I'm a happy user of GATK v3.7 running on a Win7 pc via Cygwin.
With v3.7 it was no problem to use the -L (--intervals) option.
Today I was trying the new v4.0.0.0 but ran into the following error: "java.net.URISyntaxException: Illegal character in opaque part at index 2" when I include the -L option. Without the -L option the tools run fine.
I use the following commands:
targets=E:/Pipelines/targets.bed
gatk --java-options "-Xmx8G" Mutect2 --min-pruning 3 -R $ref1 -L $targets -I ${sample}.bam -tumor ${sample} -O test.vcf
I also tried other options like putting the bed file directly in the GATK commandline or by using:
targets="E:/Pipelines/targets.bed"
and the cygwin style:
targets=/cygdrive/e/Pipelines/targets.bed
but that did not help either.
Somehow the GATK v4 tool changes the linux forward slashes to windows backslashes, which result in the error.
Do you have any clues how to solve this, so that I can keep running GATK v4 under Cygwin, with the -L option?
Thanks for the great work so far!
> Using GATK jar E:/cygwin64/home/X/GATK/v4.0.0.0/gatk-package-4.0.0.0-local.jar defined in environment variable GATK_LOCAL_JAR
Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=1 -Xmx8G -jar E:/cygwin64/home/X/GATK/v4.0.0.0/gatk-package-4.0.0.0-local.jar Mutect2 --min-pruning 3 -R E:/Agilent/SureCall_Server/Server/CommonStorage/GenomeReferences/hg19/hg19/hg19.fasta -L E:/Pipelines/targets.bed -I test.bam -tumor test -O test.vcf 15:55:12.700 WARN NativeLibraryLoader - Unable to find native library: native/gkl_compression.dll 15:55:12.700 WARN NativeLibraryLoader - Unable to find native library: native/gkl_compression.dll 15:55:15.056 INFO Mutect2 - ------------------------------------------------------------ 15:55:15.056 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.0.0.0 15:55:15.056 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/ 15:55:15.056 INFO Mutect2 - Executing as XX on Windows 7 v6.1 amd64 15:55:15.056 INFO Mutect2 - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_151-b12 15:55:15.056 INFO Mutect2 - Start Date/Time: 10 januari 2018 15:55:12 CET 15:55:15.056 INFO Mutect2 - ------------------------------------------------------------ 15:55:15.056 INFO Mutect2 - ------------------------------------------------------------ 15:55:15.056 INFO Mutect2 - HTSJDK Version: 2.13.2 15:55:15.056 INFO Mutect2 - Picard Version: 2.17.2 15:55:15.056 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 1 15:55:15.056 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 15:55:15.056 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 15:55:15.056 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 15:55:15.056 INFO Mutect2 - Deflater: JdkDeflater 15:55:15.056 INFO Mutect2 - Inflater: JdkInflater 15:55:15.056 INFO Mutect2 - GCS max retries/reopens: 20 15:55:15.056 INFO Mutect2 - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 15:55:15.056 INFO Mutect2 - Initializing engine 15:55:15.118 WARN IntelDeflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater 15:55:15.134 WARN IntelDeflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater 15:55:15.461 INFO FeatureManager - Using codec BEDCodec to read file file:///E:/Pipelines/targets.bed 15:55:15.477 INFO Mutect2 - Shutting down engine [10 januari 2018 15:55:15 CET] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 0.05 minutes. Runtime.totalMemory()=344457216 java.lang.IllegalArgumentException: Illegal character in opaque part at index 2: E:\Pipelines\targets.bed at java.net.URI.create(Unknown Source) at org.broadinstitute.hellbender.engine.FeatureInput.makeIntoAbsolutePath(FeatureInput.java:242) at org.broadinstitute.hellbender.engine.FeatureInput.toString(FeatureInput.java:314) at java.util.Formatter$FormatSpecifier.printString(Unknown Source) at java.util.Formatter$FormatSpecifier.print(Unknown Source) at java.util.Formatter.format(Unknown Source) at java.util.Formatter.format(Unknown Source) at java.lang.String.format(Unknown Source) at org.broadinstitute.hellbender.engine.FeatureDataSource.close(FeatureDataSource.java:573) at org.broadinstitute.hellbender.utils.IntervalUtils.featureFileToIntervals(IntervalUtils.java:324) at org.broadinstitute.hellbender.utils.IntervalUtils.parseIntervalArguments(IntervalUtils.java:274) at org.broadinstitute.hellbender.utils.IntervalUtils.loadIntervals(IntervalUtils.java:226) at org.broadinstitute.hellbender.cmdline.argumentcollections.IntervalArgumentCollection.parseIntervals(IntervalArgumentCollection.java:170) at org.broadinstitute.hellbender.cmdline.argumentcollections.IntervalArgumentCollection.getTraversalParameters(IntervalArgumentCollection.java:151) at org.broadinstitute.hellbender.cmdline.argumentcollections.IntervalArgumentCollection.getIntervals(IntervalArgumentCollection.java:107) at org.broadinstitute.hellbender.engine.GATKTool.initializeIntervals(GATKTool.java:376) at org.broadinstitute.hellbender.engine.GATKTool.onStartup(GATKTool.java:560) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.onStartup(AssemblyRegionWalker.java:160) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:134) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:179) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:198) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:152) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:195) at org.broadinstitute.hellbender.Main.main(Main.java:275) Caused by: java.net.URISyntaxException: Illegal character in opaque part at index 2: E:\Pipelines\targets.bed at java.net.URI$Parser.fail(Unknown Source) at java.net.URI$Parser.checkChars(Unknown Source) at java.net.URI$Parser.parse(Unknown Source) at java.net.URI.<init>(Unknown Source) ... 24 more