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CPTR-ReSeqTB / UVP

Mycobacterium tuberculosis next generation sequence analysis
MIT License
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fastQValidator subprocess call, OSError: [Errno 2] No such file or directory #2

Closed jwcodee closed 5 years ago

jwcodee commented 6 years ago

/usr/bin/uvp/scripts/UVP -q /loc/id_1.fastq.gz -r /loc/ref/genomic.fna -n test Traceback (most recent call last): File "/usr/bin/uvp/scripts/UVP", line 97, in args.verbose, ' '.join(sys.argv)) File "/usr/bin/uvp/scripts/UVP.py", line 58, in init with open("/uvp/scripts/config.yml", 'r') as ymlfile: IOError: [Errno 2] No such file or directory: '/uvp/scripts/config.yml'

I've been getting this error and I've tried adding the path to the environment before running but it still doesnt work

jwcodee commented 6 years ago

I also tried running the newest commit which solved the above issue but instead i got another problem Traceback (most recent call last): File "/usr/bin/UVP/scripts/UVP", line 98, in s.runVali() File "/usr/bin/UVP/scripts/UVP.py", line 144, in runVali self.CallCommand(['fastQValidator', valiOut + '/result.out'], [self.fastqval,'--file', self.input]) File "/usr/bin/UVP/scripts/UVP.py", line 110, in CallCommand p = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=subprocess.PIPE) File "/usr/lib64/python2.7/subprocess.py", line 711, in init__ errread, errwrite) File "/usr/lib64/python2.7/subprocess.py", line 1308, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory

Ive installed fastQvalidator and have the executable in my path but it still produces the error

mezewudo commented 5 years ago

You will want to look at the README document, you should edit file paths to fit your local machine installation.