Issue with output from CollectAllelicCounts

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jejacobs23

• August 04, 2020 22:01

Hello,

I'm using the took CollectAllelicCounts with GATK version 4.1.7.0 and I'm having difficulty with the output file.  My code is as follows:

REF=<path_to_directory>"/Homo_sapiens_assembly38.fasta"
SNPs_ONLY=<path_to_directory>"/gnomAD_sites_biallelicSNPs_only_sorted.vcf.gz"
INPUT_DIR=<path_to_input_direcotry>
OUTPUT_DIR=<path_to_output_directory>
TEMP_DIR=<path_to_temp_directory>

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 \
-O $OUTPUT_DIR/T_clean.allelicCounts.tsv
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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• 

  Genevieve Brandt (she/her)

  • August 05, 2020 18:05

  Hi jejacobs23, I am not aware of a problem where the temp directory overwrites the output file location. You may want to look at the complete command as well of the stack trace for path issues. 

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