Clara-parabricks rna-fq2bam: --sjdbOverhang

[vaibhav.a.janve]

is there a way to set the STAR --sjdbOverhang parameter in the function call? I am getting error.
"EXITING because of fatal PARAMETERS error: present --sjdbOverhang=100 is not equal to the value at the genome generation step =49
SOLUTION:

… FATAL ERROR, exiting. Exit code 105, exiting."

I am running clara-parabricks_4.0.1-1 as the node has CUDA11.8 drivers. I will try running it on node with CUDA 12.2 so I can run the latest version clara-parabricks_4.2.1-1 to see if error persists.

the sequencing was performed Paired-End 50bp. so the genome is constructed with --sjdbOverhang=49.

---

log:

[Parabricks Options Mesg]: Automatically generating ID prefix
[Parabricks Options Mesg]: Read group created for
/panfs/accrepfs.vampire/nobackup/h_vmac/user/janveva1/Project/RNAseq/ROSMAP_Monocyte/fastq/Sample_001_TAGCATAACC-
GCTATGCGCA_HK735DMXX_L002_001.R1.fastq.gz and
/panfs/accrepfs.vampire/nobackup/h_vmac/user/janveva1/Project/RNAseq/ROSMAP_Monocyte/fastq/Sample_001_TAGCATAACC-
GCTATGCGCA_HK735DMXX_L002_001.R2.fastq.gz
[Parabricks Options Mesg]: @RG\tID:HK735DMXX.2\tLB:lib1\tPL:bar\tSM:sample\tPU:HK735DMXX.2
[PB Info 2023-Dec-10 07:06:01] ------------------------------------------------------------------------------
[PB Info 2023-Dec-10 07:06:01] || Parabricks accelerated Genomics Pipeline ||
[PB Info 2023-Dec-10 07:06:01] || Version 4.0.1-1 ||
[PB Info 2023-Dec-10 07:06:01] || star ||
[PB Info 2023-Dec-10 07:06:01] ------------------------------------------------------------------------------
[PB Info 2023-Dec-10 07:06:01] … started STAR run
[PB Info 2023-Dec-10 07:06:01] … loading genome
[PB Error 2023-Dec-10 07:06:01][src/ErrorWarning.cpp:30]
EXITING because of fatal PARAMETERS error: present --sjdbOverhang=100 is not equal to the value at the genome generation step =49
SOLUTION:

… FATAL ERROR, exiting. Exit code 105, exiting.
For technical support visit Help - NVIDIA Docs
Exiting…
Please visit NVIDIA Clara - NVIDIA Docs for detailed documentation

Could not run rna_fq2bam
Exiting pbrun …

[mdemouth]

Hi @vaibhav.a.janve,

You can use the option --sjdb-overhang 49 to be in par with the number used for the genome construction.

Best
Myrieme

[vaibhav.a.janve]

Thank you, that worked!
is this in documentation or script that I can look up?
if you would please suggest equivalent options in rna-fq2bam (or where to locate them) for the following STAR alignment as I have not located many options.

STAR --runThreadN 6
–limitBAMsortRAM 31000000000
–runMode alignReads
–twopassMode Basic
–readFilesCommand zcat
–genomeDir ${ref_index}
–outFileNamePrefix ${aligned_dir}/${sample}_
–outSAMtype BAM SortedByCoordinate
–readFilesIn ${fastq_dir}${R1} ${fastq_dir}${R2}
–outSAMunmapped Within
–outSAMattributes Standard
#–quantMode GeneCounts

I appreciate you help and support.

[mdemouth]

Hi @vaibhav.a.janve ,

Please find the documentation for your version : rna_fq2bam - NVIDIA Docs