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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

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/.