GATK_UnifiedGenotyper_Unable to merge temporary Tribble output file

douym

Hi all,

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.(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.(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

chapmanb

Your system runs out of available file handles so can't open new files:

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

You can check the current number of available files with:

$ ulimit -a | grep open
open files                      (-n) 1024

GATK can be aggressive in opening files, so you'll probably have to increase your current limit.

http://stackoverflow.com/questions/34588/how-do-i-change-the-number-of-open-files-limit-in-linux

Hope this helps.