GATK does not work on Windows any longer

[teepean]

GATK doesn't seem to be working on Windows any longer, at least HaploTypeCaller crashes with the following. Tested with GATK 4.0.9.0, 4.0.11.0 and 4.1.0.0.

java.exe -jar gatk-package-4.1.0.0-local.jar HaplotypeCaller -R refa.fa -I refa.bam -O bam_chramma.vcf
java.nio.file.InvalidPathException: Illegal char <:> at index 2: /C:/Users/Teemu/AppData/Local/Temp/
        at sun.nio.fs.WindowsPathParser.normalize(Unknown Source)
        at sun.nio.fs.WindowsPathParser.parse(Unknown Source)
        at sun.nio.fs.WindowsPathParser.parse(Unknown Source)
        at sun.nio.fs.WindowsPath.parse(Unknown Source)
        at sun.nio.fs.WindowsFileSystem.getPath(Unknown Source)
        at java.nio.file.Paths.get(Unknown Source)
        at org.broadinstitute.hellbender.utils.io.IOUtils.getPath(IOUtils.java:759)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:161)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)
        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)

The last version I have tested where this still works is 4.0.8.1. It is caused most likely because of the forward slash before C:.

There are several examples of the error that can be googled. Here's one:

https://bugs.eclipse.org/bugs/show_bug.cgi?id=518079

[teepean]

According to git bisect this is the commit that is the culprit.

9125ff664902b5ac22d0c195b6350d2a0e11baec is the first bad commit
commit 9125ff664902b5ac22d0c195b6350d2a0e11baec
Author: Daniel Gómez-Sánchez <[email protected]>
Date:   Fri Aug 24 21:22:41 2018 +0200

    NIO support for TMP_DIR (#4469)

    * NIO support for TMP_DIR

:040000 040000 1e2e5ba73c9ed278665dfdee2c21a08a768b7fcd 5c74c0f3b11bc6e7a5cba909648659b18f9fd957 M      src

[cmnbroad]

@teepean We generally don't test on Windows, though we do try to keep things working there if possible. Is there any chance you could try running this branch in the same environment that previously failed, and see if it solves the problem ? Thx ?

[teepean]

@teepean We generally don't test on Windows, though we do try to keep things working there if possible. Is there any chance you could try running this branch in the same environment that previously failed, and see if it solves the problem ? Thx ?

This fixed the problem and everything else seems to be working correctly. Thank you!

[cmnbroad]

@teepean Ok, great - thx for testing that out.

[cmnbroad]

@teepean Thanks for following up, but lets leave this issue open until the fix gets merged into master.