chmccarthy
commented
4 years ago Hi Gabriel,
I think you're getting this error because Pangloss can't find either Exonerate or GeneMark-ES (see for example this S/O link as to why Python spits out this type of error). This may be because you don't have either program installed or because the paths to their respective executables (exonerate and gmes_petap.pl) aren't properly defined in your config_asp.ini file. Links to all of Pangloss' dependencies are included in the manual.
bioinfokushwaha
I have some issues executing Pangloss. I have all the paths declared in the config file, but the following error shows up: $ python Pangloss.py --pred --busco --refine --ips --go --yn00 --plots config_asp.ini /usr/lib/python2.7/dist-packages/Bio/SearchIO/init.py:211: BiopythonExperimentalWarning: Bio.SearchIO is an experimental submodule which may undergo significant changes prior to its future official release. BiopythonExperimentalWarning) Traceback (most recent call last): File "Pangloss.py", line 631, in
main()
File "Pangloss.py", line 531, in main
PanGuessHandler(*panguess_args)
File "Pangloss.py", line 151, in PanGuessHandler
exonerate_genes = PanGuess.RunExonerate(cmds, cores)
File ".../Pangloss/Pangloss/PanGuess.py", line 132, in RunExonerate
genes = farm.map(ExonerateCmdLine, cmds)
File "/usr/lib/python2.7/multiprocessing/pool.py", line 251, in map
return self.map_async(func, iterable, chunksize).get()
File "/usr/lib/python2.7/multiprocessing/pool.py", line 567, in get
raise self._value
AssertionError
As I thought this could be an exonerate bug, I tried the --no_exonerate flag, but another bug appears: $ python Pangloss.py --pred --busco --refine --ips --go --yn00 --plots --no_exonerate config_asp.ini /usr/lib/python2.7/dist-packages/Bio/SearchIO/init.py:211: BiopythonExperimentalWarning: Bio.SearchIO is an experimental submodule which may undergo significant changes prior to its future official release. BiopythonExperimentalWarning) Traceback (most recent call last): File "Pangloss.py", line 631, in
main()
File "Pangloss.py", line 531, in main
PanGuessHandler(panguess_args)
File "Pangloss.py", line 167, in PanGuessHandler
genemark_gtf = PanGuess.RunGeneMark(genome, gm_path, gm_branch, cores)
File ".../Pangloss/Pangloss/PanGuess.py", line 171, in RunGeneMark
sp.call([gm_path, "--ES", "--fungus", "--cores", cores, "--sequence", genome])
File "/usr/lib/python2.7/subprocess.py", line 523, in call
return Popen(popenargs, **kwargs).wait()
File "/usr/lib/python2.7/subprocess.py", line 711, in init
errread, errwrite)
File "/usr/lib/python2.7/subprocess.py", line 1343, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
Could you please help me solve this? I really need this analysis for an upcoming article. Thank you very much for your attention