problem with modkit pileup

[paulinecoulon]

Good morning,

I am encountering this following error:

Singularity> MicrobeMod call_methylation -b /home/pmcoulon/Data/Genomic/MicrobeMod_results/TSV292_R_mapped.bam -r /home/pmcoulon/Data/Genomic/Nanopore/TSV292_R_polishing_out/TSV292_R_polypolished_polypolca/pypolca_corrected.fasta -t 24 --min_strand_coverage 10 -o /home/pmcoulon/Data/Genomic/MicrobeMod_results/TSV292_R
25-07-31 10:20:17 INFO Running modkit: modkit pileup -t 24 /home/pmcoulon/Data/Genomic/MicrobeMod_results/TSV292_R_mapped.bam /home/pmcoulon/Data/Genomic/MicrobeMod_results/TSV292_R_low.bed -r /home/pmcoulon/Data/Genomic/Nanopore/TSV292_R_polishing_out/TSV292_R_polypolished_polypolca/pypolca_corrected.fasta --only-tabs --filter-threshold 0.66
Traceback (most recent call last):
File "/opt/conda/bin/MicrobeMod", line 220, in
microbemod.main(
File "/opt/conda/lib/python3.9/site-packages/MicrobeMod/microbemod.py", line 520, in main
low_modkit_output = run_modkit(
File "/opt/conda/lib/python3.9/site-packages/MicrobeMod/microbemod.py", line 82, in run_modkit
subprocess.check_output(cmd, shell=True, stderr=subprocess.STDOUT).decode()
File "/opt/conda/lib/python3.9/subprocess.py", line 424, in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
File "/opt/conda/lib/python3.9/subprocess.py", line 528, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command 'modkit pileup -t 24 /home/pmcoulon/Data/Genomic/MicrobeMod_results/TSV292_R_mapped.bam /home/pmcoulon/Data/Genomic/MicrobeMod_results/TSV292_R_low.bed -r /home/pmcoulon/Data/Genomic/Nanopore/TSV292_R_polishing_out/TSV292_R_polypolished_polypolca/pypolca_corrected.fasta --only-tabs --filter-threshold 0.66' returned non-zero exit status 143.

Have you any idea on how to resolve it?

Thanks

Pauline