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
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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