multiprocessing.pool.MaybeEncodingError

[pbelmann]

I'm running carveme with Python3.6 and CPLEX 12.8 and receive the following error:

  The input genome did not match sufficient genes/reactions in the database.
Traceback (most recent call last):
  File "/home/ubuntu/vendor3/bin/carve", line 395, in <module>
    p.map(f, args.input)
  File "/usr/lib/python3.6/multiprocessing/pool.py", line 266, in map
    return self._map_async(func, iterable, mapstar, chunksize).get()
  File "/usr/lib/python3.6/multiprocessing/pool.py", line 644, in get
    raise self._value
multiprocessing.pool.MaybeEncodingError: Error sending result: '<multiprocessing.pool.ExceptionWithTraceback object at 0x7f31fdcff9b0>'. Reason: 'TypeError("can't pickle SwigPyObject objects",)'

[cdanielmachado]

Can you paste here the command you ran ?

[pbelmann]

Sure:

carve -r input/*.faa &> carve.log

[cdanielmachado]

It seems there is a problem reconstructing at least one of the models, which causes the recursive mode to abort.

Could you please try the reconstructions one by one until you find the problematic one?

When you find it, can you check how many proteins are in the fasta file?

[pbelmann]

Ok, running the reconstructions one by one does not report the error. However there are fasta files where no xml is created. In the log I just see as the last lines:

18 queries aligned.
The input genome did not match sufficient genes/reactions in the database.

It would be useful to have the path of the input file reported in the log when running carveme with -r flag.

[cdanielmachado]

Thanks for the suggestion. The '-r' mode does need a more graceful failure.

Anyway, the problem with that genome is that only 18 genes could be mapped to reactions, which is below the threshold we consider sufficient to build a model.

[pbelmann]

Ok, thanks!