Error while running configuration

[sagnikbanerjee15]

Hello,

I am currently running the following command "mikado configure --list mikado_list_file --reference ../genome/Zea_mays.AGPv4.dna.toplevel.fa --mode permissive --scoring plant.yaml --copy-scoring plants.yaml -bt uniprot_sprot_plants.fasta configuration.yaml" but I am running into the following error.

2018-07-30 08:47:51,697 - to_json - configurator.py:567 - ERROR - check_json - MainProcess - (<class 'dict'>, <class 'NoneType'>)
Traceback (most recent call last):
File "/home/sagnik/.local/lib/python3.6/site-packages/Mikado/configuration/configurator.py", line 533, in check_json
(type(json_conf), type(scoring))
AssertionError: (<class 'dict'>, <class 'NoneType'>)
2018-07-30 08:47:51,698 - to_json - configurator.py:614 - ERROR - to_json - MainProcess - (<class 'dict'>, <class 'NoneType'>)
Traceback (most recent call last):
File "/home/sagnik/.local/lib/python3.6/site-packages/Mikado/configuration/configurator.py", line 612, in to_json
json_dict = check_json(json_dict, simple=simple, logger=logger)
File "/home/sagnik/.local/lib/python3.6/site-packages/Mikado/configuration/configurator.py", line 533, in check_json
(type(json_conf), type(scoring))
AssertionError: (<class 'dict'>, <class 'NoneType'>)
Traceback (most recent call last):
File "/home/sagnik/.local/lib/python3.6/site-packages/Mikado/configuration/configurator.py", line 612, in to_json
json_dict = check_json(json_dict, simple=simple, logger=logger)
File "/home/sagnik/.local/lib/python3.6/site-packages/Mikado/configuration/configurator.py", line 533, in check_json
(type(json_conf), type(scoring))
AssertionError: (<class 'dict'>, <class 'NoneType'>)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/sagnik/.local/bin/mikado", line 11, in
load_entry_point('Mikado==1.2.2', 'console_scripts', 'mikado')()
File "/opt/rit/spack-app/linux-rhel7-x86_64/gcc-4.8.5/py-setuptools-35.0.2-kvj5vuzczq4idwn7rlmg6vzklttwwpgy/lib/python3.6/site-packages/pkg_resources/init.py", line 560, in load_entry_point
return get_distribution(dist).load_entry_point(group, name)
File "/opt/rit/spack-app/linux-rhel7-x86_64/gcc-4.8.5/py-setuptools-35.0.2-kvj5vuzczq4idwn7rlmg6vzklttwwpgy/lib/python3.6/site-packages/pkg_resources/init.py", line 2648, in load_entry_point
return ep.load()
File "/opt/rit/spack-app/linux-rhel7-x86_64/gcc-4.8.5/py-setuptools-35.0.2-kvj5vuzczq4idwn7rlmg6vzklttwwpgy/lib/python3.6/site-packages/pkg_resources/init.py", line 2302, in load
return self.resolve()
File "/opt/rit/spack-app/linux-rhel7-x86_64/gcc-4.8.5/py-setuptools-35.0.2-kvj5vuzczq4idwn7rlmg6vzklttwwpgy/lib/python3.6/site-packages/pkg_resources/init.py", line 2308, in resolve
module = import(self.module_name, fromlist=['name'], level=0)
File "/home/sagnik/.local/lib/python3.6/site-packages/Mikado/init.py", line 28, in
from . import loci
File "/home/sagnik/.local/lib/python3.6/site-packages/Mikado/loci/init.py", line 13, in
from .abstractlocus import Abstractlocus
File "/home/sagnik/.local/lib/python3.6/site-packages/Mikado/loci/abstractlocus.py", line 33, in
json_conf = to_json(None)
File "/home/sagnik/.local/lib/python3.6/site-packages/Mikado/configuration/configurator.py", line 616, in to_json
errored.write(open(string).read())
FileNotFoundError: [Errno 2] No such file or directory: '/work/LAS/rpwise-lab/sagnik/data/maize/AGPv4/transcriptome/mikado.json'

Could you please help with that?

[lucventurini]

Dear @sagnikbanerjee15 ,
thank you for reporting the bug. I can reproduce it on the development branch of Mikado. I will look into it ASAP.

Many apologies for the late reply, this year I have been in the process of moving cities and getting married, which unfortunately meant I did not see this bug until now.

[lucventurini]

Dear @sagnikbanerjee15 ,
the bug is caused by an empty / invalid "plants.yaml" file within your working directory. Removing it should negate the bug.

I will work on the bug so that it is solved by the next release.

[lucventurini]

Dear @sagnikbanerjee15 ,
the bug is now fixed and will be absent from the next release of Mikado (1.3).

Thank you for reporting it, and apologies again for the late response.

Kind regards

[sagnikbanerjee15]

Thank you @lucventurini for your help.