weird python error

Question

[2405592M]

Hi people!

I downloaded this program and I'm trying to generate a tRNA database but I keep getting the following error:

Traceback (most recent call last):
  File "maketrnadb.py", line 73, in <module>
    getmaturetrnas.main(trnascan=[scanfile], genome=genomefile,gtrnafa=gtrnafafile,bedfile=dbname+"-maturetRNAs.bed",maturetrnatable=dbname+"-trnatable.txt",trnaalignment=dbname+"-trnaalign.stk",locibed=dbname+"-trnaloci.bed",maturetrnafa=dbname+"-maturetRNAs.fa")
  File "/mnt/data/BMOHAMED/TRAX/tRAX-master/getmaturetrnas.py", line 113, in main
    cmrun = subprocess.Popen(cmcommand, stdout = devnull)
  File "/home/bmohamed/miniconda2/lib/python2.7/subprocess.py", line 394, in __init__
    errread, errwrite)
  File "/home/bmohamed/miniconda2/lib/python2.7/subprocess.py", line 1047, in _execute_child
    raise child_exception
OSError: [Errno 2] No such file or directory

I can't figure out what file/directory (if any) is missing.

Please Help !!

Thanks in advance

[jared.andrews07]

What command are you calling? It sounds like you're missing arguments.

Answer 1

[bioinformatics2020]

Just by looking at the maketrnadb command, you're either missing one of the required files, or it's in a different directory than the one you are calling the script from.

maketrnadb.py --databasename=dbname --genomefile=genome.fa --trnascanfile=trnascan.txt --gtrnafafile=db-tRNAs.fa