Too many open files

The process hit the per-process limit on simultaneously open file handles

why

Tools that merge or demultiplex hold many files open at once — one per sample, per chromosome, per barcode. The default limit (often 1024) is reached quickly with a few hundred samples.

what to do

Raise the soft limit for the session (ulimit -n 4096) or ask your admin to raise the hard limit. Better where the tool supports it: merge in batches so it never needs that many handles at once.