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Possible issue with file path in bgcflow\workflow\rules\common.smk #369
Description
We had issue with following line:
Step 4. Preparing list of final outputs...
- Getting outputs for project: Lactobacillus_delbrueckii
WorkflowError in file /home/mhaahr/bgcflow/workflow/rules/common.smk, line 731:
Failed to open source file /home/mhaahr/bgcflow/workflow/../../workflow/rules.yaml
FileNotFoundError: [Errno 2] No such file or directory: '/home/mhaahr/bgcflow/workflow/../../workflow/rules.yaml'
Worked afrer updating from:
Line 731: with open(workflow.source_path(f"../../{rule_dict_path}"), "r") as file:
to:
Line 731: with open(workflow.source_path(f"../{rule_dict_path}"), "r") as file:
Activity
alpole23 commentedon Feb 12, 2025
ran into this same issue. your fix solved the problem. thanks!
shuklagyanesh21 commentedon Apr 6, 2025
At the first sight it seems to work. But does it really? Did it work for your own dataset?
I am getting a lot of "File Not Found Error" Especially when we try to build reports even if the files are processed and present in the interim folder, for some reason the summary df(s) are not being created for most rules in the tables folder (where the program looks for df(s) for building most reports).
How can such a issue be number #369 ? No one till now saw this wrong relative path calling issue which is present in plain sight? We are doing something incorrect I feel.
MatissMaleckis commentedon Jul 15, 2025
Solved the problem after doing fresh install, thank you Magnus!
georgiibondarev commentedon Nov 12, 2025
Changing Line 731 to
with open(workflow.source_path(f"../{rule_dict_path}"), "r") as file:fixed this problem for me too. Thanks, Magnus!Fix file path for rule dictionary loading
jnesme commentedon Mar 6, 2026
Run into the same issue in March 2026 - is this an abandonned project ? I am working with Tilman at DTU and happy to help @matinnuhamunada !