OSError: [Errno 13] Permission denied

[Lapo Ragionieri]

Hi everyones,
I have problem running partition finder, this is the error message I got:

....
Traceback (most recent call last):
  File "PartitionFinderProtein.py", line 25, in <module>
    sys.exit(main.main("PartitionFinderProtein", "protein"))
  File "/home/t5810admin/Documents/partitionfinder-2.1.1/partfinder/main.py", line 401, in main
    run_analysis(cfg, options)
  File "/home/t5810admin/Documents/partitionfinder-2.1.1/partfinder/main.py", line 334, in run_analysis
    anal = method(cfg, options.force_restart, options.processes)
  File "/home/t5810admin/Documents/partitionfinder-2.1.1/partfinder/analysis.py", line 66, in __init__
    self.make_tree(cfg.user_tree_topology_path)
  File "/home/t5810admin/Documents/partitionfinder-2.1.1/partfinder/analysis.py", line 192, in make_tree
    self.filtered_alignment_path, the_config.datatype, the_config.cmdline_extras, tree_scheme, self.threads)
  File "/home/t5810admin/Documents/partitionfinder-2.1.1/partfinder/raxml.py", line 124, in make_ml_topology
    run_raxml_pthreads(command, cpus)
  File "/home/t5810admin/Documents/partitionfinder-2.1.1/partfinder/raxml.py", line 77, in run_raxml_pthreads
    util.run_program(_raxml_pthreads_binary, command)
  File "/home/t5810admin/Documents/partitionfinder-2.1.1/partfinder/util.py", line 77, in run_program
    stderr=subprocess.PIPE)
  File "/home/t5810admin/anaconda2/lib/python2.7/subprocess.py", line 711, in __init__
    errread, errwrite)
  File "/home/t5810admin/anaconda2/lib/python2.7/subprocess.py", line 1343, in _execute_child
    raise child_exception
OSError: [Errno 13] Permission denied

Can anyone gives some help?

Many thanks
Lapo

[Rob Lanfear]

Hi Lapo,

It looks from this like you might not have permission to run things on the processor you are trying to use. It could be a number of things, but to help out, can you provide the following information:

1. What OS you are using

2. The commandline you used

3. The output you get (please copy all of it, and attach as a text file) when you re-run the same analysis adding '-v -p 1' at the command line.

4. The output you get if you cd to the /programs folder and type 'ls -lh' (or whatever you need to do on your OS to see the file permissions in that folder).

Cheers,

Rob