OSError: [Errno 24] Too many open files

[zihhuafang]

Hi,

I have a question regarding this particular error for HPC users.

We wanted to run quantseqpool_analysis using the script with the repo here (https://github.com/Lexogen-Tools/quantseqpool_analysis).
I ran into the known issue for idemux as too many open files as we pooled 22 libraries which consisted of 2112 samples on a Novaseq S4 flowcell.
With the number of samples, I would need to run ulimit -n 5120.
For an HPC cluster user, I am unable to increase the limit since I am non-root user (The OS of our cluster is CentOS Linux release 7.9.2009 with max user processes (-u) = 4096). ​

What would be the alternative here?
Run idemux per library after demultiplexed i5/i7 with bcl2fastq?
Would that be an potential issue for the undetermined reads?

Appreciate your insight.
Thanks.
Zih-Hia