Megalodon not producing any output, sitting idle

[bastian-wur]

Hi everyone,

I'm trying to use Megalodon, but I'm totally failing to do so. I have confirmed that I can run guppy on my data with a model to detect modified bases, and the output has the right SAM flags for modified bases. But if I run Megalodon, the process just sits there, and does nothing (around 1% CPU for more than 10 days now, whereas base calling goes within a few minutes).

my command: megalodon --outputs mods --processes 20 --guppy-config dna_r10.4_e8.1_modbases_5hmc_5mc_cg_fast.cfg --output-directory /nfs/research/biomics/Transfer/myname/nanopore_methylation_test_data/results_test_4 --overwrite --guppy-server-path /nfs/research/biomics/Software/ont-guppy-cpu/bin/guppy_basecall_server /nfs/research/biomics/Transfer/myname/nanopore_methylation_test_data

What's wrong with my command? I'm confused.

Best regards, Bastian