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Comments (6)

Hi,

i have SNPs from another SNP caller which does not produce vcf files so i wanted to convert those using the VariantsToVCF walker. I used the following command:

java -Xmx2g -jar  /PATH/TO/GenomeAnalysisTK.jar -T VariantsToVCF -R reference.fa -o mySNPs.vcf --variant mySNPs.bed

GATK version 2.7-4

i took a bed file as input which had the following format:

chr1    895 896
chr1    941 942
chr1    1096    1097
...

The walker runs without any error message but i get an empty vcf file (0B, nothing) apart from a mySNPs.vcf.idx and a mySNPs.bed.idx file.

Any idea how to fix that?

Thanks a lot!!!

Best wishes, Karin

Comments (7)

Hi,

I am getting the following error when running UnifiedGenotyper (Unexpectedly couldn't find valid codec for temporary output file). Any advice on what might be going wrong?

Thanks

run with java option -Djava.io.tmpdir=/data/wildmice/scratch/scratch
v2.1-11-g13c0244
Program Args: -T UnifiedGenotyper -R ref/NCBIM37_um.fa -I   /data/wildmice/bams/wilddom/wildmus101_A.realigned.bam -I /data/wildmice/bams/wilddom/wildmus211_A.realigned.bam -I /data/wildmice/bams/wilddom/wildmus218_A.realigned.bam -I /data/wildmice/bams/wilddom/wildmus227_A.realigned.bam -I /data/wildmice/bams/wilddom/wildmus231_A.realigned.bam -I /data/wildmice/bams/wilddom/wildmus234_A.realigned.bam -I /data/wildmice/bams/wilddom/wildmus236_A.realigned.bam -I /data/wildmice/bams/wilddom/wildmus246_A.realigned.bam -I /data/wildmice/bams/wilddom/wildmus303_A.realigned.bam -I /data/wildmice/bams/wilddom/wildmus310_A.realigned.bam -I /data/wildmice/bams/wilddom/wildmus311_A.realigned.bam -I /data/wildmice/bams/wilddom/wildmus313_A.realigned.bam -I /data/wildmice/bams/wilddom/wildmus314_A.realigned.bam -I /data/wildmice/bams/wilddom/wildmus327_A.realigned.bam -I /data/wildmice/bams/wilddom/wildmus329_A.realigned.bam -I /data/wildmice/bams/wilddom/wildmus330_A.realigned.bam -I /data/wildmice/bams/wilddom/wildmus334_A.realigned.bam -I /data/wildmice/bams/wilddom/wildmus34_A.realigned.bam -I /data/wildmice/bams/wilddom/wildmus44_A.realigned.bam -I /data/wildmice/bams/wilddom/wildmus54_A.realigned.bam -o scratch/forBQSR.dom.chr2.vcf -nt 36 -rf BadCigar -L 2

##### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace
org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Unexpectedly couldn't find valid codec for temporary output file /data/wildmice/scratch/scratch/org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub2878319150678783116.tmp
        at org.broadinstitute.sting.gatk.io.storage.VariantContextWriterStorage.mergeInto(VariantContextWriterStorage.java:190)
        at org.broadinstitute.sting.gatk.io.storage.VariantContextWriterStorage.mergeInto(VariantContextWriterStorage.java:53)
        at org.broadinstitute.sting.gatk.executive.OutputMergeTask.merge(OutputMergeTask.java:48)
        at org.broadinstitute.sting.gatk.executive.HierarchicalMicroScheduler.mergeExistingOutput(HierarchicalMicroScheduler.java:263)
        at org.broadinstitute.sting.gatk.executive.HierarchicalMicroScheduler.execute(HierarchicalMicroScheduler.java:105)
        at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:265)
        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)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 2.1-11-g13c0244):
##### 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: Unexpectedly couldn't find valid codec for temporary output file /data/wildmice/scratch/scratch/org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub2878319150678783116.tmp
##### ERROR ------------------------------------------------------------------------------------------