Issue in running last_align rule

[priyambial123]

Hello,

I have been facing issues with conda libraries. So, I have installed micromamba and started using using it. For the PacBio workflow. I kept the all the existing rule scripts and directories and updated only the environment using the command:

mamba create -c conda-forge -c bioconda -n pb-human-wgs snakemake=6.15.3 tabulate=0.8.10 pysam=0.16.0.1 python=3

I faced no issue running the first step in the workflow (process_smrtcells.smk). But, last few steps in second step (process_sample.smk) didn't get completed. It stops in the last_align step (tandem genotyping). Log file shows bus error. Please find the attached log files. Is this a memory issue or bug.

log.txt benchmark.log

Thank you

Priya

[williamrowell]

It's hard to tell based on the log, but given that we haven't been having any trouble with this rule for a wide variety of samples, I think it's more likely to be a memory issue than a bug.

Now that we have an internal tool to genotype tandem repeats (TRGT), we'll deprecate tandem-genotypes in future releases. I'd recommend disabling it by commenting out line 15 in config.yaml:

sample_targets:
  - pbsv_vcf  # req: alignment in config['smrtcells_targets']
  - deepvariant  # req: alignment in config['smrtcells_targets']
  - whatshap  # req: deepvariant
  - coverage  # req: whatshap
  - kmers  # req: kmers in config['smrtcells_targets']
  - assembly
  #- tandem-genotypes  # req: whatshap
  - trgt  # req: whatshap
  - 5mc_cpg_pileup # req: whatshap; also requires uBAM input with basemods

This should allow you to move past this error without having to troubleshoot resource requirements.

[priyambial123]

Thank you, it worked