[wgs-assembler-users] Failusre to resume extendClearRanges job

[Quan, X. <x....@im...>]

Dear All

My celera failed in the extendClearRanges stage. The job extendClearRanges-scaffold.0017585.sh failed with the following error:
"examining gap 2089 from lcontig 252777756 (orient: F, pos: 1843.074083, 6837.074083) to rcontig 819682 (orient: R, pos: 8597.736468, 6893.736468), size: 56.6
62385
ReplaceEndUnitigInContig()-- contig 252777756 unitig 210835 isLeft(0)
contig 252777756
len 4994
(::::sequences)
data.unitig_coverage_stat 0.000000
data.unitig_microhet_prob 1.000000
data.unitig_status        X
data.unitig_unique_rept   X
data.contig_status        U
data.num_frags            1271
data.num_unitigs          2
insertMultiAlign()-- ERROR: multialign 252777756 C has invalid fragment/unitig layout (length 4992) -- exceeds bounds of consensus sequence (length 4994).
extendClearRanges: MultiAlignStore.C:327: void MultiAlignStore::insertMultiAlign(MultiAlignT*, bool, bool): Assertion `GetMultiAlignLength(ma) <= GetMultiAli
gnLength(ma, true)' failed.
/ax3-savolainenlab/analysis/Plants/Genomics/Celera/fullrun1/7-1-ECR/extendClearRanges-scaffold.0017585.sh: line 18: 116736 Aborted                 /apps/wgs/
2012-11-02//Linux-amd64/bin/extendClearRanges -g /ax3-savolainenlab/analysis/Plants/Genomics/Celera/fullrun1/Howea.gkpStore -t /ax3-savolainenlab/analysis/Pl
ants/Genomics/Celera/fullrun1/Howea.tigStore -n 16 -c Howea -b 0017585 -e 0051439 -i 1 -S 3936
----------------------------------------END Thu Nov  8 15:06:42 2012 (4402 seconds)
----------------------------------------START Thu Nov  8 15:06:42 2012
/ax3-savolainenlab/analysis/Plants/Genomics/Celera/fullrun1/7-1-ECR/extendClearRanges-scaffold.0051443.sh
----------------------------------------END Thu Nov  8 15:06:42 2012 (0 seconds)
ERROR: Failed with signal HUP (1)
================================================================================

runCA failed.

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

 at /apps/wgs/2012-11-02//bin/runCA line 1391
        main::caFailure('extendClearRanges failed', '/ax3-savolainenlab/analysis/Plants/Genomics/Celera/fullrun1/7...') called at /apps/wgs/2012-11-02//bin/r
unCA line 5111
        main::eCR('7-1-ECR', undef, 1) called at /apps/wgs/2012-11-02//bin/runCA line 5206
        main::scaffolder() called at /apps/wgs/2012-11-02//bin/runCA line 6146

----------------------------------------
Last few lines of the relevant log file (/ax3-savolainenlab/analysis/Plants/Genomics/Celera/fullrun1/7-1-ECR/extendClearRanges-scaffold.0051443.err):


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

extendClearRanges failed
"
So the problem is that it didn't success and didn't produce the *.ckp.17 file needed by the following extendClearRanges-scaffold.0051443.sh. But it store a success information in some log file (I don't know which log file) so I can not re-start the extendClearRanges-scaffold.0017585.sh or skip it to the next job. 

I will really appreciate it for any help!


Thanks very much! 

Dr. Xueping Quan
Imperial College London