8000 Error in rule convert_individual_overview running TOBIAS 0.12.10 · Issue #75 · loosolab/TOBIAS · GitHub
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Error in rule convert_individual_overview r 8000 unning TOBIAS 0.12.10 #75

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Knetsy opened this issue Jun 9, 2021 · 2 comments
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Error in rule convert_individual_overview running TOBIAS 0.12.10 #75

Knetsy opened this issue Jun 9, 2021 · 2 comments
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@Knetsy
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Knetsy commented Jun 9, 2021 •
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Hi,
I ran TOBIAS in the past and it gave us meaningful results :) ! Now I have a new experiment and I am running TOBIAS 0.12.10 (after running into the issue #64) using the snakemake pipeline and I encountered an error at the rule convert_individual_overview. Looking at the log files it seems to be a problem with R installing packages and the error displayed is : "ERROR: failed to lock directory ...".

I have attached the log as well as an example of the error message for the transcription factor SPI1 for more clarity.

Thank you in advance for your help!

Deborah
@msbentsen
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Hi,

I had a look at this - you are right that something is going wrong with that rule. I think it might be an issue with the initial install of the 'wilson' package. I will see if I can get it solved within the next couple of days.

If you don't need those files, you can also tell snakemake to just keep going even if some rules fail. This is done by appending --keep-going to the snakemake call on the commandline. This will ensure that all other rules finish as planned. Hope you can use this as a temporary solution.

Best Mette

@msbentsen msbentsen added the bug Something isn't working label Jun 14, 2021
@msbentsen
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I just made some updates to the snakemake respository, which should solve the issue. I split some of the packages into individual conda environments, so the first run of the pipeline might take a little longer due to building the new environments. Also, if you use the same output folder, please delete the "wilson" folder before re-running the pipeline - that will ensure that wilson is re-installed (this time correctly).

Please let me know if this solves the issue, thanks!

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