Hi all,
I keep getting the following errors with my deposition jobs in i2 version
8.0.002:
"-ERROR- adding_stats_to_mmcif_i2_gui:19 Failed instantiating plugin object”
and
"-ERROR- adding_stats_to_mmcif_i2_gui:48 Error in wrapper
adding_stats_to_mmcif_i2 0.1:: Error in the plugin script startProcess”
I’ve pasted the stdout.txt log below the email. The same files are confirmed to
result in a successful job in CCP4 7, and I get the same result with any
dataset I try. Any thoughts?
Thanks,
Alex
runTask Script raw Input Arguments
['/Applications/ScienceApps/ccp4-8.0/Frameworks/Python.framework/Versions/Current/lib/python3.7/site-packages/ccp4i2/bin/runTask.py',
'/Users/snow/CCP4I2_PROJECTS/BmTAL_apo_AR7867/CCP4_JOBS/job_51/input_params.xml']
runTask Script top_path(CCPI2dir) and __file__ variables
/Applications/ScienceApps/ccp4-8.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/ccp4i2
/Applications/ScienceApps/ccp4-8.0/Frameworks/Python.framework/Versions/Current/lib/python3.7/site-packages/ccp4i2/bin/runTask.py
what is going on ? loadConfig
ccp4i2 version 1.1.0
ccp4i2 source revision 6539
Running QApplication to support asyncronous sub-processes
None
None
Starting Project Manager
Current schema version: ('0.1.22', '23-09-2016')
CCP4i2 opening database file /Users/snow/.CCP4I2/db/database.sqlite
updateDbSchema 0.1.22 23-09-2016
Starting Project Manager - DONE
CRunPlugin.run before setupComAndLog
Starting <class 'core.CCP4DataManager.CDataManager'> 0.0009248256683349609
{'sequence': '', 'nCopies': '1', 'polymerType': 'PROTEIN', 'name': '',
'description': '', 'source': ''}
<class 'core.CCP4ModelData.CAsuContentSeq'>
<PySide2.QtCore.SignalInstance object at 0x11fac63b0>
<class 'core.CCP4ModelData.CDictDataFile'>
<PySide2.QtCore.SignalInstance object at 0x11fac6310>
{'sequence': '', 'nCopies': '1', 'polymerType': 'PROTEIN', 'name': '',
'description': '', 'source': ''}
<class 'core.CCP4ModelData.CAsuContentSeq'>
<PySide2.QtCore.SignalInstance object at 0x11fac6590>
PROCESSMANAGER running command:
/Applications/ScienceApps/ccp4-8.0/bin/cmtzjoin -mtzout
/Users/snow/CCP4I2_PROJECTS/BmTAL_apo_AR7867/CCP4_JOBS/job_51/mergedForMakingCif.mtz
-mtzin
/Users/snow/CCP4I2_PROJECTS/BmTAL_apo_AR7867/CCP4_JOBS/job_45/HKLOUT_0-observed_data.mtz
-colin Iplus,SIGIplus,Iminus,SIGIminus -colout
F_SIGF_Iplus,F_SIGF_SIGIplus,F_SIGF_Iminus,F_SIGF_SIGIminus -mtzin
/Users/snow/CCP4I2_PROJECTS/BmTAL_apo_AR7867/CCP4_JOBS/job_45/HKLOUT_0-observed_data_asFPAIR.mtz
-colin Fplus,SIGFplus,Fminus,SIGFminus -colout
F_SIGF_Fplus,F_SIGF_SIGFplus,F_SIGF_Fminus,F_SIGF_SIGFminus -mtzin
/Users/snow/CCP4I2_PROJECTS/BmTAL_apo_AR7867/CCP4_JOBS/job_45/FREERFLAG.mtz
-colin FREER -colout FREERFLAG_FREER -mtzin
/Users/snow/CCP4I2_PROJECTS/BmTAL_apo_AR7867/CCP4_JOBS/job_49/49_bmtal_apo_ar7867_fphiout_prosmart_refmac.mtz
-colin F,PHI -colout FPHIOUT_F,FPHIOUT_PHI -mtzin
/Users/snow/CCP4I2_PROJECTS/BmTAL_apo_AR7867/CCP4_JOBS/job_49/49_bmtal_apo_ar7867_diffphiout_prosmart_refmac.mtz
-colin F,PHI -colout DIFFPHIOUT_F,DIFFPHIOUT_PHI >
/Users/snow/CCP4I2_PROJECTS/BmTAL_apo_AR7867/CCP4_JOBS/job_51/log_mtzjoin.txt
Process finished: 1 exit code: 0 exit status: 0 time: 13:48:25 05/Jul/2022
scaledunmerged path is None
Failed adding program version to parent job None None
Error report from extracting output data to database
None -WARNING- CDbApi:173 Possible job output file does not exist
MMCIFOUT
/Users/snow/CCP4I2_PROJECTS/BmTAL_apo_AR7867/CCP4_JOBS/job_51/51_bmtal_apo_ar7867_mmcifout_adding_stats_to_mmcif_i2.cif
None -WARNING- CDbApi:173 Possible job output file does not exist
CIFREFLECTIONS
/Users/snow/CCP4I2_PROJECTS/BmTAL_apo_AR7867/CCP4_JOBS/job_51/51_bmtal_apo_ar7867_cifreflections_adding_stats_to_mmcif_i2.cif
None -WARNING- CDbApi:173 Possible job output file does not exist
DIFFPHIOUT
/Users/snow/CCP4I2_PROJECTS/BmTAL_apo_AR7867/CCP4_JOBS/job_51/51_bmtal_apo_ar7867_diffphiout_adding_stats_to_mmcif_i2.mtz
None -WARNING- CDbApi:173 Possible job output file does not exist
FPHIOUT
/Users/snow/CCP4I2_PROJECTS/BmTAL_apo_AR7867/CCP4_JOBS/job_51/51_bmtal_apo_ar7867_fphiout_adding_stats_to_mmcif_i2.mtz
None -WARNING- CDbApi:173 Possible job output file does not exist
COOTSCRIPTOUT
/Users/snow/CCP4I2_PROJECTS/BmTAL_apo_AR7867/CCP4_JOBS/job_51/51_bmtal_apo_ar7867_cootscriptout_adding_stats_to_mmcif_i2.scm
Exporting project meta-data as XML file:
/Users/snow/CCP4I2_PROJECTS/BmTAL_apo_AR7867/DATABASE.db.xml
exportProjectXml 2dd631487da911eb8ec85ce0c5cd3c28
/Users/snow/CCP4I2_PROJECTS/BmTAL_apo_AR7867/DATABASE.db.xml
Backing up after top-level job finished
----------------------------------------backupDB----------------------------------------
Writing to /var/folders/s6/npngzdbs4m517mms5m50pmvh0000gn/T/tmpm94ikk47
Saved backup database to
/Users/snow/.CCP4I2/db/database_sqlite_backup-05072022-134825
31
['/Users/snow/.CCP4I2/db/database_sqlite_backup-05072022-123047']
/Users/snow/.CCP4I2/db/database_sqlite_backup-05072022-123047
Deleting temporary files for 51 adding_stats_to_mmcif_i2
['/Users/snow/CCP4I2_PROJECTS/BmTAL_apo_AR7867/CCP4_JOBS/job_51/log_mtzjoin.txt']
quitThread <core.CCP4PluginScript.CRunPlugin(0x6000004aeb80) at 0x115272e10>
--
Alex Snow (He/Him/His)
PhD Student
ID: 201015406
ORCID: 0000-0002-7475-7175
Department of Chemistry, YSBL
University of York
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