Has anyone here worked with CNCI before? I'm just about exhausted trying to figure out what I'm doing wrong.
So, I tried the following:
python CNCI.py candidate_lncs.gtf -g -o test -m ve -p 16 -d ./dbase GRCm38.primary_assembly.genome.fa
and I recieved the following error:
name@server %57> CNCI.py -f candidate_lncs.gtf -g -o test -m ve -p 16 -d ~/dataBase/GRCm38.2bit /home/pgian1/src/CNCI sh: 1: twoBitToFa: not found Traceback (most recent call last): File "CNCI.py", line 533, in <module> GtfInFiles = open(fastaFiles) IOError: [Errno 2] No such file or directory: 'candidate_lncs.gtf.fa'
It looks to me that CNCI is trying to read my GTF file as a fasta file. I'm not sure why though. I have tried different versions of python, changing my path, etc and nothing is working. Any help at all is appreciated!! Or if someone could find a protocol or something that demonstrates CNCIs usage. I have found nothing so far