Error: reads weren't basecalled

[Arkadiy-Garber]

Could you please help me troubleshoot this:

root@nanodisco:~$ nanodisco preprocess -p 24 -f 2748_NP_methylation/fast5_pass/single_barcode12/ -s barcode12 -o 2748_NP_methylation/fastq_pass/barcode12/assembly/ -r 2748_NP_methylation/fastq_pass/barcode12/assembly/assembly.fasta

[2023-02-26 23:44:13] Localize all fast5 files.
[2023-02-26 23:44:13] Found 110340 fast5 files.
[2023-02-26 23:44:13] Extract sequences from fast5.
[2023-02-26 23:44:21] All fast5 files processed.
Warning message:
In extract.sequence(path_input, base_name, path_output, nb_threads, :
110340 reads weren't basecalled.
No reads were extracted. Please check that -f/--path_fast5 is correct.

This is after the reads were converted from multi-read format to single-read format. Sequencing was done using the new version 10 flow cells.

Thanks,
Arkadiy

[touala]

Hello @Arkadiy-Garber,

Unfortunately, the current version of nanodisco do not handle R10 datasets (only R9). Furthermore, fast5 with multi-read format can be used directly. I've recently shared a short example of analysis here.

Alan

[Arkadiy-Garber]

Hi @touala,

Thanks for the response. So do you think we would be able to use nanodisco on our data if we go through the steps outlined in the Issue#64 that you linked?

Cheers,
Arkadiy

[touala]

You currently cannot use nanodisco with R10.4.1 datasets. Is it your dataset type?

Alan

[touala]

But we are actively working on a R10.4.1 enabled version of nanodisco.

[oohas2000]

How can I download earlier versions of guppy?