search

novoalab / EpiNano

Detection of RNA modifications from Oxford Nanopore direct RNA sequencing reads (Liu*, Begik* et al., Nature Comm 2019)
GNU General Public License v2.0
109 stars 31 forks source link

Error with EpiNano Predict #121

Closed agouru55 closed 1 year ago

agouru55 commented 2 years ago

Hello! I am running into the following error when running Epinano_Predict with the pre-trained RRACH motif.:

Commad:  EpiNano/Epinano_Predict.py -m rrach.q3.mis3.del3.linear.dump -p alignment.sorted.chr1.plus_strand.per.site.5mer.csv -cl 8,13,23 --out_prefix rna_mod
Traceback (most recent call last):
  File "EpiNano/Epinano_Predict.py", line 73, in <module>
    mod_col = int (args['modification_status_column']) - 1 if args['modification_status_column'] else None
ValueError: invalid literal for int() with base 10: 'rrach.q3.mis3.del3.linear.dump'

The prior steps all seemed to work properly. How can I address this error? Thanks so much!

enovoa commented 1 year ago

Hi @agouru55 apologies for the slow reply - were you able to solve this issue? Otherwise please let me know. Thanks!

Huanle commented 1 year ago

Hi @agouru55 ,

It's my bad for this late reply. The error msg indicates that the column number that you passed is not valid. Do you mind sharing a few lines of your input for me to help with debugging?

enovoa commented 1 year ago

Hi @agouru55 i assume this has been solved. If not please reopen. Thanks!