[wgs-assembler-users] Consensus and extendClearRanges failure

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

Dear All

My hybrid assembly (with about 131GB Illumina reads and 2GB 454 reads).  Now it failed at the extendClearRanges stage. But when I checked all the stage. I found that in the 5-consensus/ folder, there are 110 jobs, only 60 of them succeed (with both err and success output file). Below is the last few lines of the job61.err
"NumColumnsInUnitigs             = 261474722
NumGapsInUnitigs                = 280587
NumRunsOfGapsInUnitigReads      = 11234803
NumColumnsInContigs             = 0
NumGapsInContigs                = 0
NumRunsOfGapsInContigReads      = 0
NumAAMismatches                 = 0
NumVARRecords                   = 0
NumVARStringsWithFlankingGaps   = 0
NumUnitigRetrySuccess           = 0

WARNING:  Total number of unitig failures = 1

Consensus did NOT finish successfully."

Should I re-run the consensus and how can to make the failed consensus jobs succeed?

The failure information in file extendClearRanges-scaffold.0017585.err is
"FRG type R ident 757459763 container  94540021 parent  94540021 hanginsertMultiAlign()-- ERROR: multialign 636535 C has invalid fragment/unitig layout (lengt
h 2214) -- exceeds bounds of consensus sequence (length 2215).
extendClearRanges: MultiAlignStore.C:327: void MultiAlignStore::insertMultiAlign(MultiAlignT*, bool, bool): Assertion `GetMultiAlignLength(ma) <= GetMultiAli
gnLength(ma, true)' failed.
     57      0 position   2106   2185
FRG type R ident 757459764 container  94540021 parent  94540021 hang     57      0 position   2106   2185
FRG type R ident 930433904 container  94540021 parent  94540021 hang     61      0 position   2185   2110
UTG type X ident    636535 position      0   2214 num_instances 0"

Can I follow this instruction to restart it
http://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=Extend_clear_ranges_failure?

Thanks very much!






Dr. Xueping Quan

Imperial College London