search

google-code-export / nmrrestrntsgrid

Automatically exported from code.google.com/p/nmrrestrntsgrid
0 stars 0 forks source link

Rerun with all models #146

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
E.g. 1D3Z has only 1 model processed.

Original issue reported on code.google.com by jurge...@gmail.com on 16 Dec 2008 at 12:19

GoogleCodeExporter commented 9 years ago 
And some others too I expect.

Original comment by jurge...@gmail.com on 16 Dec 2008 at 12:20

GoogleCodeExporter commented 9 years ago 
I would like to keep Vincent informed of this issue's progress.

Original comment by jurge...@gmail.com on 14 Jan 2009 at 8:52

GoogleCodeExporter commented 9 years ago 
I'm testing with the oceans 12 entries, now.

Original comment by jurge...@gmail.com on 14 Jan 2009 at 12:30

GoogleCodeExporter commented 9 years ago

Original comment by jurge...@gmail.com on 22 Jan 2009 at 6:59

GoogleCodeExporter commented 9 years ago 
[deleted comment]
GoogleCodeExporter commented 9 years ago 
I still miss 96 entries:

From 4340 only 4244 are in DOCR with XML.

Original comment by jurge...@gmail.com on 27 Jan 2009 at 1:59

GoogleCodeExporter commented 9 years ago 
45 entries give an error in the per entry log:

find . -name "*.log" | xargs grep ERROR | sort

/1b4c.log:ERROR 1b4c after executing Wattos script file: 
/big/docr/workspace/nmrrestrntsgrid/scripts/wcf/ExportForNRG.wcf see log file: 
1b4c_DOCR.log
./1b4c.log:ERROR 1b4c found in doExportsForGrid
./1ckr.log:ERROR 1ckr found in doExportsForGrid
./1ckr.log:ERROR 1ckr in 
/big/docr/workspace/recoord/python/recoord2/msd/exportCns.py
./1d0w.log:ERROR: 1d0w No addMissingAtoms input star file: 
/big/docr/NRG/star/1d0w/1d0w_merge.str
./1d0w.log:ERROR: perhaps a previous phase was not done yet?
./1dx1.log:ERROR 1dx1 Wattos script 1dx1.wcf failed; not continueing
./1eci.log:ERROR 1eci after executing Wattos script file: 
/big/docr/workspace/nmrrestrntsgrid/scripts/wcf/ExportForNRG.wcf see log file: 
1eci_DOCR.log
./1eci.log:ERROR 1eci found in doExportsForGrid
./1f8h.log:ERROR 1f8h Wattos script 1f8h.wcf failed; not continueing
./1fb9.log:ERROR: 1fb9 No addMissingAtoms input star file: 
/big/docr/NRG/star/1fb9/1fb9_merge.str
./1fb9.log:ERROR: perhaps a previous phase was not done yet?
./1ghh.log:ERROR 1ghh after executing Wattos script file: 
/big/docr/workspace/nmrrestrntsgrid/scripts/wcf/ExportForNRG.wcf see log file: 
1ghh_DOCR.log
./1ghh.log:ERROR 1ghh found in doExportsForGrid
./1his.log:ERROR 1his Wattos script 1his.wcf failed; not continueing
./1hit.log:ERROR 1hit Wattos script 1hit.wcf failed; not continueing
./1j6t.log:ERROR 1j6t Wattos script 1j6t.wcf failed; not continueing
./1j6y.log:ERROR 1j6y Wattos script 1j6y.wcf failed; not continueing
./1jtw.log:ERROR 1jtw Wattos script 1jtw.wcf failed; not continueing
./1lfu.log:ERROR 1lfu found in doExportsForGrid
./1lfu.log:ERROR 1lfu in 
/big/docr/workspace/recoord/python/recoord2/msd/exportCyana.py
./1m39.log:ERROR 1m39 after executing Wattos script file: 
/big/docr/workspace/nmrrestrntsgrid/scripts/wcf/ExportForNRG.wcf see log file: 
1m39_DOCR.log
./1m39.log:ERROR 1m39 found in doExportsForGrid
./1mit.log:ERROR 1mit found in doExportsForGrid
./1mit.log:ERROR 1mit in 
/big/docr/workspace/recoord/python/recoord2/msd/exportCns.py
./1nao.log:ERROR 1nao in Wattos assign script
./1qe7.log:ERROR 1qe7 found in doExportsForGrid
./1qe7.log:ERROR 1qe7 in 
/big/docr/workspace/recoord/python/recoord2/msd/exportCns.py
./1r2n.log:ERROR 1r2n Wattos script 1r2n.wcf failed; not continueing
./1r9v.log:ERROR 1r9v in 
/big/docr/workspace/recoord/python/recoord2/msd/linkNmrStarData.py
./1rf8.log:ERROR 1rf8 after executing Wattos script file: 
/big/docr/workspace/nmrrestrntsgrid/scripts/wcf/ExportForNRG.wcf see log file: 
1rf8_DOCR.log
./1rf8.log:ERROR 1rf8 found in doExportsForGrid
./1s4a.log:ERROR 1s4a in 
/big/docr/workspace/recoord/python/recoord2/msd/linkNmrStarData.py
./1soc.log:ERROR 1soc in 
/big/docr/workspace/recoord/python/recoord2/msd/linkNmrStarData.py
./1vrc.log:ERROR 1vrc Wattos script 1vrc.wcf failed; not continueing
./1wa8.log:ERROR 1wa8 after executing Wattos script file: 
/big/docr/workspace/nmrrestrntsgrid/scripts/wcf/ExportForNRG.wcf see log file: 
1wa8_DOCR.log
./1wa8.log:ERROR 1wa8 found in doExportsForGrid
./1xnt.log:ERROR 1xnt after executing Wattos script file: 
/big/docr/workspace/nmrrestrntsgrid/scripts/wcf/ExportForNRG.wcf see log file: 
1xnt_DOCR.log
./1xnt.log:ERROR 1xnt found in doExportsForGrid
./1yl8.log:ERROR 1yl8 in 
/big/docr/workspace/recoord/python/recoord2/msd/linkNmrStarData.py
./1yl9.log:ERROR 1yl9 in 
/big/docr/workspace/recoord/python/recoord2/msd/linkNmrStarData.py
./2con.log:ERROR 2con Wattos script 2con.wcf failed; not continueing
./2exg.log:ERROR 2exg Wattos script 2exg.wcf failed; not continueing
./2f40.log:ERROR 2f40 in Wattos assign script
./2fce.log:ERROR 2fce Wattos script 2fce.wcf failed; not continueing
./2gbh.log:ERROR 2gbh in 
/big/docr/workspace/recoord/python/recoord2/msd/linkNmrStarData.py
./2hvu.log:ERROR: 2hvu No input mmCIF file: 
/dumpzone/pdb/pdb/data/structures/divided/mmCIF/hv/2hvu.cif.gz
./2jn3.log:ERROR 2jn3 found in merge log file; will now grep for ERROR again.
./2jn3.log:    >   ERROR: molecule CHENODEOXYCHOLIC ACID does not have any 
molResidues! Chain creation aborted...
./2jnd.log:ERROR 2jnd in 
/big/docr/workspace/recoord/python/recoord2/msd/linkNmrStarData.py
./2ju5.log:ERROR 2ju5 after executing Wattos script file: 
/big/docr/workspace/nmrrestrntsgrid/scripts/wcf/ExportForNRG.wcf see log file: 
2ju5_DOCR.log
./2ju5.log:ERROR 2ju5 found in doExportsForGrid
./2jue.log:ERROR 2jue in 
/big/docr/workspace/recoord/python/recoord2/msd/linkNmrStarData.py
./2jvp.log:ERROR: 2jvp No input mmCIF file: 
/dumpzone/pdb/pdb/data/structures/divided/mmCIF/jv/2jvp.cif.gz
./2k9e.log:ERROR 2k9e in 
/big/docr/workspace/recoord/python/recoord2/msd/linkNmrStarData.py
./2new.log:ERROR 2new Wattos script 2new.wcf failed; not continueing
./2o4y.log:ERROR 2o4y after executing Wattos script file: 
/big/docr/workspace/nmrrestrntsgrid/scripts/wcf/ExportForNRG.wcf see log file: 
2o4y_DOCR.log
./2o4y.log:ERROR 2o4y found in doExportsForGrid
./2p7c.log:ERROR 2p7c after executing Wattos script file: 
/big/docr/workspace/nmrrestrntsgrid/scripts/wcf/ExportForNRG.wcf see log file: 
2p7c_DOCR.log
./2p7c.log:ERROR 2p7c found in doExportsForGrid
./2px9.log:ERROR 2px9 in 
/big/docr/workspace/recoord/python/recoord2/msd/linkNmrStarData.py
./7hsc.log:ERROR 7hsc found in doExportsForGrid
./7hsc.log:ERROR 7hsc in 
/big/docr/workspace/recoord/python/recoord2/msd/exportCns.py

I will try to debug those issues related to Wattos now.
Wim, could you try looking at the python related?

Original comment by jurge...@gmail.com on 28 Jan 2009 at 11:43

GoogleCodeExporter commented 9 years ago 
Fixed 1b4c
Obsoletes by now: 2jvp 2hvu
Leaves 42 entries...

Original comment by jurge...@gmail.com on 28 Jan 2009 at 2:02

GoogleCodeExporter commented 9 years ago 
Halve way thru the list is reduced to:

jd:stella/perEntry/ find . -name "*.log" | xargs grep ERROR | sort
./1j6t.log:ERROR 1j6t Wattos script 1j6t.wcf failed; not continueing
./1j6y.log:ERROR 1j6y Wattos script 1j6y.wcf failed; not continueing
./1jtw.log:ERROR 1jtw Wattos script 1jtw.wcf failed; not continueing
./1lfu.log:ERROR 1lfu found in doExportsForGrid
./1lfu.log:ERROR 1lfu in 
/Users/jd/workspace34/recoord/python/recoord2/msd/exportCyana.py
./1m3v.log:ERROR 1m3v Wattos script 1m3v.wcf failed; not continueing
./1mit.log:ERROR 1mit found in doExportsForGrid
./1mit.log:ERROR 1mit in 
/Users/jd/workspace34/recoord/python/recoord2/msd/exportCns.py
./1nao.log:ERROR 1nao in Wattos assign script
./2e4j.log:WARNING 2e4j found more than 1000 ERRORs in log file
./2edu.log:WARNING 2edu found more than 1000 ERRORs in log file
./2hm9.log:ERROR 2hm9 in Wattos assign script
./2jox.log:WARNING 2jox found more than 1000 ERRORs in log file
./2jrn.log:WARNING 2jrn found more than 1000 ERRORs in log file
./2jro.log:WARNING 2jro found more than 1000 ERRORs in log file
./2jrt.log:WARNING 2jrt found more than 1000 ERRORs in log file
./2jsx.log:WARNING 2jsx found more than 1000 ERRORs in log file
./2juy.log:ERROR: 2juy No addMissingAtoms input star file: 
/Users/jd/NRG/star/2juy/2juy_merge.str
./2juy.log:ERROR: perhaps a previous phase was not done yet?
./2nsw.log:WARNING 2nsw found more than 1000 ERRORs in log file

Original comment by jurge...@gmail.com on 29 Jan 2009 at 12:43

GoogleCodeExporter commented 9 years ago 
Actually, removing the oldies leaves only already checked entries:
./1j6t.log:ERROR 1j6t Wattos script 1j6t.wcf failed; not continueing
./1j6y.log:ERROR 1j6y Wattos script 1j6y.wcf failed; not continueing
./1jtw.log:ERROR 1jtw Wattos script 1jtw.wcf failed; not continueing
./1lfu.log:ERROR 1lfu found in doExportsForGrid
./1lfu.log:ERROR 1lfu in 
/Users/jd/workspace34/recoord/python/recoord2/msd/exportCyana.py
./1m3v.log:ERROR 1m3v Wattos script 1m3v.wcf failed; not continueing
./1mit.log:ERROR 1mit found in doExportsForGrid
./1mit.log:ERROR 1mit in 
/Users/jd/workspace34/recoord/python/recoord2/msd/exportCns.py
./1nao.log:ERROR 1nao in Wattos assign script

Leaves a list of 19 entries committed in revision 125:
http://code.google.com/p/nmrrestrntsgrid/source/browse/trunk/nmrrestrntsgrid/dat
a/problemEntryList.csv

All problems noted are now transfered to other issues so I'm closing this issue.

Original comment by jurge...@gmail.com on 29 Jan 2009 at 1:23