I am trying to run Parabricks DeepVariant on some BAMs aligned to the UCSC hg19 reference. They had been aligned to the softmasked reference, but in my troubleshooting I made a BED file listing all the non-masked regions from the hardmasked reference, used that with --interval-file and still had the problem. When the software reaches chr20 at around 60 megabases, I get the error:
[src/PBBgzfFile.cpp:893] Data already present in output., expected absent == 1, exiting. Here is my bash script, for reference:
#!/bin/bash #SBATCH --account=gpu-sids-sponsored #SBATCH --partition=gpu-core-sponsored #SBATCH --nodes=1 #SBATCH --ntasks=1 #SBATCH --cpus-per-task=24 #SBATCH --mem-per-cpu=7500M #SBATCH --gpus=1 #SBATCH --time=0-03:00:00 #SBATCH --job-name=parabricks #SBATCH --mail-type=ALL #SBATCH --mail-user=Lindsay.Clark@seattlechildrens.org #SBATCH --chdir=/data/hps/assoc/private/sids/user/lclar5/logs CONTAINER=/data/hps/assoc/public/bioinformatics/container/rare-disease-wf/nvcr.io-nvidia-clara-clara-parabricks-4.4.0-1.img INCSV=/data/hps/assoc/private/sids/user/lclar5/ramirez_2025-06_rare-disease-wf/samples/SIDS_bams_2025-06-25_test10.csv OUTDIR=/data/hps/assoc/private/sids/user/lclar5/ramirez_2025-06_rare-disease-wf/results/gvcfs FASTA=/data/hps/assoc/public/bioinformatics/annotations/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hg19.fa INTERVALS=/data/hps/assoc/private/sids/user/lclar5/ramirez_2025-06_rare-disease-wf/assets/hg19_chrom_nonmasked.bed TMP=/data/hps/assoc/private/sids/user/lclar5/temp_parabricks mkdir -p $OUTDIR ROW=1 SAMPLE_ID=`head $INCSV -n $(($ROW + 1)) | tail -n 1 | cut -d , -f 3` BAM=`head $INCSV -n $(($ROW + 1)) | tail -n 1 | cut -d , -f 4` echo $SAMPLE_ID echo $BAM mkdir -p "$TMP/$SAMPLE_ID" apptainer exec --bind /data/hps/assoc --nv \ $CONTAINER \ pbrun deepvariant \ --ref $FASTA \ --in-bam $BAM \ --out-variants "$OUTDIR/$SAMPLE_ID.g.vcf.gz" \ --interval-file $INTERVALS \ --num-gpus 1 \ --gvcf \ --tmp-dir "$TMP/$SAMPLE_ID" rm "$OUTDIR/$SAMPLE_ID.vcf"