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Un arrêt de service aura lieu le lundi 27 mars de 17h à 21h pour maintenance.
Il ne sera plus possible d’utiliser forgemia ni d’accéder aux dépôts (git, container, packages…) pendant cette période.

  • OmnicrobeOmnicrobe
  • Extended Microorganisms Taxonomy
  • Issues
  • #15
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Issue created Apr 03, 2022 by Mouhamadou Ba@mandiaybaOwner

execution étape rewrite-taxonomy.snakefile

extended-microorganisms-taxonomy installé et toutes les étapes passent sauf la dernière concernant rewrite-taxonomy.snakefile. est-ce qu'il aurait des choses spécifiques à faire absentes du README ?

l'erreur est au niveau de la rule all qui ne retrouve pas ces inputs : repro

ssh front.migale.inrae.fr
/work_projet/omnicrobe_data/tm_workflow/extended-microorganisms-taxonomy
conda activate snakemake-6.9.1
snakemake --nolock --verbose --printshellcmds --use-singularity --use-conda --reason --latency-wait 60 --jobs 5 --snakefile rewrite-taxonomy.snakefile --cluster "qsub -v PYTHONPATH='' -l mem_free=24G -V -cwd -e log/ -o log/ -q short.q,long.q" --dryrun
Building DAG of jobs...
Full Traceback (most recent call last):
  File "/usr/local/genome/Anaconda3/envs/snakemake-6.9.1/lib/python3.9/site-packages/snakemake/__init__.py", line 699, in snakemake
    success = workflow.execute(
  File "/usr/local/genome/Anaconda3/envs/snakemake-6.9.1/lib/python3.9/site-packages/snakemake/workflow.py", line 763, in execute
    dag.init()
  File "/usr/local/genome/Anaconda3/envs/snakemake-6.9.1/lib/python3.9/site-packages/snakemake/dag.py", line 179, in init
    job = self.update([job], progress=progress, create_inventory=True)
  File "/usr/local/genome/Anaconda3/envs/snakemake-6.9.1/lib/python3.9/site-packages/snakemake/dag.py", line 801, in update
    raise exceptions[0]
  File "/usr/local/genome/Anaconda3/envs/snakemake-6.9.1/lib/python3.9/site-packages/snakemake/dag.py", line 759, in update
    self.update_(
  File "/usr/local/genome/Anaconda3/envs/snakemake-6.9.1/lib/python3.9/site-packages/snakemake/dag.py", line 920, in update_
    raise MissingInputException(job.rule, missing_input)
snakemake.exceptions.MissingInputException: Missing input files for rule all:
output/finish.txt

MissingInputException in line 5 of /work_projet/omnicrobe_data/tm_workflow/extended-microorganisms-taxonomy/rewrite-taxonomy.snakefile:
Missing input files for rule all:
output/finish.txt
Edited Apr 04, 2022 by Mouhamadou Ba
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