Error while running LILO

[el-mat]

Dear, I get the following error while running LILO. Any idea what could be the problem?

/bin/bash: /home/minion/anaconda3/envs/LILO/etc/profile.d/conda.sh: No such file or directory

CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
To initialize your shell, run

    $ conda init <SHELL_NAME>

Currently supported shells are:
  - bash
  - fish
  - tcsh
  - xonsh
  - zsh
  - powershell

See 'conda init --help' for more information and options.

IMPORTANT: You may need to close and restart your shell after running 'conda init'.


/bin/bash: line 2: scaffold_builder.py: command not found
sed: can't read reads_24h_Scaffold.fasta: No such file or directory
[Wed Aug 10 11:12:28 2022]
Error in rule scaffold:
    jobid: 1
    output: reads_24h_Scaffold.fasta
    shell:
        source $CONDA_PREFIX/etc/profile.d/conda.sh
                conda activate scaffold_builder
                scaffold_builder.py -i 75 -t 3693 -g 80000 -r /home/minion/lilo-test/ASFV.reference.fasta -q reads_24h/polished_trimmed.fa -p reads_24h
                sed -i '1 s/^.*$/>reads_24h_Lilo_scaffold/' reads_24h_Scaffold.fasta
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Job failed, going on with independent jobs.
Exiting because a job execution failed. Look above for error message
Complete log: /home/minion/lilo-test/.snakemake/log/2022-08-10T111227.425486.snakemake.log

Kind regards, Elisabeth