[wgs-assembler-users] Issue with 3-overlapper

[Alex B. <aj...@gm...>]

Hi Celera Community,

I'm using celera 8.3 and getting an error message I can't seem to make
heads or tails of:

----------------------------------------START Thu Aug 27 08:13:38 2015

/global/common/genepool/jgi/assemblers/celera/8.3/Linux-amd64/bin/overlapStore
-u
/global/homes/a/ajbrandt/bscratch/h/celera_attempt/h_parallel/hp.ovlStore
/global/homes/a/ajbrandt/bscratch/h/celera_attempt/h_parallel/3-overlapcorrection/hp.erates
>
/global/homes/a/ajbrandt/bscratch/h/celera_attempt/h_parallel/3-overlapcorrection/overlapStore-update-erates.err
2>&1

----------------------------------------END Thu Aug 27 08:14:17 2015 (39
seconds)

ERROR: Failed with signal HUP (1)

================================================================================


runCA failed.


----------------------------------------

Stack trace:


 at /usr/common/jgi/assemblers/celera/8.3/Linux-amd64/bin/runCA line 1649.

main::caFailure('failed to apply the overlap corrections',
'/global/homes/a/ajbrandt/bscratch/h/celera_attempt/h...') called at
/usr/common/jgi/assemblers/celera/8.3/Linux-amd64/bin/runCA line 4569

main::overlapCorrection() called at
/usr/common/jgi/assemblers/celera/8.3/Linux-amd64/bin/runCA line 6557


----------------------------------------

Last few lines of the relevant log file
(/global/homes/a/ajbrandt/bscratch/h/celera_attempt/h_parallel/3-overlapcorrection/overlapStore-update-erates.err):


ERROR: iNum 291211181897 != orig->ovs.numOverlapsTotal 418401494276


I get that there must be some discrepancy between iNum and the number of
total overlaps, but I have no idea how to fix the problem (what steps to
rerun, etc).


Thanks

Alex