[wgs-assembler-users] runCA stopped while updating overlapStore - how to resume???

[Christoph H. <chr...@gm...>]

Dear users and developers,

I have the following problem: In my assembly process I have just 
completed the fragment- and overlap error correction. Unfortunately 
runCA stopped in the subsequent updating of the overlapStore, because of 
an incorrectly set time limit..
If I am trying to resume the assembly now, I get the following error:
----------------------------------------START Mon Jul  9 11:05:53 2012
/xanadu/home/chrishah/programmes/wgs-7.0/Linux-amd64/bin/overlapStore -u 
/projects/nn9201k/Celera/work2/salaris1/salaris.ovlStore 
/projects/nn9201k/Celera/work2/salaris1/3-overlapco
rrection/salaris.erates> 
/projects/nn9201k/Celera/work2/salaris1/3-overlapcorrection/overlapStore-update-erates.err 
2>&1
----------------------------------------END Mon Jul  9 11:05:54 2012 (1 
seconds)
ERROR: Failed with signal HUP (1)
================================================================================

runCA failed.

----------------------------------------
Stack trace:

  at /usit/titan/u1/chrishah/programmes/wgs-7.0/Linux-amd64/bin/./runCA 
line 1237
         main::caFailure('failed to apply the overlap corrections', 
'/projects/nn9201k/Celera/work2/salaris1/3-overlapcorrection/o...') 
called at /usit/titan/u1/chrishah/programmes/wgs
-7.0/Linux-amd64/bin/./runCA line 4077
         main::overlapCorrection() called at 
/usit/titan/u1/chrishah/programmes/wgs-7.0/Linux-amd64/bin/./runCA line 5880

----------------------------------------
Last few lines of the relevant log file 
(/projects/nn9201k/Celera/work2/salaris1/3-overlapcorrection/overlapStore-update-erates.err):

AS_OVS_openBinaryOverlapFile()-- Failed to open 
'/projects/nn9201k/Celera/work2/salaris1/salaris.ovlStore/0001~' for 
reading: No such file or directory

----------------------------------------
Failure message:

failed to apply the overlap corrections



So it can obviously not find the file /salaris.ovlStore/0001~. The 
reason is, from what I can see, that the /salaris.ovlStore/0001~ file 
has already been updated to /salaris.ovlStore/0001 before it stopped. In 
fact it seems to have stopped after updating /salaris.ovlStore/0249 (of 
430). Is there a way to tell runCA to continue from  
/salaris.ovlStore/0250~, instead of from 0001~, which is obviously not 
there any more??
Another solution I was thinking of is to run the previous overlapStore 
command again manually (the one that was done before starting the 
frgcorr and ovlcorr: 
/xanadu/home/chrishah/programmes/wgs-7.0/Linux-amd64/bin/overlapStore -c 
/projects/nn9201k/Celera/work2/salaris1/salaris.ovlStore.BUILDING -g 
/projects/nn9201k/Celera/work2/salaris1/salaris.gkpStore  -i 0 -M 14000 
-L /projects/nn9201k/Celera/work2/salaris1/salaris.ovlStore.list  > 
/projects/nn9201k/Celera/work2/salaris1/salaris.ovlStore.err 2>&1) to 
restore the status from before the frgcorr and ovlcorr steps, before 
resuming runCA. This should restore the 0001~ file, right? The most 
important thing is that I want to avoid rerunning the frgcorr and 
ovlcorr steps, because these steps were really resource intensive.

I would really appreciate any comments or suggestions to my problem! 
Thanks in advance for your help!

much obliged,
Christoph

University of Oslo