Error in Nanopolish indexing

[aman21392]

I am using the latest Dorado basecaller for basecalling, and I’ve noticed that the summary file it generates seems to differ from the one produced by Guppy. When I attempt to run nanopolish index, I receive the following warning:

warning: detected invalid summary file entries for 1737 of 1820 fast5 files These files will be indexed without using the summary file, which is slow.

I suspect this issue arises due to differences in the summary file format between Dorado and Guppy. Does this mean I cannot use your pipeline (e.g., for detecting m5C or m6A modifications) if I use Dorado for basecalling?

I appreciate any help you can provide.

[EduEyras]

Hi,

thanks for your email.

We'll soon make the new models available here: https://github.com/comprna/SWARM

SWARM will work with dorado

Please stay tuned!

Thanks

Eduardo

On Wed, 14 May 2025 at 03:52, Aman kumar singh @.***> wrote:

aman21392 created an issue (comprna/CHEUI#46) https://github.com/comprna/CHEUI/issues/46

I am using the latest Dorado basecaller for basecalling, and I’ve noticed that the summary file it generates seems to differ from the one produced by Guppy. When I attempt to run nanopolish index, I receive the following warning:

warning: detected invalid summary file entries for 1737 of 1820 fast5 files These files will be indexed without using the summary file, which is slow.

I suspect this issue arises due to differences in the summary file format between Dorado and Guppy. Does this mean I cannot use your pipeline (e.g., for detecting m5C or m6A modifications) if I use Dorado for basecalling?

I appreciate any help you can provide.

— Reply to this email directly, view it on GitHub https://github.com/comprna/CHEUI/issues/46, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADCZKB7MI3AUNZKFI5LUXND26IWNJAVCNFSM6AAAAAB5BI2IJWVHI2DSMVQWIX3LMV43ASLTON2WKOZTGA3DAOBRGUYTONQ . You are receiving this because you are subscribed to this thread.Message ID: @.***>