Error in rule uncompress_genome

[louphey]

Hello, ljyanesm

Another error was encountered while running command "daijin assemble --cores 30 daijin.yaml" with mikado v2.2.3 yesterday according to the Daijin tutorial https://mikado.readthedocs.io/en/latest/Tutorial/Daijin_tutorial/#step-2-running-the-assemble-part

If I want to continue running the command, I have to copy Reference/Drosophila_melanogaster.BDGP6.dna.toplevel.fa to Dmelanogaster/0-reference/genome.fa"

The following is error message .

Error in rule uncompress_genome:
jobid: 0
output: Dmelanogaster/0-reference/genome.fa

RuleException:
TypeError in line 470 of /home/app/miniconda2/envs/mikado/lib/python3.8/site-packages/Mikado/daijin/assemble.smk:
symlink: dst should be string, bytes or os.PathLike, not OutputFiles
File "/home/app/miniconda2/envs/mikado/lib/python3.8/site-packages/snakemake/executors/init.py", line 2326, in run_wrapper
File "/home/app/miniconda2/envs/mikado/lib/python3.8/site-packages/Mikado/daijin/assemble.smk", line 470, in __rule_uncompress_genome
File "/home/app/miniconda2/envs/mikado/lib/python3.8/site-packages/snakemake/executors/init.py", line 568, in _callback
File "/home/app/miniconda2/envs/mikado/lib/python3.8/concurrent/futures/thread.py", line 57, in run
File "/home/app/miniconda2/envs/mikado/lib/python3.8/site-packages/snakemake/executors/init.py", line 554, in cached_or_run
File "/home/app/miniconda2/envs/mikado/lib/python3.8/site-packages/snakemake/executors/init.py", line 2357, in run_wrapper
Exiting because a job execution failed. Look above for error message
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /path/to/.snakemake/log/2021-03-27T100112.595247.snakemake.log

[lucventurini]

Dear @louphey

Thank you again for your bug report. We will investigate, it's probably something minor as we test that part of the pipeline constantly before releasing.

We will try to update you tomorrow.

Kind regards,

[lucventurini]

Dear @louphey

Thank you for pointing this out, there was indeed a bug. I just fixed it, and I am revising the tutorial as well.

Many thanks again.

Kind regards,
Luca Venturini