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Old 08-25-2012, 08:25 PM   #1
MissDona
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Location: beijing

Join Date: Nov 2011
Posts: 17
Unhappy Error while running GATK UnifiedGenotyper

Hi everyone!
I've been analyzing some illumina whole exome sequencing data these days. yesterday I used GATK(version 2.0) UnifiedGenotyper to call snps and indels with the following commands:
run_gatk.sh
-T UnifiedGenotyper
-R GRCh37/human_g1k_v37.fasta
-I GATK_recal_result.bam
-glm BOTH
--dbsnp reference/dbsnp_134.b37.vcf
-stand_call_conf 50
-stand_emit_conf 10
-o raw2.vcf
-dcov 200
--num_threads 10

After running theses commands, I got a vcf file which is very small(when I checked the vcf file, I found these called snps and indels are all from Chromosome1)
The error message is as follows:
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace
org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Unable to merge temporary Tribble output file.
at org.broadinstitute.sting.gatk.executive.HierarchicalMicroScheduler.mergeExistingOutput(HierarchicalMicroScheduler.java:269)
at org.broadinstitute.sting.gatk.executive.HierarchicalMicroScheduler.execute(HierarchicalMicroScheduler.java:105)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:269)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
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:93)
Caused by: org.broad.tribble.TribbleException$MalformedFeatureFile: Unable to parse header with error: /rd/tmp/org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub8005277156701491219.tmp (Too many open files), for input source: /rd/tmp/org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub8005277156701491219.tmp
at org.broad.tribble.TribbleIndexedFeatureReader.readHeader(TribbleIndexedFeatureReader.java:104)
at org.broad.tribble.TribbleIndexedFeatureReader.<init>(TribbleIndexedFeatureReader.java:58)
at org.broad.tribble.AbstractFeatureReader.getFeatureReader(AbstractFeatureReader.java:69)
at org.broadinstitute.sting.gatk.io.storage.VariantContextWriterStorage.mergeInto(VariantContextWriterStorage.java:182)
at org.broadinstitute.sting.gatk.io.storage.VariantContextWriterStorage.mergeInto(VariantContextWriterStorage.java:52)
at org.broadinstitute.sting.gatk.executive.OutputMergeTask.merge(OutputMergeTask.java:48)
at org.broadinstitute.sting.gatk.executive.HierarchicalMicroScheduler.mergeExistingOutput(HierarchicalMicroScheduler.java:263)
... 6 more
Caused by: java.io.FileNotFoundException: /rd/tmp/org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub8005277156701491219.tmp (Too many open files)
at java.io.FileInputStream.open(Native Method)
at java.io.FileInputStream.<init>(FileInputStream.java:120)
at org.broad.tribble.util.ParsingUtils.openInputStream(ParsingUtils.java:56)
at org.broad.tribble.TribbleIndexedFeatureReader.readHeader(TribbleIndexedFeatureReader.java:96)
... 12 more
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 2.0-39-gd091f72):
##### 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 website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Unable to merge temporary Tribble output file.
##### ERROR ------------------------------------------------------------------------------------------
Would you please help me solve it ? Thanks a lot
Dona
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Old 08-25-2012, 11:28 PM   #2
PeteH
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Location: Melbourne

Join Date: Jun 2010
Posts: 64
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You'll likely have more luck getting an answer to your question by reading the GATK documentation and then posting a question at the official GATK forums (http://gatkforums.broadinstitute.org/), as stated in your error message.
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Old 08-26-2012, 02:10 AM   #3
Bukowski
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Location: UK

Join Date: Jan 2010
Posts: 390
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As already said, ask the GATK developers, they're very responsive to questions.

Having said that I had a very similar issue with an older release:

/rd/tmp/org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub8005277156701491219.tmp (Too many open files)

Might suggest that you've hit the per-user ulimit, on our servers I had to up the ulimit for users running UG (although the bug that was creating this issue in the 1.x series was subsequently fixed).
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Old 08-26-2012, 03:39 AM   #4
MissDona
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Location: beijing

Join Date: Nov 2011
Posts: 17
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Thanks a lot!
I sent this error message to the server programmer, after he changed some of the system configure (in /etc/security/limit.conf), I run these commands again with num_threads reducing to 2, and it worked~
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Old 08-26-2012, 03:41 AM   #5
MissDona
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thanks!
I have solved this problem with the server programmer's help
some of the system configre(in /etc/sequrity/limit.conf)should be changed
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