problem with running tradis pipeline multiple

[gaworj]

Hello,

When I try to run following command using quatradis:

tradis pipeline multiple -v -n 12 -o quatradis_out fastqs_filtered_sizecut_all.txt genome.fa

this error appears:
Traceback (most recent call last):
File "/home/jang/anaconda3/envs/mamba/envs/albatradis/bin/tradis", line 293, in
main()
File "/home/jang/anaconda3/envs/mamba/envs/albatradis/bin/tradis", line 285, in main
args.func(args)
File "/home/jang/anaconda3/envs/mamba/envs/albatradis/bin/tradis", line 202, in run_multiple_pipeline
tradis.run_multi_tradis(args.fastqs, args.reference,
File "/home/jang/anaconda3/envs/mamba/envs/albatradis/lib/python3.9/site-packages/quatradis/tradis.py", line 142, in run_multi_tradis
pipeline = find_pipeline_file()
File "/home/jang/anaconda3/envs/mamba/envs/albatradis/lib/python3.9/site-packages/quatradis/tradis.py", line 101, in find_pipeline_file
if os.path.exists(exe_path):
File "/home/jang/anaconda3/envs/mamba/envs/albatradis/lib/python3.9/genericpath.py", line 19, in exists
os.stat(path)
TypeError: stat: path should be string, bytes, os.PathLike or integer, not NoneType

What I'm doing wrong?

The same input files work smoothly in bacteria_tradis.

Bests,
Jan

[sbastkowski]

Hi Jan, we are aware of this issue and are in the process of fixing it. In the meantime we strongly encouraged to use docker for running the multiple pipeline. I will update you asap on the progress.