One of our group has been using the newly updated PanDDA (0.2.12 in ccp4
7.0.058) to look at some data previously processed with PanDDA. It dies with
an error on unpickling a pickle file (see errors below).
My guess is that changes have left it unable to read some pickle files from
previous versions. I’ve tried running pandda.analyse on the tutorial data and
it completes without errors.
Can anyone shed some light on this?
TIA,
Chris
---%<---
PanDDA is running on Ubuntu 16.0.4 LTS with CCP4 7.0.058. The command was:
pandda.analyse data_dirs="/work/<redacted>/foop/"
out_dir="/<redacted>/pandda/pandda_analyse" min_build_datasets=30
max_new_datasets=500 grid_spacing=0.5 cpus=8 events.order_by=cluster_size
pdb_style='pandda_in_*.pdb' mtz_style='pandda_in_*_map_coeffs.mtz'
recalculate_statistical_maps=no existing_datasets=reprocess
reference.pdb="/work/<redacted>/pandda/pandda_analyse/reference/reference.pdb"
reference.mtz="/work/<redacted>/pandda/pandda_analyse/reference/reference.mtz"
The error is:
<…>
Checking for existing analyses
------------------------------------->>>
Looking for pickled files from previous runs in: pickled_data
-> Loading reference grid
Unpickling File: pickled_data/grid.pickle
-> Loading reference dataset
Unpickling File: pickled_data/reference_dataset.pickle
Runtime: 00 hours:00 minutes:00 seconds
############################################## <~~~>
###############################################
### PanDDA exited with an error
###
############################################## <~~~>
###############################################
------------------------------------->>>
Traceback (most recent call last):
File
"/common/app/ccp4/7.0.0/ccp4-7.0/lib/python2.7/site-packages/panddas-0.2.12-py2.7.egg/pandda/analyse/__init__.py",
line 1081, in run
pandda_analyse_main(pandda=pandda)
File
"/common/app/ccp4/7.0.0/ccp4-7.0/lib/python2.7/site-packages/panddas-0.2.12-py2.7.egg/pandda/analyse/__init__.py",
line 1020, in pandda_analyse_main
pandda.run_analysis_init()
File
"/common/app/ccp4/7.0.0/ccp4-7.0/lib/python2.7/site-packages/panddas-0.2.12-py2.7.egg/pandda/analyse/classes.py",
line 771, in run_analysis_init
self.load_pickled_objects()
File
"/common/app/ccp4/7.0.0/ccp4-7.0/lib/python2.7/site-packages/panddas-0.2.12-py2.7.egg/pandda/analyse/classes.py",
line 821, in load_pickled_objects
self.datasets.set_reference(dataset=self.unpickle(self.pickle_handler.get_file('reference_dataset')))
File
"/common/app/ccp4/7.0.0/ccp4-7.0/lib/python2.7/site-packages/panddas-0.2.12-py2.7.egg/giant/manager.py",
line 82, in unpickle
return easy_pickle.load(pickle_file)
File
"/common/app/ccp4/7.0.0/ccp4-7.0/lib/py2/site-packages/cctbx_project/libtbx/easy_pickle.py",
line 80, in load
return cPickle.loads(_open(file_name, "rb").read())
AttributeError: 'module' object has no attribute 'ElectronDensityMap'
------------------------------------->>>
############################################## <~~~>
###############################################
### PanDDA exited with an error
###
############################################## <~~~>
###############################################
--
Dr Chris Richardson :: Sysadmin, structural biology, icr.ac.uk
The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company
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