I'm using the took CollectAllelicCounts with GATK version 22.214.171.124 and I'm having difficulty with the output file. My code is as follows:
srun mkdir <path_to_temp_directory>
srun $GATK/gatk --java-options "-Xmx3g" CollectAllelicCounts \
-L $SNPs_ONLY \
-I $INPUT_DIR/recal_reads.cram \
-R $REF \
--tmp-dir $TEMP_DIR \
srun rm -rf <path_to_temp_directory>
I'm using my institution's cluster computing environment which utilizes scratch space for the temp directory. This is created at the beginning of the job and then deleted at the end of the job. The job finishes without error, but there is no output file. Is there something about using a Temp Directory that overwrites the usual output file location? Any assistance would be greatly appreciated.
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