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Mikado self comparison bug #194

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lucventurini opened this issue Jul 10, 2019 · 0 comments
Closed

Mikado self comparison bug #194

lucventurini opened this issue Jul 10, 2019 · 0 comments
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@lucventurini
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lucventurini commented Jul 10, 2019

From @gemygk:
On a minor note, I think the Mikado –self comparison does need some fixing though. Please find additional information below:

WD:

/ei/workarea/group-ga/Projects/CB-GENANNO-432_10+wheat_genomes_annotation/Analysis/mikado_compare/Julius/mikado-20190705_7f87abe/julius_HC

CMD:

sbatch -c 6 --mem 123G -o out_mikado_compare.%j.log -p ei-cb -J julius_HC --wrap "source mikado-20190705_7f87abe && mikado compare -r julius_HC.gff --self --processes 6"

ERROR:

Process FinalAssigner-7:

Traceback (most recent call last):

  File "/usr/local/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap

    self.run()

  File "/usr/local/lib/python3.7/site-packages/Mikado/scales/compare.py", line 295, in run

    self.assigner.load_result(dbname)

  File "/usr/local/lib/python3.7/site-packages/Mikado/scales/assigner.py", line 222, in load_result

    object_hook=msgpack_convert))

  File "msgpack/_unpacker.pyx", line 201, in msgpack._cmsgpack.unpackb

  File "/usr/local/lib/python3.7/site-packages/Mikado/scales/assigner.py", line 55, in msgpack_convert

    return ResultStorer(state=o['value'])

  File "/usr/local/lib/python3.7/site-packages/Mikado/scales/resultstorer.py", line 72, in __init__

    self._load_dict(state)

  File "/usr/local/lib/python3.7/site-packages/Mikado/scales/resultstorer.py", line 108, in _load_dict

    setattr(self, key, self.types[index](state[key]))

  File "/usr/local/lib/python3.7/site-packages/Mikado/scales/resultstorer.py", line 38, in to_int_tuple

    return tuple([int(tup)])

ValueError: invalid literal for int() with base 10: '4,10'

2019-07-08 16:31:00,355 - main_queue - compare.py:758 - INFO - compare - MainProcess – Finished
@lucventurini lucventurini added this to the 2.0 milestone Jul 10, 2019
@lucventurini lucventurini reopened this Jul 10, 2019
@lucventurini lucventurini added this to Closed in Version 2 Oct 15, 2020
lucventurini added a commit to lucventurini/mikado that referenced this issue Feb 11, 2021
* Refactored the functions that were crashing ResultStorer
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