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
CNCI is trying to open your files as a Fasta file, becauase the first thing the program does if you provide GTF files is convert them to fasta. Almost certainly this conversion is failing and CNCI is therefore unable to open the FASTA file it thinks it should have created. 

Looking at the CNCI source code, the conversion is done in two steps. The first uses a perl script from CNCI's own directory to convert the GTF file to a bed file. The second uses twoBitToFa to convert said bed file to a FASTA file. The failure could be either one of these two steps. 

Thus I would try to the following commands to see which fail:

    perl PATH_TO_CNCI//gtf2Bed.pl candidate_lncs.gtf >  candidate_lncs.gtf.bed
    twoBitToFa -bed=candidate_lncs.gtf.bed ~/dataBase/GRCm38.2bit candidate_lncs.gtf.fa