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adnaniazi / tailfindr

An R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA and DNA reads.
https://www.cbu.uib.no/valen/
GNU General Public License v3.0
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Unexpected token '--fast5_out' on command-line. #46

Open xcarmengrandix opened 1 year ago

xcarmengrandix commented 1 year ago

Hi,

I am trying to basecall my fast5 files. I have done it many times with the following code:

"C:\Program Files\OxfordNanopore\MinKNOW\guppy\bin\guppy_basecaller.exe" \ --config rna_r9.4.1_70bps_hac.cfg \ --input_path \path\to\raw\reads\folder \ --recursive \ --save_path \path\to\save\basecalled\data\to\ --fast5_out \ --trim_strategy none \ --num_callers 1 \ --cpu_threads_per_caller 8 \ 2>&1 | tee logfile.txt

But now I get this error: Unexpected token '--fast5_out' on command-line.

If I remove --fast5_out from the code, it works. Did something change?

Thanks for your help!

Carmen

adnaniazi commented 1 year ago

Hi,

May be you are using the latest version of basecaller which no longer supports outputting of FAST5 file. Try switching to Guppy version less than v6.3.2. RNA basecalling model performance is the same between older and latest Guppy versions. The older version can output FAST5 files, while the latest versions only produce FASTQ files.

xcarmengrandix commented 1 year ago

Hi, Thank you for the quick reply. Do you know by any chance where I can find previous versions or how to downgrade it? Nanopore allows to download only the most recent one.

adnaniazi commented 1 year ago

Do the following:

  1. Visit the Downloads page to find the link for the latest Guppy for your platform https://community.nanoporetech.com/downloads
  2. Visit the link below to find which versions of guppy are actually available: https://community.nanoporetech.com/downloads/guppy/release_notes
  3. Note down the version number that you want to download.
  4. Change the version number in the download URL (in step 0) of latest guppy version to the version number that you are interested in (that you found in step 2).

So if the download URL of latest Guppy is https://cdn.oxfordnanoportal.com/software/analysis/ont-guppy-cpu_6.4.6_linux64.tar.gz

then I just need to change 6.4.6 to 6.2.1 to download the old version for CPU Guppy that still supports FAST5 output. The download link for CPU Guppy will then be: https://cdn.oxfordnanoportal.com/software/analysis/ont-guppy-cpu_6.2.1_linux64.tar.gz

xcarmengrandix commented 1 year ago

It now works! Thank you :)