Will BaseRecalibrator overwrite an existing .grp file? Where are the tmp files stored?

I've been running BaseRecalibrator for a while, and I've just realized that I have an empty file with the same name I've given to BaseRecalibrator as output (it may have been created from a previous aborted run). Will the tool write to this file when it is finished (ETA ~19 hours), or will it exit with an error? Also, are there any intermediate files created in generating the recalibration table, and if so, where should I look for them (output directory, log directory, directory from which I called GATK, ...)?

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  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @sorrywm‌

    Hi,

    The file will be overwritten without exiting with an error.

    The temp files are stored in whatever directory is set up as the java temp directory in your java settings.

    -Sheila

  • sorrywmsorrywm Member

    Thank you, Sheila! Is this the default behavior of all GATK walkers, to overwrite any pre-existing files specified with -o and to pass intermediate files to the java temp directory? I found information about overwriting behavior in the documentation for some tools but not all.

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