Hi, I am trying to run the tool FindBreakpointEvidenceSpark. I have successfully produced the required kmers and the tool seems to run for several minutes until it finally stops without producing output.
I have read in past issues that memory usage might be a problem and have tried to accomodate for it using the -Xmx option.
a) GATK version used: gatk4: 184.108.40.206 through singularity (/cvmfs/singularity.galaxyproject.org/all/gatk4:220.127.116.11--0)
b) Exact command used:
singularity exec /cvmfs/singularity.galaxyproject.org/all/gatk4:18.104.22.168--0 gatk --java-options "-Xmx75g -DGATK_STACKTRACE_ON_USER_EXCEPTION=true" FindBreakpointEvidenceSpark \
-R /mnt/SCRATCH/domniman/references/ssa_selected/Simon_Final2021_Ssa_selected.fa -I /mnt/SCRATCH/domniman/2014G_NO_Males_1169_D03_RG.bam \
--aligner-index-image /mnt/SCRATCH/domniman/references/ssa_selected/Simon_Final2021_Ssa_selected.fa.img \
--kmers-to-ignore /mnt/users/domniman/ag_fish/kmers_to_ignore.txt -O /mnt/SCRATCH/domniman/assembly.sam \
--tmp-dir /mnt/SCRATCH/domniman/tmp -L ssa03
Entire error log:
Due to length of the complete log (37.671 lines) I attach it as a separate link: https://www.dropbox.com/s/n7q5dco4z5t3moz/gatk%20error%20log%20.txt?dl=0
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