some jobs would get stuck with this error messages.


INFO 17:12:16,425 HelpFormatter - ---------------------------------------------------------------------------------
INFO 17:12:16,428 HelpFormatter - The Genome Analysis Toolkit (GATK) v1.4-25-g23e7f1b, Compiled 2012/02/08 04:59:00
INFO 17:12:16,428 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 17:12:16,428 HelpFormatter - Please view our documentation at http://www.broadinstitute.org/gsa/wiki
INFO 17:12:16,428 HelpFormatter - For support, please view our support site at http://getsatisfaction.com/gsa
INFO 17:12:16,429 HelpFormatter - Program Args: -T UnifiedGenotyper -glm BOTH -stand_call_conf 30 -stand_emit_conf 30 -R reference/S288Cseq/S288C.fasta -o ./BWA/FP-973-5-4NQO-B.vcf -I ./BWA/FP-973-5-4NQO-B.mdup.realign.bam
INFO 17:12:16,429 HelpFormatter - Date/Time: 2012/02/12 17:12:16
INFO 17:12:16,429 HelpFormatter - ---------------------------------------------------------------------------------
INFO 17:12:16,429 HelpFormatter - ---------------------------------------------------------------------------------
INFO 17:12:16,458 GenomeAnalysisEngine - Strictness is SILENT
INFO 17:12:31,572 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 17:12:31,588 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace
org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Unable to write data to BAM schedule file.
at org.broadinstitute.sting.gatk.datasources.reads.BAMSchedule.write(BAMSchedule.java:311)
at org.broadinstitute.sting.gatk.datasources.reads.BAMSchedule.<init>(BAMSchedule.java:150)
at org.broadinstitute.sting.gatk.datasources.reads.BAMScheduler.getNextOverlappingBAMScheduleEntry(BAMScheduler.java:263)
at org.broadinstitute.sting.gatk.datasources.reads.BAMScheduler.advance(BAMScheduler.java:170)
at org.broadinstitute.sting.gatk.datasources.reads.BAMScheduler.populateFilteredIntervalList(BAMScheduler.java:99)
at org.broadinstitute.sting.gatk.datasources.reads.BAMScheduler.createOverMappedReads(BAMScheduler.java:62)
at org.broadinstitute.sting.gatk.datasources.reads.IntervalSharder.shardOverMappedReads(IntervalSharder.java:54)
at org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource.createShardIteratorOverMappedReads(SAMDataSource.java:1135)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.getShardStrategy(GenomeAnalysisEngine.java:450)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:230)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:122)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:90)
Caused by: java.io.IOException: No space left on device
at sun.nio.ch.FileDispatcher.write0(Native Method)
at sun.nio.ch.FileDispatcher.write(FileDispatcher.java:57)
at sun.nio.ch.IOUtil.writeFromNativeBuffer(IOUtil.java:122)
at sun.nio.ch.IOUtil.write(IOUtil.java:93)
at sun.nio.ch.FileChannelImpl.write(FileChannelImpl.java:224)
at org.broadinstitute.sting.gatk.datasources.reads.BAMSchedule.write(BAMSchedule.java:306)
... 13 more
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 1.4-25-g23e7f1b):
##### ERROR
##### ERROR Please visit the wiki to see if this is a known problem
##### ERROR If not, please post the error, with stack trace, to the GATK forum
##### ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki
##### ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa
##### ERROR
##### ERROR MESSAGE: Unable to write data to BAM schedule file.
##### ERROR ------------------------------------------------------------------------------------------
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Old 02-12-2012, 02:23 PM   #2
swbarnes2
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Doesn't "No space left on device" means pretty much like what it looks like?
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Old 02-12-2012, 04:26 PM   #3
bjchen
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Uh... I have about 500G on the drive where I have GATK and my bam files. Each of my bam file is only about 1G. So I don't think that drive does not have enough space (please correct me if I am wrong). But I suspect the program utilizes some other drive for temporary files. So I am wondering if there is any way I can get around this.

Thanks.
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Old 02-12-2012, 05:27 PM   #4
adaptivegenome
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This is actually an issue with JVM (if it is true your temp space is located in a spot where there is no free space). Try this:

java -Djava.io.tmpdir=/temp/ [and then the resets of the command] where /temp is whatever spot you want to write temp files.
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Old 02-12-2012, 07:56 PM   #5
bjchen
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Setting -Djava.io.tmpdir seems to work! Thanks a lot!!
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Old 02-13-2012, 12:21 AM   #6
Bukowski
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Quote:
Originally Posted by swbarnes2 View Post
Doesn't "No space left on device" means pretty much like what it looks like?
I've also hit this when ulimit is exhausted with GATK, so not always
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