GatherVCFs error - provider not installed
I am trying to create a panel of normal following this guide - https://gatk.broadinstitute.org/hc/en-us/articles/360035531132--How-to-Call-somatic-mutations-using-GATK4-Mutect2
I have split the genome into chromosomes and created genomic DB using them. However, when trying to combine the output from CreateSomaticPanelOfNormals, I'm getting a weird error. Any help is appreciated!
REQUIRED for all errors and issues:
a) GATK version used: v4.2.6.1
b) Exact command used:
time gatk GatherVcfs -I chr1:1-123463784.vcf.gz \
-I chr1:123463784-248956422.vcf.gz -I chr2:1-92988518.vcf.gz -I \
chr2:92988518-242193529.vcf.gz -I chr3.vcf.gz -I chr4.vcf.gz -I \
chr5.vcf.gz -I chr6.vcf.gz -I chr7.vcf.gz -I chr8.vcf.gz -I \
chr9.vcf.gz -I chr10.vcf.gz -I chr11.vcf.gz -I chr12.vcf.gz -I \
chr13.vcf.gz -I chr14.vcf.gz -I chr15.vcf.gz -I chr16.vcf.gz -I \
chr17.vcf.gz -I chr18.vcf.gz -I chr19.vcf.gz -I chr20.vcf.gz -I \
chr21.vcf.gz -I chr22.vcf.gz -I chrX.vcf.gz -I chrY.vcf.gz -I \
chrM.vcf.gz -O pon.vcf.gz
c) Entire program log:
[Fri Dec 02 15:41:33 IST 2022] picard.vcf.GatherVcfs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2155347968
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
java.nio.file.FileSystemNotFoundException: Provider "chr1" not installed
at java.nio.file.Paths.get(Paths.java:147)
at htsjdk.io.HtsPath.toPath(HtsPath.java:158)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1384)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:482)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:472)
at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:566)
at picard.vcf.GatherVcfs.doWork(GatherVcfs.java:95)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:308)
at org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutor.instanceMain(PicardCommandLineProgramExecutor.java:37)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
at org.broadinstitute.hellbender.Main.main(Main.java:289)
-
Any updates on this? Am I doing something wrong?
Please sign in to leave a comment.
1 comment