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draeger-lab / SABINE

Prediction of the binding specificity of transcription factors using support vector regression
GNU General Public License v3.0
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Invalid base directory. Aborting. Base directory: tmp/validator_tmp/ #2

Open papelypluma opened 2 years ago

papelypluma commented 2 years ago

Hi SABINE developers, thank you for developing and sharing this tool with the community. I managed to install SABINE based on the instructions. However, running ./sabine -check-install gives me the following output:

Invalid base directory. Aborting. Base directory: tmp/validator_tmp/

I'm wondering if this is something that needs to be addressed prior to running SABINE, although I tested SABINE on TFpredict's output (sample fasta file included assuming that it's a human sequence) (as SABINE input). It worked, but it didn't have any predictions as to what the DNA binding motif is.

Thanks a lot for the help!

draeger commented 2 years ago

@papelypluma Thank you for your feedback. Would you mind sharing a sample data set (could also be a reduced one) via email (andreas.draeger@uni-tuebingen.de)? This makes it easier to reproduce the problem.

papelypluma commented 2 years ago

Hi @draeger. Thank you for looking into this.

draeger commented 2 years ago

The script runs after creating the folder tmp directly in the SABINE main folder. This problem won't appear in next versions because it is now calling the method File.mkdirs instead of mkdir. SABINE attempted to create multiple folders at once but couldn't.