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Welcome to the Maize_WGS_Build wiki!

More information:

• YouTube: GATK Workshop 2019 by Broad Institute (GATK4)
• Bioinformatic Workbook: GATK Best Practices Workflow
• GATK Papers (for citation)
• Recent Papers using GATK on PubMed

GATK can indicate multiple types of pipelines (e.g. HaplotypeCaller for germline variants and Mutect2 for cell somatic variants). For more information, please visit https://gatk.broadinstitute.org/hc/en-us/articles/360035890491-Somatic-calling-is-NOT-simply-a-difference-between-two-callsets#:~:text=HaplotypeCaller%20is%20designed%20to%20call,for%20the%20other%20use%20case.

This pipeline is a Nextflow version of the GATK HaplotypeCaller pipeline.

Possible Errors and How to Fix Them

Singularity pull times out

Error Message on Atlas

[-        ] process > run_SortVCF                    -
[-        ] process > calc_DPvalue                   -
[-        ] process > gatk_VariantFiltration         -
[-        ] process > keep_only_pass                 -
Pulling Singularity image shub://aseetharam/gatk:latest [cache /project/isu_gif_vrsc/Jennifer/github/Maize_WGS_Build/work/singularity/aseetharam-gatk-latest.img]
WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /project/isu_gif_vrsc/Jennifer/github/Maize_WGS_Build/work/singularity -- Use env variable NXF_SINGULARITY_CACHEDIR to specify a different location
Error executing process > 'prep_reads:paired_FastqToSAM (BioSample17)'

Caused by:
  Failed to pull singularity image
  command: singularity pull  --name aseetharam-gatk-latest.img shub://aseetharam/gatk:latest > /dev/null
  status : 255
  message:
    [31mFATAL:   While pulling shub image: failed to get manifest for: shub://aseetharam/gatk:latest: no response received from singularity hub

Fix

singularity pull  --name aseetharam-gatk-latest.img shub://aseetharam/gatk:latest
mv aseetharam-gatk-latest.img work/singularity/.

Slurm requires an account

Error on Atlas

Command output:
  sbatch: error: You must specify an account!
  sbatch: error: E.g.: #SBATCH -A <account> |OR| --account=<account>
  sbatch: error: Batch job submission failed: Unspecified error

Fix: use the atlas profile -profile atlas,singularity

${NEXTFLOW} run main.nf \
  --genome test-data/ref/b73_chr1_150000001-151000000.fasta \
  --reads "test-data/fastq/*_{R1,R2}.fastq.gz" \
  -profile atlas,singularity \
  -resume

Fix Java TMPDIR runs out of space during IO. Fix requires setting environment variables, something like below:

export _JAVA_OPTIONS=-Djava.io.tmpdir=/ptmp/GIF/Username/
export TMPDIR=“tmpdir” 

To-Do List

• Add parameter to specify slurm account name
• Add download data options (sratoolkit etc...)
• Increase wall time for certain slurm processes