search

fanglab / nanodisco

nanodisco: a toolbox for discovering and exploiting multiple types of DNA methylation from individual bacteria and microbiomes using nanopore sequencing.
Other
66 stars 7 forks source link

unexpected error during read extraction process using nanodisco preprocess #73

Open tweedle828 opened 1 year ago

tweedle828 commented 1 year ago

Hi,

I'm using nanodisco to analyze the WGA dataset (https://www.ncbi.nlm.nih.gov/biosample/SAMEA111521248). I used the following command and I don't know why I got following error there...

Thanks for your help.

nanodisco preprocess -p 8 -f E1_WGA_even_coverage_fast5 -s E1_WGA_even_coverage_fast5 -o ../analysis/E1_WGA_even_coverage_fast5 -r ../reference/SC452.fasta

nanodisco preprocess -p 8 -f B2_WGA -s B2_WGA -o ../analysis/B2_WGA -r ../reference/SC419.fasta [2023-06-20 18:40:08] Localize all fast5 files. [2023-06-20 18:40:08] Found 66 fast5 files. [2023-06-20 18:40:08] Extract sequences from fast5. Processed fast5 [-------------------------] 0% eta: ?s (elapsed: 00:00:00) Error in { : task 1 failed - "task 1 failed - "task 21 failed - "non-character argument""" Calls: extract.sequence -> %dopar% -> Execution halted Unexpected error during read extraction process.

touala commented 11 months ago

Hello @tweedle828,

Were those fast5 basecalled? I've wrote a simple example for nanodisco processing here.

Please let me know if this help.

Alan