Open shelkmike opened 1 year ago
I encountered the same problem too, and I think mybe fast_circ.py import donovo.py without the option of '--cuff'. But I konw little about python to edit the .py file, sorry
@bakillersky
I've found a solution for this problem. After "fast_circ.py denovo" stops with this error, I run "CIRCexplorer2 denovo" separately with a command like this:
CIRCexplorer2 denovo --ref=$path_to_the_file_with_information_on_genes --genome=$path_to_the_reference --bed=./CIRCexplorer2_results/back_spliced_junction.bed --cuff=./CIRCexplorer2_results/assemble/ --tophat=./CIRCexplorer2_results/alignment/tophat --output=./CIRCexplorer2_results/denovo/
Here, "CIRCexplorer2_results" is the folder where "fast_circ.py denovo" wrote its results to.
@shelkmike You are such a genius!!! thank you so much
When running "fast_circ.py denovo" from the latest version of CIRCexplorer2, I encountered the following error: