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fanglab / nanodisco

nanodisco: a toolbox for discovering and exploiting multiple types of DNA methylation from individual bacteria and microbiomes using nanopore sequencing.
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Error: reads weren't basecalled #67

Open Arkadiy-Garber opened 1 year ago

Arkadiy-Garber commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

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

Alan

touala commented 1 year ago

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

oohas2000 commented 1 year ago

How can I download earlier versions of guppy?