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

[marcus1487]

Megalodon is being deprecated so I would recommend using Guppy, Bonito or Dorado.

Megalodon has not been tested with the modified base guppy models so it may be an issue with this. The current recommendation for calling mods from megalodon is to pass in the --remora-model option. Also note that running the guppy backend on cpu only resources will likely be very slow and may be contributing to this issue.

[bastian-wur]

You guys need to make an overview somewhere what you're still developing or what not, and for what purpose. Trying to figure out what tool to use for Nanopore data confronts someone with 4+ different tools developed by you guys alone, without a clear idea what's still developed or for what purpose to use :/.

I managed to run my data with guppy in the meantime though.