Guppy default modified base calling configuration file doesn't exist

[JayVaz18]

Hello,

I am trying to run guppy for modified base calling and then use your package to extract the data. However, do you know why the configuration file provided on the Nanopore Guppy Modified Base Calling Toolkit website doesn't exist in the data folder?

Here is the command I used:

guppy_basecaller -i /Users/jakevazquez18/Desktop/guppy -s /Users/jakevazquez18/Desktop/guppy/fast5/mod_out2 --num_caller 10 --records_per_fastq 0 --fast5_out -c dna_r9.4.1_450bps_modbases_dam-dcm-cpg_hac.cfg

And got this error:

/Desktop/ont-guppy-cpu/data/dna_r9.4.1_450bps_modbases_dam-dcm-cpg_hac.cfg does not exist!

Can somebody help me understand why? The only configurations file I see in the data folder for DNA base modifications are for 5mC but not 6mA.

[fbrennen]

Hi @JayVaz18 -- apologies, the documentation is slightly out of date. We updated the modified base models in Guppy 4.5.2, and removed the olds. You should be able to get it to work using this configuration file: dna_r9.4.1_modbases_5mc_hac.cfg