Empty .bedGraph.gz and .bismark.cov.gz files

[geethavenk]

Description of the bug

Hi, I am using methylseq and for one of the samples, the .bedGraph.gz and .bismark.cov.gz files are empty. When I checked the .command.err file, I see the following error.
"Failed to open filehandle: Too many open files at /usr/local/bin/bismark2bedGraph line 279, line 7034081."
I did not have this problem before while processing the samples.

Command used and terminal output

nextflow run nf-core/methylseq \
  -r 2.6.0 \
  --input /samplesheets/samplesheet_sample_m.csv \
  --outdir /output/sample_m \
  --unmapped \
  --em_seq \
  --meth_cutoff 1 \
  --bismark_index /ucsc/BismarkIndex/ \
  -c gvenk_mod.config


Output:
Now writing methylation information for file >>CpG_OT_sample_m_1_val_1_bismark_bt2_pe.deduplicated.txt.gz<< to individual files for each chromosome
Failed to open filehandle: Too many open files at /usr/local/bin/bismark2bedGraph line 279, <IN> line 7034081.
Finished BedGraph conversion ...

Relevant files

No response

System information

Nextflow version - 23.10.1
Hardware - HPC

[sateeshperi]

TODO: add --scaffolds option to docs
https://felixkrueger.github.io/Bismark/options/methylation_extraction/#bedgraph-specific-options

[sateeshperi]

@geethavenk Kindly update whether the above param helps with the reported issue