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
Do you have
twoBitToFain your path. Taking a quick look at the source code here and the error it seems since
twoBitToFais not in the path the required fasta file creation failed.
The user edited the other question to say that
twoBitToFais in the PATH variable ( Error from CNCI usage (coding non coding index) What to do? )
Thank you. Yes,
twoBitToFais in my path.
This a duplicate of this question.
Yes, I wanted to ask a formal question and this was more of just a forum post to just connect with others who have also used CNCI. I apologize if this violated etiquette.
Is this the absolute minimum example that you are trying to run?, i.e., you have followed some tutorial line by line and are running the commands exactly as per the tutorial?
Be wary of, e.,g., character encodings. For example, there are a few different encodings of the hyphen, which can often affect command line parameter parsing. Also, if you work between a Windows and Mac/Linux system, be wary of end-line character encodings in your files.
I had a look at the GitHub landing page ( https://github.com/www-bioinfo-org/CNCI ), in fact, and I am not sure that you are running it correctly (?). Please try:
Thank you Kevin for the advice, I was unable to find a CNCI tutorial so this is based purly off the github page. I am a newbie/beginner so if anyone knows of a tutorial I would appreciate the guidance.