How did you install Flair?
- bioconda (e.g.
conda create -n flair -c conda-forge -c bioconda flair)
What happened?
I've been encountering resource exhaustion issues when running flair_transcriptome on SLURM HPC job submission systems. After investigating the code, I think I identified the root cause:
The --threads argument (default: 4) controls the multiprocessing pool size, but each worker process independently launches minimap2 with the same thread count. This results in 4 processes × 4 minimap2 threads = 16 total threads, far exceeding the expected allocation specified by the user.
This will result in the jobs being killed for exceeding the expected resource consumption.
Example
flair_transcriptome -b reads.bam -g genome.fa # User expects ~4 threads by default
# Actually spawns: 4 worker processes + (4 × 4 minimap2 threads) = 16 threads
Potential Fixes:
- Reduce minimap2 threads per worker to 1
- Add separate --minimap_threads argument, or
- Default --threads to 1 to prevent surprise resource consumption.
Thank you,
Max
How did you install Flair?
conda create -n flair -c conda-forge -c bioconda flair)What happened?
I've been encountering resource exhaustion issues when running
flair_transcriptomeon SLURM HPC job submission systems. After investigating the code, I think I identified the root cause:The --threads argument (default: 4) controls the multiprocessing pool size, but each worker process independently launches
minimap2with the same thread count. This results in 4 processes × 4 minimap2 threads = 16 total threads, far exceeding the expected allocation specified by the user.This will result in the jobs being killed for exceeding the expected resource consumption.
Example
Potential Fixes:
Thank you,
Max