[wgs-assembler-users] wgs failed at frgcorr.sh step

[Christian D. <chr...@gm...>]

Hi,

I  run wgs-8.2beta until the assembler went idle on one of the overlap
correction steps (frgcorr.sh). Obviously, one of the early fragments didn't
finish, as frgcorr.sh for this fragment was running for 15h and the log
file contained only the first few row up to ### Using 20 pthreads. The
assembler stopped the correction only a few fragments after the idle one.
I killed the idle process and executed the fragcorr.sh command for this
fragment manually. After that, I run runCA again with the original command
and immediatly got the failure message:

"gatekeeper failed to add fragments"

As this didn't seem to work, I renamed the folder 3-overlapcorrection and
run runCA again leading to the same error message.
I thought that starting with the step before the error correction could
work and run:

/software/wgs-8.2beta/Linux-amd64/bin/overlapStoreBuild  -o
/cabog/CA/genome.ovlStore.BUILDING  -g /cabog/CA/genome.gkpStore  -M 8192
-L /cabog/CA/genome.ovlStore.list  > /cabog/CA/genome.ovlStore.err 2>&1

The log file genome.ovlStore.err contains the following:

gkStore_open()--  ERROR!  Incorrect element sizes; code and store are
incompatible.
  gkLibrary:                    store   216   code   216 bytes
  gkPackedFragment:             store    24   code    24 bytes
  gkNormalFragment:             store    48   code    48 bytes
  gkStrobeFragment:             store    48   code    48 bytes
  AS_READ_MAX_NORMAL_LEN_BITS:  store    16   code    18

Is it possible to restart the assembly at this point?
 What steps do I have to take to "rescue" the assembly results up to this
point (23 days of calculation time)

Thanks
Chris