Emisam
commented
7 years ago Thanks for testing the software and providing information about bugs. Hopefully I will be able to fix this error soon.
I was able to reproduce the error in python 2.7. The reason we get this error is because in python 2.7 the multiprocessing module does not support pickling of instance methods. So I need to fix this by adding some extra code, but that will take a couple of days before I find the time to do it.
The multiprocessing module was reworked to support this in python 3.x, so a temporary solution is to create an environment on your machine for python 3.x and run the program from there.
I will update the issue when I've fixed so it works for 2.7 again. Best wishes
dpchris
I installed genome_update with pip as showed in the README : pip install genome_update pip install genome_update --upgrade
but when I try to download genomes, I get this error \:
genome_update -g "Brucella" -p 8
_... Adding new isolate CMUL 031 to species: Brucella sp. Adding new isolate CMUL 035 to species: Brucella sp. Adding new isolate CMUL 034 to species: Brucella sp. Downloading jobs.... Traceback (most recent call last): File "/usr/local/bin/genome_update", line 11, in
sys.exit(main())
File "/usr/local/lib/python2.7/dist-packages/genome_update/main.py", line 92, in main
download(yaml, args.name, args.name, args.output, args.parallel)
File "/usr/local/lib/python2.7/dist-packages/genome_update/main.py", line 102, in download
newdict = dwon.download_jobs(parallel, job)
File "/usr/local/lib/python2.7/dist-packages/genome_update/downloader.py", line 42, in download_jobs
pool.map(self.download, jobs)
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
cPickle.PicklingError: Can't pickle <type 'instancemethod'>: attribute lookup builtin.instancemethod failed
same with genome_update -g "Brucella"