Hello,
For some reason when I run the germline pipeline with v4.1.0-1, the output shows that the pipeline is run twice. This does not happen with v4.0.0-1.
Here is the command line that I used:
docker run --gpus ‘“device=0,1,2,3”’ --rm --volume /lvol/haruna/parabricks/Ref:/ref_data --volume /lvol/haruna/parabricks:/input_data --volume /lvol/haruna:/outputdir --volume /lvol/haruna:/workdir --workdir /workdir --env TCMALLOC_MAX_TOTAL_THREAD_CACHE_BYTES=268435456 nvcr.io/nvidia/clara/clara-parabricks:4.1.0-1 pbrun germline --ref /ref_data/Homo_sapiens_assembly38.fasta --in-fq /input_data/Data1/S1_1.fastq.gz /input_data/Data1/S1_2.fastq.gz ‘@RG\tID:foo\tLB:lib1\tPL:tong\tSM:20\tPU:unit1’ ‘–bwa-options=-K 10000000’ --knownSites /ref_data/Homo_sapiens_assembly38.known_indels.vcf --num-gpus 4 --out-bam /outputdir/out1/S1.bam --out-recal-file /outputdir/out1/S1.recal.txt --out-variants /outputdir/out1/S1.vcf --tmp-dir /workdir --num-cpu-threads 16 --gpusort –gpuwrite
And here is the output that shows how it was run twice:
haruna@o184i053:~/parabricks$ grep “Program:” S1_4_1.o184i081.lvol.out
[PB Info 2023-Oct-11 17:24:57] || Program: GPU-BWA mem, Sorting Phase-I ||
[PB Info 2023-Oct-11 17:25:14] || Program: Sorting Phase-II ||
[PB Info 2023-Oct-11 17:27:06] || Program: Marking Duplicates, BQSR ||
[PB Info 2023-Oct-11 17:34:48] || Program: GPU-GATK4 HaplotypeCaller ||
[PB Info 2023-Oct-11 17:45:36] || Program: GPU-BWA mem, Sorting Phase-I ||
[PB Info 2023-Oct-11 17:45:53] || Program: Sorting Phase-II ||
[PB Info 2023-Oct-11 17:47:45] || Program: Marking Duplicates, BQSR ||
[PB Info 2023-Oct-11 17:55:15] || Program: GPU-GATK4 HaplotypeCaller ||
haruna@o184i053:~/parabricks$
Thank you so much!
Haruna