Dear Martin, Here you are! I cannot fin the diagnostics.xml Armando
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stderr.txt
Description: application/applefile
runTask Script raw Input Arguments
['/Applications/ccp4-9/Frameworks/Python.framework/Versions/Current/lib/python3.9/site-packages/ccp4i2/bin/runTask.py',
'/Users/xalbert/Armando/0_1_Current/SOS3_Alejandra/Bsk5486x12/Refine_new/CCP4_JOBS/job_8/input_params.xml']
runTask Script top_path(CCPI2dir) and __file__ variables
/Applications/ccp4-9/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ccp4i2
/Applications/ccp4-9/Frameworks/Python.framework/Versions/Current/lib/python3.9/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/xalbert/.CCP4I2/db/database.sqlite
updateDbSchema 0.1.22 23-09-2016
Starting Project Manager - DONE
CRunPlugin.run before setupComAndLog
Starting <class 'core.CCP4DataManager.CDataManager'> 0.0013203620910644531
<class 'core.CCP4ModelData.CPdbDataFile'>
<PySide2.QtCore.SignalInstance object at 0x118557910>
<class 'core.CCP4XtalData.CMapCoeffsDataFile'>
<PySide2.QtCore.SignalInstance object at 0x118557af0>
<class 'core.CCP4XtalData.CMapCoeffsDataFile'>
<PySide2.QtCore.SignalInstance object at 0x118557b30>
<class 'core.CCP4ModelData.CPdbDataFile'>
<PySide2.QtCore.SignalInstance object at 0x118557b70>
<class 'core.CCP4ModelData.CPdbDataFile'>
<PySide2.QtCore.SignalInstance object at 0x118557c30>
<class 'core.CCP4ModelData.CPdbDataFile'>
<PySide2.QtCore.SignalInstance object at 0x118557cb0>
<class 'core.CCP4ModelData.CPdbDataFile'>
<PySide2.QtCore.SignalInstance object at 0x118557d30>
<class 'core.CCP4ModelData.CPdbDataFile'>
<PySide2.QtCore.SignalInstance object at 0x118557b90>
<class 'core.CCP4ModelData.CPdbDataFile'>
<PySide2.QtCore.SignalInstance object at 0x118557e10>
<class 'core.CCP4ModelData.CPdbDataFile'>
<PySide2.QtCore.SignalInstance object at 0x118557e90>
<class 'core.CCP4ModelData.CPdbDataFile'>
<PySide2.QtCore.SignalInstance object at 0x118557f10>
<class 'core.CCP4ModelData.CPdbDataFile'>
<PySide2.QtCore.SignalInstance object at 0x118557f90>
<class 'core.CCP4ModelData.CPdbDataFile'>
<PySide2.QtCore.SignalInstance object at 0x118557fd0>
<class 'core.CCP4ModelData.CDictDataFile'>
<PySide2.QtCore.SignalInstance object at 0x118557d90>
<class 'core.CCP4ModelData.CDictDataFile'>
<PySide2.QtCore.SignalInstance object at 0x118557d90>
<class 'core.CCP4ModelData.CDictDataFile'>
<PySide2.QtCore.SignalInstance object at 0x118557d90>
<class 'core.CCP4ModelData.CDictDataFile'>
<PySide2.QtCore.SignalInstance object at 0x118557d90>
<class 'core.CCP4ModelData.CDictDataFile'>
<PySide2.QtCore.SignalInstance object at 0x118557f90>
<class 'core.CCP4ModelData.CDictDataFile'>
<PySide2.QtCore.SignalInstance object at 0x118557f90>
<class 'core.CCP4ModelData.CDictDataFile'>
<PySide2.QtCore.SignalInstance object at 0x118557f90>
<class 'core.CCP4ModelData.CDictDataFile'>
<PySide2.QtCore.SignalInstance object at 0x118557f90>
<class 'core.CCP4ModelData.CDictDataFile'>
<PySide2.QtCore.SignalInstance object at 0x118557f90>
<class 'core.CCP4ModelData.CDictDataFile'>
<PySide2.QtCore.SignalInstance object at 0x118557f90>
reading file number 1
reading diff file number 1
Running process coot asyncronously using QProcess
PROCESSMANAGER running command:
coot --no-state-script --python --script
/Users/xalbert/Armando/0_1_Current/SOS3_Alejandra/Bsk5486x12/Refine_new/CCP4_JOBS/job_8/script.py
>
/Users/xalbert/Armando/0_1_Current/SOS3_Alejandra/Bsk5486x12/Refine_new/CCP4_JOBS/job_8/log.txt
startQProcess process says finished 134
PySide2.QtCore.QProcess.ExitStatus.NormalExit
Process finished: 1 exit code: 134 exit status:
PySide2.QtCore.QProcess.ExitStatus.NormalExit time: 09:18:16 19/Nov/2024
CPluginScript.handleProcessFailed processId 1 exitStatus 0 exitCode 134
self._runningProcessId 1
CCP4Utils.getProgramVersion m1 ('/Applications/ccp4-9/coot_py2/libexec/',
'-bin')
Failed adding program version to parent job coot None
Error report from extracting output data to database
None -WARNING- CDbApi:173 Possible job output file does not
exist
/Users/xalbert/Armando/0_1_Current/SOS3_Alejandra/Bsk5486x12/Refine_new/CCP4_JOBS/job_8/8_sos3h57n_rev_xyzout_coot_rebuild_0.pdb
None -WARNING- CDbApi:173 Possible job output file does not
exist
/Users/xalbert/Armando/0_1_Current/SOS3_Alejandra/Bsk5486x12/Refine_new/CCP4_JOBS/job_8/8_sos3h57n_rev_xyzout_coot_rebuild_1.pdb
None -WARNING- CDbApi:173 Possible job output file does not
exist
/Users/xalbert/Armando/0_1_Current/SOS3_Alejandra/Bsk5486x12/Refine_new/CCP4_JOBS/job_8/8_sos3h57n_rev_xyzout_coot_rebuild_2.pdb
None -WARNING- CDbApi:173 Possible job output file does not
exist
/Users/xalbert/Armando/0_1_Current/SOS3_Alejandra/Bsk5486x12/Refine_new/CCP4_JOBS/job_8/8_sos3h57n_rev_xyzout_coot_rebuild_3.pdb
None -WARNING- CDbApi:173 Possible job output file does not
exist
/Users/xalbert/Armando/0_1_Current/SOS3_Alejandra/Bsk5486x12/Refine_new/CCP4_JOBS/job_8/8_sos3h57n_rev_xyzout_coot_rebuild_4.pdb
None -WARNING- CDbApi:173 Possible job output file does not
exist
/Users/xalbert/Armando/0_1_Current/SOS3_Alejandra/Bsk5486x12/Refine_new/CCP4_JOBS/job_8/8_sos3h57n_rev_xyzout_coot_rebuild_5.pdb
None -WARNING- CDbApi:173 Possible job output file does not
exist
/Users/xalbert/Armando/0_1_Current/SOS3_Alejandra/Bsk5486x12/Refine_new/CCP4_JOBS/job_8/8_sos3h57n_rev_xyzout_coot_rebuild_6.pdb
None -WARNING- CDbApi:173 Possible job output file does not
exist
/Users/xalbert/Armando/0_1_Current/SOS3_Alejandra/Bsk5486x12/Refine_new/CCP4_JOBS/job_8/8_sos3h57n_rev_xyzout_coot_rebuild_7.pdb
None -WARNING- CDbApi:173 Possible job output file does not
exist
/Users/xalbert/Armando/0_1_Current/SOS3_Alejandra/Bsk5486x12/Refine_new/CCP4_JOBS/job_8/8_sos3h57n_rev_xyzout_coot_rebuild_8.pdb
None -WARNING- CDbApi:173 Possible job output file does not
exist
/Users/xalbert/Armando/0_1_Current/SOS3_Alejandra/Bsk5486x12/Refine_new/CCP4_JOBS/job_8/8_sos3h57n_rev_xyzout_coot_rebuild_9.pdb
None -WARNING- CDbApi:173 Possible job output file does not
exist
/Users/xalbert/Armando/0_1_Current/SOS3_Alejandra/Bsk5486x12/Refine_new/CCP4_JOBS/job_8/8_sos3h57n_rev_dictout_coot_rebuild_0.cif
None -WARNING- CDbApi:173 Possible job output file does not
exist
/Users/xalbert/Armando/0_1_Current/SOS3_Alejandra/Bsk5486x12/Refine_new/CCP4_JOBS/job_8/8_sos3h57n_rev_dictout_coot_rebuild_1.cif
None -WARNING- CDbApi:173 Possible job output file does not
exist
/Users/xalbert/Armando/0_1_Current/SOS3_Alejandra/Bsk5486x12/Refine_new/CCP4_JOBS/job_8/8_sos3h57n_rev_dictout_coot_rebuild_2.cif
None -WARNING- CDbApi:173 Possible job output file does not
exist
/Users/xalbert/Armando/0_1_Current/SOS3_Alejandra/Bsk5486x12/Refine_new/CCP4_JOBS/job_8/8_sos3h57n_rev_dictout_coot_rebuild_3.cif
None -WARNING- CDbApi:173 Possible job output file does not
exist
/Users/xalbert/Armando/0_1_Current/SOS3_Alejandra/Bsk5486x12/Refine_new/CCP4_JOBS/job_8/8_sos3h57n_rev_dictout_coot_rebuild_4.cif
None -WARNING- CDbApi:173 Possible job output file does not
exist
/Users/xalbert/Armando/0_1_Current/SOS3_Alejandra/Bsk5486x12/Refine_new/CCP4_JOBS/job_8/8_sos3h57n_rev_dictout_coot_rebuild_5.cif
None -WARNING- CDbApi:173 Possible job output file does not
exist
/Users/xalbert/Armando/0_1_Current/SOS3_Alejandra/Bsk5486x12/Refine_new/CCP4_JOBS/job_8/8_sos3h57n_rev_dictout_coot_rebuild_6.cif
None -WARNING- CDbApi:173 Possible job output file does not
exist
/Users/xalbert/Armando/0_1_Current/SOS3_Alejandra/Bsk5486x12/Refine_new/CCP4_JOBS/job_8/8_sos3h57n_rev_dictout_coot_rebuild_7.cif
None -WARNING- CDbApi:173 Possible job output file does not
exist
/Users/xalbert/Armando/0_1_Current/SOS3_Alejandra/Bsk5486x12/Refine_new/CCP4_JOBS/job_8/8_sos3h57n_rev_dictout_coot_rebuild_8.cif
None -WARNING- CDbApi:173 Possible job output file does not
exist
/Users/xalbert/Armando/0_1_Current/SOS3_Alejandra/Bsk5486x12/Refine_new/CCP4_JOBS/job_8/8_sos3h57n_rev_dictout_coot_rebuild_9.cif
Exporting project meta-data as XML file:
/Users/xalbert/Armando/0_1_Current/SOS3_Alejandra/Bsk5486x12/Refine_new/DATABASE.db.xml
exportProjectXml 1c8089e6a58e11ef844f3c7d0a01d6b0
/Users/xalbert/Armando/0_1_Current/SOS3_Alejandra/Bsk5486x12/Refine_new/DATABASE.db.xml
Backing up after top-level job finished
----------------------------------------backupDB----------------------------------------
Writing to /var/folders/nm/q06wlbzs10x2zk84n3yyl1xm0000gn/T/tmpj6qivmfu
Saved backup database to
/Users/xalbert/.CCP4I2/db/database_sqlite_backup-19112024-091816
31
['/Users/xalbert/.CCP4I2/db/database_sqlite_backup-18112024-102137']
/Users/xalbert/.CCP4I2/db/database_sqlite_backup-18112024-102137
quitThread <core.CCP4PluginScript.CRunPlugin(0x600000f5d0e0) at 0x11645ea00>
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> El 19 nov 2024, a las 10:21, Martin Malý <martin.maly...@email.cz> escribió: > > Dear Armando, > If a job fails, there should be also shown files diagnostics.xml, stderr.txt > and stdout.txt. Please can you send them to us here? > Cheers, > Martin > > > On 19/11/2024 08:25, Armando Albert wrote: >> Dear all, >> >> I am trying to run coot from CCP4i2 and I’ve got the following message: >> >> Error Report for Job 6: Manual model building - COOT >> -ERROR- Ccoot_rebuild:56 Error in wrapper coot_rebuild >> 0.0:: External process exited with exit code != 0 >> Process: coot >> -ERROR- Ccoot_rebuild:47 Error in wrapper coot_rebuild >> 0.0:: Error in checking external process after completion >> exit status and code: 0 134 >> >> And, of course, it does not run. >> >> Any hint? >> >> (CCP4-9 on MacOS Sonoma) >> >> Armando >> >> ######################################################################## >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> >> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing >> list hosted by www.jiscmail.ac.uk, terms & conditions are available at >> https://www.jiscmail.ac.uk/policyandsecurity/ > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing > list hosted by www.jiscmail.ac.uk, terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/ ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
