GATK: unable to write data to BAM schedule file

[bjchen]

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 ------------------------------------------------------------------------------------------

[swbarnes2]

Doesn't "No space left on device" means pretty much like what it looks like?

[bjchen]

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.

[adaptivegenome]

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.

[bjchen]

Setting -Djava.io.tmpdir seems to work! Thanks a lot!!

[Bukowski]

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