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MarkDuplicateSpark does not find file though it is there
Hi GATK Team.
I got the following error when using MarkDupliactesSpark tool:
A USER ERROR has occurred: Couldn't write file /media/Berechnungen/190218_NB501654_0110_AHT7VFBGX9/0046-19_Exom (Intelligenzminderung)/0046-19.dedup.bam because writing failed with exception File file:/media/Berechnungen/190218_NB501654_0110_AHT7VFBGX9/0046-19_Exom%20(Intelligenzminderung)/0046-19.dedup.bam.parts/header does not exist
I looked at the specified path and the
header file is in the right directory.
Is it possible, that MDSpark replaces a space in the filepath to %20 and at the end does not replace it back to space, so it does not finde the
Thanks in advance