search

hasindu2008 / f5c

Ultra-fast methylation calling and event alignment tool for nanopore sequencing data (supports CUDA acceleration)
https://hasindu2008.github.io/f5c/docs/overview
MIT License
144 stars 26 forks source link

Error in eventalign #113

Closed Tomcxf closed 1 year ago

Tomcxf commented 2 years ago

Well, I test f5c to index, it really faster than before. It works! but when I use f5c to eventalign, it print out on screen: [E::faidx_adjust_position] The sequence "NM_001035539.1" not found [E::faidx_adjust_position] The sequence "NM_001035539.1" not found ...... [get_rank::WARNING] A None ACGT base found : U [get_rank::WARNING] A None ACGT base found : U [get_rank::WARNING] A None ACGT base found : U ...... Now it has run two hours, and there is nothing written in output file I don't know what's wrong with it. Or it is just normal. Thank you!

hasindu2008 commented 2 years ago

Hi

First can I confirm if your date is DNA or RNA? If the data is RNA, make sure you specify --rna option to f5c eventalign. Then that warning on U should disappear.

On that warning about the contig not found, what are you specifying to -g option? Make sure if that genome you specify to -g is the same as the reference you used to generate the BAM file?

hasindu2008 commented 2 years ago

@Tomcxf Any updates on this?

Tomcxf commented 2 years ago

Sorry to reply so late. The problem has been solve through your advise Thank you!

hasindu2008 commented 2 years ago

How is the runtime performance like? Was there an improvement?

Tomcxf commented 2 years ago

yes, it can improve time greatly! Thank you for your donation to ONT!