Open lssb opened 2 years ago
Hi Issb, I'm having the exact same problem as you are with CLEAR, and I was wondering if you were ever able to find out what was causing the issue. I'm not sure where the error could be coming from; the CLEAR source code shows the .tmp file being made so I'm not sure why it can't be found.
It turns out the problem was that the I had the wrong versions of GenePredtoGTF/GTFtoGenePred installed. I specifically had to run the follow commands in my anaconda environment to get the pipeline to work:
conda install -c bioconda ucsc-genepredtogtf=366
conda install -c bioconda ucsc-gtftogenepred=366
It turns out the problem was that the I had the wrong versions of GenePredtoGTF/GTFtoGenePred installed. I specifically had to run the follow commands in my anaconda environment to get the pipeline to work:
conda install -c bioconda ucsc-genepredtogtf=366 conda install -c bioconda ucsc-gtftogenepred=366
I did install the version of these genepredtogtf and gtftogenepred, however, still the genePred.tmp not generated, I am not sure, why it could not be found. Many thanks for helping.
Hi, Thanks for CLEAR. I am in troubles using CLEAR and looking for solutions. I need your help and this is the error log.