Dear Maria, Could you please try deleting the file /home/msa/CCP4I2_PROJECTS/TRT84A11C/DATABASE.db.xml ?
I think that this file is corrupted (empty) and that this is causing the problems. Best wishes, Stuart McNicholas On Wed, 24 Jul 2024 at 12:22, Marian Oliva <[email protected]> wrote: > > Dear all, > > Since yesterday I’m having some issues for running of ccp4i2. At the begging > I though it was a disk space memory problem but it wasn´t. I have re-install > ccp4 (indeed, I have tried with ccp4-8 and ccp4-9 installations) with the > same result. I can run all other programs (ccp4, ccp4cloud…) but ccp4i2. > > My machine is Ubuntu 22.04.4 and I have the error messages shown below when > trying to execute ccp4i2. > > Any help will be really appreciate > > Best, > Marian > > Running CCP4i2 browser from: > /opt/xtal/ccp4-9/lib/python3.9/site-packages/ccp4i2 > Python 3.9.18 (main, Feb 15 2024, 15:40:47) > [GCC 9.3.1 20200408 (Red Hat 9.3.1-2)] > Qt version 5.15.3 > > ccp4i2 version 1.1.0 > ccp4i2 source revision 6539 > CPrintHandler saving print output to directory: > /home/msa/.CCP4I2/logs/started_1721818556 > None > None > Starting Project Manager > Current schema version: ('0.1.22', '23-09-2016') > CCP4i2 opening database file /home/msa/.CCP4I2/db/database.sqlite > updateDbSchema 0.1.22 23-09-2016 > Starting Project Manager - DONE > Starting Job Controller > Starting Job Controller - DONE > Rebuilding DATABASE.db.xml for project /home/msa/CCP4I2_PROJECTS/TRT35C51 > exportProjectXml a25752da1bc311ee8776afbed6b8f83a > /home/msa/CCP4I2_PROJECTS/TRT35C51/DATABASE.db.xml > Rebuilding DATABASE.db.xml for project /home/msa/CCP4I2_PROJECTS/TRT84A11B > exportProjectXml 15ec8f74f27611eea3f08fdd9b93c48d > /home/msa/CCP4I2_PROJECTS/TRT84A11B/DATABASE.db.xml > Rebuilding DATABASE.db.xml for project /home/msa/CCP4I2_PROJECTS/TRT84A11C > exportProjectXml 3c81ce1af31611eea3f08fdd9b93c48d > /home/msa/CCP4I2_PROJECTS/TRT84A11C/DATABASE.db.xml > Traceback (most recent call last): > File "/opt/xtal/ccp4-9/lib/python3.9/site-packages/ccp4i2/bin/browser.py", > line 109, in <module> > startBrowser(sys.argv[1:], app=app, splash=splash) > File > "/opt/xtal/ccp4-9/lib/python3.9/site-packages/ccp4i2/utils/startup.py", line > 248, in startBrowser > createMissingDATABASEdbXML() > File > "/opt/xtal/ccp4-9/lib/python3.9/site-packages/ccp4i2/utils/startup.py", line > 177, in createMissingDATABASEdbXML > tree = parse_from_unicode(s) > File > "/opt/xtal/ccp4-9/lib/python3.9/site-packages/ccp4i2/utils/startup.py", line > 173, in parse_from_unicode > return etree.fromstring(s, parser=utf8_parser) > File "src/lxml/etree.pyx", line 3222, in lxml.etree.fromstring > File "src/lxml/parser.pxi", line 1877, in lxml.etree._parseMemoryDocument > File "src/lxml/parser.pxi", line 1765, in lxml.etree._parseDoc > File "src/lxml/parser.pxi", line 1127, in lxml.etree._BaseParser._parseDoc > File "src/lxml/parser.pxi", line 601, in > lxml.etree._ParserContext._handleParseResultDoc > File "src/lxml/parser.pxi", line 711, in lxml.etree._handleParseResult > File "src/lxml/parser.pxi", line 640, in lxml.etree._raiseParseError > File "<string>", line 1 > lxml.etree.XMLSyntaxError: Document is empty, line 1, column 1 > > > ________________________________ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## 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/
