[wgs-assembler-users] Stuck at consensusAfterScaffolder

[<mic...@ip...>]

Hello, 

After several restarts of an assembly with error-corrected PacBio reads using CA 8.0, i got stuck at the consensusAfterScaffolder stage. Removing consensus.sh and rerunning the assembly couldnt overcome the following error (at end of post). 
I found a earlier post about consensusAfterScaffolder  - problems (in CA 6.0 i think) in the tracker but wasnt sure if its solution is still valid for CA 8.0. 
Attached is one of the 3 error-files which didnt succeed (from 8-consensus/ ). 

When looking at the error-files in 8-consensus/ i found two of them terminating with: 

#IncBaseCount i out of range (possibly non ACGTN letter?)ctgcns: MultiAlignment_CNS.C:193: int IncBaseCount(BaseCount*, char): Assertion `0' failed.
#
#Failed with 'Aborted'

and one with: 

# Failed with 'Segmentation fault'




$less runCA.sge.out.10

ENV: SGE_TASK_ID needs to be unset, done.
/data/users/mmoser/Celera/main/assembly20.11.13/8-consensus/peaxi_026 failed -- no .success.
/data/users/mmoser/Celera/main/assembly20.11.13/8-consensus/peaxi_056 failed -- no .success.
/data/users/mmoser/Celera/main/assembly20.11.13/8-consensus/peaxi_057 failed -- no .success.
================================================================================

runCA failed.

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

 at /home/mmoser/CELERA/wgs-8.0/Linux-amd64/bin/runCA line 1501
        main::caFailure('3 consensusAfterScaffolder jobs failed; remove /data/users/mm...', undef) called at /home/mmoser/CELERA/wgs-8.0/Linux-amd64/bin/runCA line 5542
        main::postScaffolderConsensus() called at /home/mmoser/CELERA/wgs-8.0/Linux-amd64/bin/runCA line 6317

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

3 consensusAfterScaffolder jobs failed; remove /data/users/mmoser/Celera/main/assembly20.11.13/8-consensus/consensus.sh to try again