m6anet dataprep does not generate output from nanopolish eventalign input

[rhliii]

Dear m6Anet developers,

Thank you for your great work on m6Anet. I am currently trying to use the pipeline with input generated from nanopolish eventalign, but encountered an issue during the dataprep stage. Despite successfully generating the eventalign.txt file, the m6anet dataprep step did not produce any output files

Below is the exact command-line pipeline I used:
`nanopolish eventalign
--reads "$fq"
--bam "$bam"
--genome "$GENOME"
--scale-events
--signal-index
--summary "$out_dir/summary.txt"
--threads 30 > "$out_dir/eventalign.txt"

m6anet dataprep
--eventalign "$out_dir/eventalign.txt"
--out_dir "$out_dir"
--n_processes 20

m6anet inference
--input_dir "$out_dir"
--out_dir "$out_dir"
--n_processes 20
--num_iterations 1000
`
File structure after running dataprep：

Preview of eventalign.txt content:

Preview of eventalign.index content:

Data.info only has the title: (transcript_id, read_index, pos_start, pos_end)

I noticed that similar issues have been mentioned in other posts. I also tried removing rows in the eventalign.txt file where the 10th column (model_kmer) is NNNNN, and then reran m6anet dataprep, but unfortunately no output was generated. I would really appreciate your guidance on how to resolve this issue.

I would greatly appreciate it if you could let me know whether there might be an issue with the format of my eventalign.txt, or if any additional preprocessing or formatting is required before running dataprep.

Thank you very much in advance for your time and support!

Best regards

[yuukiiwa]

Hi @rhliii,

Can you share the first 10 lines of your gtf and fasta files, please?

Thanks!

Best wishes,
Yuk Kei

[rhliii]

Hi @yuukiiwa ,

Thank you very much for your quick response, and my sincere apologies for not providing the file details in time.
Below are the first 10 lines of my GTF and FASTA files. If anything looks inconsistent or sub‑optimal, I’d be very grateful for your guidance.

Mus_musculus.GRCm38.101.gtf：

Mus_musculus.GRCm38.cdna.all.fa：

Many thanks again for your outstanding work!

Best wishes

[yuukiiwa]

Hi @rhliii,

The transcript_id in the fasta and the eventalign.txt file has the transcript version, whereas the gtf does not have that. Here are two ways you can solve it:

1. Replace the transcript_id in the gtf file with the transcript_id with transcript version ENSMUSTxxxxxxxx.X and run m6anet dataprep again

2. Strip the transcript version (ENSMUSTxxxxxxxx.X --> ENSMUSTxxxxxxxx) in the fasta file and run minimap2 and eventalign again.

Thanks!

Best wishes,
Yuk Kei