GATK won't produce figures while analyzing covariates to generate 'recal_plots.pdf'
I am using GATK to call variants (following guide: https://gencore.bio.nyu.edu/variant-calling-pipeline-gatk4/)
On step 12 you analyze covariates using the before and after recalibration table. I have seen figures like this online and I am not having any plots being produced.
I have had zero problems with GATK up until this point.
#!/bin/bash
#SBATCH -J gatk_recal_plots_YPD_0_S1
#SBATCH -A gts-rros3
#SBATCH -N 1 --ntasks-per-node=24
#SBATCH --mem-per-cpu=8G
#SBATCH -t 4:00:00
#SBATCH -o gatk_recal_plots_YPD_0_S1.out
cd $SLURM_SUBMIT_DIR
ml gatk
ml anaconda3
conda activate r-environment
export R_LIBS_USER=/storage/programs/r_packages:$R_LIBS_USER
gatk AnalyzeCovariates -before /storage/home/BaseRecalibrator/YPD_0_S1_Recal_Data.table -after /storage/home/BQSR2/YPD_0_S1_post_recal_data.table -plots /storage/home/AnalyzeCovariates/YPD_0_S1_recal_plots.pdf
This is my only output.
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GenoMax
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mgranada3 •
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mgranada3 •
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Your cluster may be missing libraries etc to create the PDF plots (this looks like a cluster job submission) on your cluster. Did you check the log file for the job to see if you have any pointers for this?