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pedronachtigall / CodAn

CDS prediction in transcripts
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Stuck at CDS Prediction #10

Open limpengken opened 3 years ago

limpengken commented 3 years ago

Hi, CodAn always stuck at the CDS prediction step. Can you help me? I made sure that my python version = 3.7 and the lines of my fasta file did not exceed 1.2k characters. I installed Codan using conda in a new environment following the tutorial.

This is the command I used:

codan.py -t ./CodAn_output/good.Psilotum_nudum_transcripts_90.fasta -c 3 -m ./CodAn_models/PLANTS_partial/ -s plus

I am stuck here:

2021-09-23 16:41:06 >>>> starting CodAn (v1.1 June 2021)... transcript file -> ./CodAn_output/good.Psilotum_nudum_transcripts_90.fasta model -> ./CodAn_models/PLANTS_partial/ strand prediction -> plus number of threads -> 3 2021-09-23 16:41:06 >>>> CDS prediction...

pedronachtigall commented 2 years ago

Hi @limpengken ,

Sorry for the slow response. Did you solve this issue? If not, try to specify the entire PATH to the model or the PATH from the working directory to the model (i.e., remove the "./" from model PATH). Do this to the transcript file also.

Hope that this helps you, please let me know if are still having issues.

Best, Pedro