Module not found tqtm after install with conda

[RxLoutre]

Hello there !

I have installed NanoCaller with conda (mamba) :

mamba install -c bioconda nanocaller

I install this within its own environnement with no other tool in it.

And then trying to call nanocaller, I get the following error :

Nanocaller --bam myBam.bam --ref my_ref.fasta --cpu 4 --mode snps

NanoCaller command and arguments are saved in the following file: SequencingProjects/202408/analysis/Flongle/ASC410/sushi/args
Traceback (most recent call last):
  File "/miniconda3/envs/nanocaller/bin/NanoCaller", line 186, in <module>
    run(args)
  File "/miniconda3/envs/nanocaller/bin/NanoCaller", line 13, in run
    from nanocaller_src import snpCaller, indelCaller
  File "/miniconda3/envs/nanocaller/bin/nanocaller_src/snpCaller.py", line 2, in <module>
    from tqdm import tqdm
ModuleNotFoundError: No module named 'tqdm'

I find this odd, but as I try to fix the issue by installling the requested package with conda, it shows it is actually already installed.

Any idea of what is going on here ? :)

Thank you for your help !

Best,

Roxane

[umahsn]

Hi Roxane,

The problem could be that the correct python installation is not being used by NanoCaller. Can you activate the nanocaller environment and run the following commands in terminal?

echo $PATH
python -c 'import sys; print(sys.executable)'
echo $CONDA_PREFIX

Best,
Umair