Unsupported number of states

[mmahlke]

Hi! New Megalodon user. I'm getting this error I don't understand:

[guppy/error] Unsupported number of states: 1. State count should be a positive power of 4.. Error initialising basecall server using port: ipc:///scratch/slurm-364559/2f15-b630-de9b-5edb. Aborting.

Any help would be very appreciated!

My command: megalodon
fast5_pass
--guppy-server-path $guppy_path
--guppy-params "--model_file /ihome/crc/install/guppy/ont-guppy_gpu_6.1.2/data/dna_r9.4.1_e8.1_modbases_5mc_cg_hac.jsn"
--guppy-config /ihome/crc/install/guppy/ont-guppy_gpu_6.1.2/data/dna_r9.4.1_e8.1_modbases_5mc_cg_hac.cfg
--output-directory out_081022_1
--outputs basecalls mappings mod_basecalls mod_mappings mods
--reference chm13.draft_v1.1.fasta
--mod-motif Z N 0
--devices 0 1
--processes 20
--verbose-read-progress 3

Guppy server log: [guppy/message] ONT Guppy basecall server software version 6.1.2+e0556ff, client-server API version 11.0.0, minimap2 version 2.22-r1101 log path: out_081022_1/guppy_log chunk size: 2000 chunks per runner: 256 max queued reads: 2000 num basecallers: 4 num socket threads: 2 max returned events: 50000 gpu device: cuda:0 cuda:1 kernel path:
runners per device: 4 Use of this software is permitted solely under the terms of the end user license agreement (EULA).By running, copying or accessing this software, you are demonstrating your acceptance of the EULA. The EULA may be found in /ihome/crc/install/guppy/ont-guppy_gpu_6.1.2/bin

2022-08-10 10:40:47.430185 [guppy/info] crashpad_handler not supported on this platform. 2022-08-10 10:40:47.430800 [guppy/info] Listening on port ipc:///scratch/slurm-364559/2f15-b630-de9b-5edb. 2022-08-10 10:40:47.524441 [guppy/error] Unsupported number of states: 1. State count should be a positive power of 4.. Error initialising basecall server using port: ipc:///scratch/slurm-364559/2f15-b630-de9b-5edb. Aborting. 2022-08-10 10:40:47.524924 [guppy/message] The basecall server has shut down successfully.

[marcus1487]

We are working to deprecate megalodon at the moment. Are you able to run this basecalling model from Guppy standalone?

[mmahlke]

Thank you! Deprecate--as in permanently? Is the plan to integrate modified base calling into guppy directly?

[marcus1487]

Remora modified base calling has been included in Guppy since version 6.1.1 (March 2022; login required) and will be in Dorado (replacement for Guppy) shortly. So yes the idea is to permanently deprecate megalodon.