I am using the rna_fq2bam pipeline in parabricks v3.8.0.1.
I have prepared a genome index beforehand with the most recent version of STAR from GitHub. The genome index works with the GitHub version of STAR. However, when I am trying to use that genome index with the parabricks rna_fq2bam pipeline, I get an error (see below).
Ideally I would like to build the index with STAR from parabricks as as well, to work only with one version, but it is not clear how to do that because the pipeline isolates me from using STAR directly. Could you please advise how to build a matching genome index that works with the STAR version used in parabricks v3.8.0.1?
Here is the error::
[kratz@gcg01 ~]$ pbrun rna_fq2bam --in-fq SRR5927736_GSM2740270_HUVECs_Late_passage_rep2_Homo_sapiens_RNA-Seq_1.fastq.gz SRR5927736_GSM2740270_HUVECs_Late_passage_rep2_Homo_sapiens_RNA-Seq_2.fastq.gz --genome-lib-dir gbuild --output-dir sample_X/ --out-bam OUT_BAM --ref gindex/GRCh38.primary_assembly.genome.fa
Please visit NVIDIA Clara - NVIDIA Docs for detailed documentation[Parabricks Options Mesg]: Automatically generating ID prefix
[Parabricks Options Mesg]: Read group created for
/home/kratz/SRR5927736_GSM2740270_HUVECs_Late_passage_rep2_Homo_sapiens_RNA-Seq_1.fastq.gz and
/home/kratz/SRR5927736_GSM2740270_HUVECs_Late_passage_rep2_Homo_sapiens_RNA-Seq_2.fastq.gz
[Parabricks Options Mesg]: @RG\tID:SRR5927736.1.1\tLB:lib1\tPL:bar\tSM:sample\tPU:SRR5927736.1.1
[PB Info 2023-Apr-30 10:01:02] ------------------------------------------------------------------------------
[PB Info 2023-Apr-30 10:01:02] || Parabricks accelerated Genomics Pipeline ||
[PB Info 2023-Apr-30 10:01:02] || Version 3.8.0-1 ||
[PB Info 2023-Apr-30 10:01:02] || star ||
[PB Info 2023-Apr-30 10:01:02] || Contact: Parabricks-Support at […]
[PB Info 2023-Apr-30 10:01:02] ------------------------------------------------------------------------------
[PB Info 2023-Apr-30 10:01:03] … started STAR run
[PB Info 2023-Apr-30 10:01:03] … loading genome
[PB Error 2023-Apr-30 10:01:03][src/ErrorWarning.cpp:30]
EXITING: FATAL INPUT ERROR: unrecognized parameter name “genomeType” in input “genomeParameters.txt”
SOLUTION: use correct parameter name (check the manual)… FATAL ERROR, exiting. Exit code 102, exiting.
For technical support visit […]
Exiting…Could not run rna_fq2bam
Exiting pbrun …