Better error reporting when making trees

[ctSkennerton]

When prodigal isn't in your path you get a very vague error message, which due to the parallel nature of the code points to an uninformative part of the source (see below). A check for the required external dependancies before getting into this would help a lot.

src/gtdblite.py trees create --output ~/test_genome_tree --all_genomes --marker_set_ids 3 --no_tree
24377 genomes contain 975080 uncalculated markers.
These markers need to be calculated in order to build the tree. More markers means more waiting. Continue using 1 threads? (y/N): y
Breaking calculation into 49 chunks of up to 500 genomes.
Calculating chunk 1 of 49....
Prodigal complete for 102 of 500 genomes (chunk 1 of 49),
Prodigal complete for 189 of 500 genomes (chunk 1 of 49),
Prodigal complete for 276 of 500 genomes (chunk 1 of 49),
Prodigal complete for 363 of 500 genomes (chunk 1 of 49),
Prodigal complete for 449 of 500 genomes (chunk 1 of 49),
Prodigal complete for 500 of 500 genomes (chunk 1 of 49),
Exception caught. Dumping info.
Traceback (most recent call last):
  File "src/gtdblite.py", line 664, in <module>
    result = args.func(db, args)
  File "src/gtdblite.py", line 128, in CreateTreeData
    return db.MakeTreeData(marker_id_list, genome_id_list, args.out_dir, "gtdblite", args.profile, profile_config_dict, not(args.no_tree))
  File "/export/data1/sw/GTDBLite/src/gtdblite/GenomeDatabase.py", line 1550, in MakeTreeData
    prodigal_dir = async_result.get()
  File "/opt/qiime/1.8.0/python-2.7.3-release/lib/python2.7/multiprocessing/pool.py", line 528, in get
    raise self._value
OSError: [Errno 2] No such file or directory