RNA to bam issue, dont know how to generate index

Hello everyone,

I’m facing an issue with Parabricks rna_fq2bam and STAR genome indexing. Despite regenerating the STAR indices, Parabricks throws an error:

EXITING: FATAL INPUT ERROR: unrecognized parameter name "genomeType" in input "genomeParameters.txt"
SOLUTION: use correct parameter name (check the manual)

Steps taken:

  1. Manually installed STAR.
  2. Generated genome indices:
    STAR --runMode genomeGenerate \
        --genomeDir /home/$USER/Ref/ \
        --genomeFastaFiles /home/$USER/Ref/Mus_musculus.GRCm39.dna.primary_assembly.fa \
        --sjdbGTFfile /home/$USER/Ref/Mus_musculus.GRCm39.108.gtf \
        --sjdbOverhang 99 \
        --runThreadN 12
    
  3. Ran Parabricks:
    docker run --rm --gpus all --volume $(pwd)/Data:/workdir/Data --volume $(pwd)/Output:/outputdir --volume $(pwd)/Ref:/workdir/Ref \
        nvcr.io/nvidia/clara/clara-parabricks:4.0.0-1 \
        pbrun rna_fq2bam \
        --in-fq /workdir/Data/322ndSMCLID16_S8_L001_R1_001.fastq.gz /workdir/Data/322ndSMCLID16_S8_L001_R2_001.fastq.gz \
        --genome-lib-dir /workdir/Ref/ \
        --output-dir /outputdir/ \
        --ref /workdir/Ref/Mus_musculus.GRCm39.dna.primary_assembly.fa \
        --out-bam /outputdir/output.bam
    

Has anyone faced similar issues or know how to resolve this? Thanks in advance!

Best,
Owais

Which version of STAR are you using to generate the index? The Parabricks version of STAR is compatible with the 2.7.2a CPU-only version of STAR.

1 Like

Confirmed solution. Using the STAR 2.7.2a version of STAR that is compatible with Parabricks 4.3 worked. Also, use the path to the directory generated by STAR as the genome library pathway.

Step 1:
Create the genome directory using compatible STAR (2.7.2a)

 STAR --runThreadN 16      --runMode genomeGenerate      --genomeDir /home/$USER/genomeDir      --genomeFastaFiles /home/$USER/ref/REFERENCE_FILE.fa      --sjdbGTFfile /home/owais_siddiqi/ref/ANNOTATED_FILE.gtf      --sjdbOverhang 100

STEP 2:
Run NVIDIA parabricks 4.3 after pulling its docker image

docker run --rm --gpus all     --volume /home/$USER/data:/workdir/data     --volume /home/$USER/genomeDir:/workdir/genomeDir     --volume /home/$USER/output:/outputdir     --volume /home/$USER/ref:/workdir/ref     --workdir /workdir/data     nvcr.io/nvidia/clara/clara-parabricks:4.3.1-1     pbrun rna_fq2bam     --in-fq /workdir/data/SEQ_DATA R1.fastq.gz /workdir/data/SEQ_DATA R2.fastq.gz     --genome-lib-dir /workdir/genomeDir     --output-dir /outputdir     --ref /workdir/ref/REFERENCE_FILE.fa     --out-bam /outputdir/aligned_reads.bam     --read-files-command zcat

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