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Picard/GATK MergeVcfs throws errors

Dear all,
I am following your guidelines for germline SNP detection in GATK 4. Nevertheless, I cannot complete the concatenation of region-wise gvcfs.
Using GATK MergeVcfs I get the following error:
/package/sequencer/java/8/bin/java -jar -XX:+UseSerialGC -verbose:GC -Xmx8g -Djava.io.tmpdir=/scratch/cluster/seqcore/temp/smith/package/sequencer/gatk/current/gatk-package-4.0.1.1-local.jar MergeVcfs --INPUT ./03_GATK/core_L11935-2_Mystique.chrEBV.gvcf --INPUT ./03_GATK/core_L11935-2_Mystique.chrUn_KI270742v1.gvcf --OUTPUT ./03_GATK/core_L11935-2_Mystique.gvcf

[Fri Feb 09 13:20:55 CET 2018] MergeVcfs --INPUT ./03_GATK/core_L11935-2_Mystique.chrEBV.gvcf --INPUT ./03_GATK/core_L11935-2_Mystique.chrUn_KI270742v1.gvcf --OUTPUT ./03_GATK/core_L11935-2_Mystique.gvcf --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 1 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX true --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Fri Feb 09 13:20:55 CET 2018] Executing as smith@bromhidrosophobie.molgen.mpg.de on Linux 4.14.17.mx64.205 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_25-b17; Deflater: Intel; Inflater: Intel; Picard version: Version:4.0.1.1

java.lang.IllegalArgumentException: Illegal character in fragment at index 1: ##fileformat=VCFv4.2
at java.net.URI.create(URI.java:852)
at htsjdk.samtools.util.IOUtil.getPath(IOUtil.java:1134)
at htsjdk.samtools.util.IOUtil.lambda$unrollPaths$2(IOUtil.java:1088)
at htsjdk.samtools.util.IOUtil$$Lambda$29/1967434886.accept(Unknown Source)
at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:183)
at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.Iterator.forEachRemaining(Iterator.java:116)
at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:512)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:502)
at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:150)
at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:173)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418)
at htsjdk.samtools.util.IOUtil.unrollPaths(IOUtil.java:1085)
at htsjdk.samtools.util.IOUtil.unrollFiles(IOUtil.java:1050)
at picard.vcf.MergeVcfs.doWork(MergeVcfs.java:164)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:269)
at org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutor.instanceMain(PicardCommandLineProgramExecutor.java:24)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:153)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:195)
at org.broadinstitute.hellbender.Main.main(Main.java:277)
Caused by: java.net.URISyntaxException: Illegal character in fragment at index 1: ##fileformat=VCFv4.2
at java.net.URI$Parser.fail(URI.java:2848)
at java.net.URI$Parser.checkChars(URI.java:3021)
at java.net.URI$Parser.parse(URI.java:3067)
at java.net.URI.(URI.java:588)
at java.net.URI.create(URI.java:850)

Applying the picard commands I get the following:
/package/sequencer/java/8/bin/java -jar -XX:+UseSerialGC -verbose:GC -Xmx8g -Djava.io.tmpdir=/scratch/cluster/seqcore/temp/smith/package/sequencer/picard-tools/current/picard.jar MergeVcfs INPUT=./03_GATK/core_L11935-2_Mystique.chrEBV.gvcf INPUT=./03_GATK/core_L11935-2_Mystique.chrUn_KI270742v1.gvcf OUTPUT= ./03_GATK/core_L11935-2_Mystique.gvcf

13:24:51.701 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/package/sequencer/picard-tools/2.12.1/picard.jar!/com/intel/gkl/native/libgkl_compression.so
[Fri Feb 09 13:24:51 CET 2018] MergeVcfs INPUT=[./03_GATK/core_L11935-2_Mystique.chrEBV.gvcf, ./03_GATK/core_L11935-2_Mystique.chrUn_KI270742v1.gvcf] OUTPUT=./03_GATK/core_L11935-2_Mystique.gvcf VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false

Exception in thread "main" htsjdk.samtools.SAMException: Cannot read non-existent file: /project/seqcore-cluster/data/superhero/chrUn_KI270742v1 186727 . C .. END=186739 GT:DP:GQ:MIN_DP:PL 0/0:9:0:4:0,0,0
at htsjdk.samtools.util.IOUtil.assertFileIsReadable(IOUtil.java:347)
at htsjdk.samtools.util.IOUtil.assertFileIsReadable(IOUtil.java:334)
at htsjdk.samtools.util.IOUtil.unrollFiles(IOUtil.java:948)
at picard.vcf.MergeVcfs.doWork(MergeVcfs.java:98)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:268)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:98)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:108)

I appreciate any help on this issue.
Best
Stefan

Answers

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