MLST error
Closed this issue · 8 comments
I was running Campype using my own Vibrio datasets, including 1 V. parahaemolyticus, 6 V. alginolyticus, and 17 V. diabolicus.
Because V. alginolyticus and V. diabolicus generate only 4 columns of house keeping gene in MLST, but V. parahaemolytiucs generate 7 columns. So, there is a error in generating uneven column of this file.
Then I tried to skip the process, including deactivate mlst analysis in config file, changing campype.py program file. I also tried adding reference genome, and even change species name in the input_files, but none of those attempts work.
campype.1.log
campype.2.log
MLST(1).txt
We apologize for the error and we are trying to solve it as soon as possible as also happened here #140 (comment). We will get back to you when solved, including the error in the CSV report. Sorry for the inconveniences
Thanks very mcuh for your reply!! I am looking forward to when when you solve the problem.
@sdvjucw The issue with the csv report (campype.2.log) has just been solved. Please, updated CamPype and rerun again making sure you deactivate the MLST analysis.
We are working to solve the error you encountered in campype.1.log.
Hi~ Thanks for the update! Could you please publish a example input_files for assembled genomes? I can't run campype in Fastq mode with my personal computer.
Here you have: input_files.csv
Hi! I really appreciate your fast reply. Unfortunately here is another error happened in Prokka.
campype.log
the data I put in were the contigs file generated by SPAdes.
I would really appreciate it if you could fix it or tell me if I made mistake.
Hi @sdvjucw . I that error is addressed in the FAQ section of the repository.
Please try running prokka --setupdb on your terminal after activating campype env (conda activate campype).
@JoseBarbero I just successfully generated final report without running mlst. It is very kind of you for helping me run this pipeline.