From: Brian W. <th...@gm...> - 2015-07-23 15:21:54
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Did you do a code update between starting the assembly and now? If you have the source code, change AS_READ_MAX_NORMAL_LEN_BITS in file AS_global.H from 18 to 16. The ovlStore is likely OK. The issue is hopefully configuration of the frgCorr (and ovlCorr) stages. These are both I/O intense and big memory, and finding a tradeoff is sometimes hard. Post your config, please (and describe the hardware you're running on). Failing that, you can turn this step off: doFragmentCorrection=0 (IIRC). I'd suggest a slight increase in unitigger (bogart, the bat* parameters) error rates to adjust for the uncorrected overlaps. b On Thu, Jul 23, 2015 at 10:29 AM, Christian Dreischer < chr...@gm...> wrote: > > 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 (>20 days of calculation time) > > Thanks > Chris > > > > ------------------------------------------------------------------------------ > > _______________________________________________ > wgs-assembler-users mailing list > wgs...@li... > https://lists.sourceforge.net/lists/listinfo/wgs-assembler-users > > |