FindBreakpointEvidenceSpark sudden shutdown

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Domniki Manousi

• March 07, 2022 12:01

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: 4.2.0.0 through singularity (/cvmfs/singularity.galaxyproject.org/all/gatk4:4.2.0.0--0) 

b) Exact command used: 

singularity exec /cvmfs/singularity.galaxyproject.org/all/gatk4:4.2.0.0--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

Best,

Domniki

 

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  Genevieve Brandt (she/her)

  • March 07, 2022 22:31

  Hi Domniki Manousi,

  Thank you for writing in and bringing this to our attention. It looks like this could be a bug so I have created a ticket on github so that our developers can take a look.

  You can track the progress here: https://github.com/broadinstitute/gatk/issues/7710

  Best,

  Genevieve

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  Genevieve Brandt (she/her)

  • March 10, 2022 22:03

  Hi Domniki Manousi,

  I have an update from our development team. We are wondering if you have unmapped reads in the BAM? This tool is meant to be run on a BAM aligned to a reference file.

  Best,

  Genevieve

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  Domniki Manousi

  • March 11, 2022 06:26

  dear Genevieve Brandt (she/her)

  thank you for you fast reply

  the bam file was originally aligned to the same reference file that I used on the tool.
  I tried using samtools to retain only mapped reads on the .bam file and re-run FindBreakpointEvidenceSpark, however that did not improve the situation.

  Best,
  Domniki 

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  Genevieve Brandt (she/her)

  • March 11, 2022 19:58

  Thanks for replying directly - let me know if you need anything else.

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