Fast5 not getting proccesed.

[AlbertoOsorio]

Hi, I have just installed bonito via pip and I also found some fast5 files to test it, but when I enter the command to start basecalling ( bonito basecaller dna_r10.4_e8.1_sup@v3.4 /path_to_file.fast5 > basecalls.bam or bonito basecaller dna_r10.4_e8.1_sup@v3.4 /path_to_folder > basecalls.bam ) the following happens:

loading model dna_r10.4_e8.1_sup@v3.4 outputting unaligned bam completed reads: 0
duration: 0:00:00 samples per second 0.0E+00 done

I tried uninstalling the pip installation and installing the source version but I have the exact same issue that way

[AlbertoOsorio]

I also have a small non realted question, The source installation includes reamora?

[iiSeymour]

Hi @AlbertoOsorio

Can you confirm you are passing a directory that contains one or more *.fast5 files inside? By default, bonito will only call the files inside the directory specified. If the files are inside subdirectories then you can add --recursive to process them all.

Yes, bonito depends on remora so installing bonito will also install remora.

[AlbertoOsorio]

Thanks for replying @iiSeymour !! Yes, the directory is fine I even tried to pass a single fast5 file directly into the CLI and I got the same results, my os is popos 21.04 I think it might be because of that so I am trying the installation again in a vm of ubuntu 20.04.

[oskesr]

Hi @AlbertoOsorio , I have the same issue as yours on Ubuntu 20.04. Any success with your VM installation ?

[AlbertoOsorio]

I tried to install on ubuntu 20.04. Currently I am running on a different issue because y also want to install megalodon and other ont programs, I might test again with a fresh installation in a few days @oskesr

[AlbertoOsorio]

I am also trying windows installation. As soon as I get updates I'll tell you