[wgs-assembler-users] Removing Problematic Scaffolds

[Corey W. <cor...@gm...>]

It appears that I have a problematic scaffold killing my assembly. Reading
the documentation suggests removing the assertion in the source then
re-compiling and re-running.

I was wondering instead if it were possible to somehow skip this scaffold
or otherwise prevent it from crashing?

As an aside, how does WGS do with reads that were sequenced with the
intention of overlapping sometimes called dovetailing? Should that be
precomputed  with FLASH or is WGS smart enough to handle them in their
paired form?

CreateAContigInScaffold()-- new contig 29939425 in scaffold 4725
WARNING:  NEGATIVE VARIANCE in creating contig 29939425.  Set to
6.191102e+03 based on extremal orig contig, but contig 5687395
(non-extremal) has min variance 5.129192e+03
RecomputeOffsetsInScaffold() returned RECOMPUTE_MERGE_CONTIG on scaffold
4725; scaffold modified, keep trying
CleanupAScaffold() Processing total multialign of 10483
CleanupAScaffold() Error: Undoing jiggle fpr 29439904 failed multi-align,
backing out changes
CreateAContigInScaffold()-- new contig 29939426 in scaffold 4725
CreateAContigInScaffold()-- new contig 29939427 in scaffold 4725
ScaffoldSanity()--  contig 29439904 in scaffold 4725 -- negative gap
variance -30.072749 on positive gap size 590.491808
ScaffoldSanity()-- scaffold 4725 has 1 problems.
ScaffoldSanity()-- Contig   745958 at         0 +- 0           to     10360
+- 269          ctg len     10360  gap to next        42 +- 715
ScaffoldSanity()-- Contig  8923661 at     10402 +- 984         to     10584
+- 989          ctg len       182  gap to next         6 +- 1112
ScaffoldSanity()-- Contig 29432576 at     10590 +- 2101        to     29067
+- 2582         ctg len     18477  gap to next        26 +- 512
ScaffoldSanity()-- Contig  5500353 at     29094 +- 3093        to     29678
+- 3109         ctg len       584  gap to next       -20 +- -557
ScaffoldSanity()-- Contig 29439904 at     29658 +- 2552        to     39557
+- 2809         ctg len      9899  gap to next        57 +- 1509
ScaffoldSanity()-- Contig 29939425 at     39614 +- 4318        to     50470
+- 4600         ctg len     10856  gap to next       137 +- 989
ScaffoldSanity()-- Contig   547439 at     50607 +- 5589        to     50693
+- 5591         ctg len        86  gap to next        79 +- 1287
ScaffoldSanity()-- Contig 29939426 at     50773 +- 6878        to     64864
+- 7244         ctg len     14091  gap to next        -1 +- 205
ScaffoldSanity()-- Contig   261117 at     64863 +- 7449        to     67408
+- 7515         ctg len      2545  gap to next        26 +- 292
ScaffoldSanity()-- Contig   928325 at     67433 +- 7808        to     76417
+- 8041         ctg len      8984  gap to next       -18 +- 1160
ScaffoldSanity()-- Contig 29385733 at     76400 +- 9201        to     83279
+- 9380         ctg len      6879  gap to next       -13 +- 124
ScaffoldSanity()-- Contig   849822 at     83266 +- 9504        to     92248
+- 9738         ctg len      8982  gap to next         3 +- 292
ScaffoldSanity()-- Contig  5428042 at     92251 +- 10030       to     92807
+- 10044        ctg len       556  gap to next       121 +- 454
ScaffoldSanity()-- Contig 29427826 at     92927 +- 10498       to    110977
+- 10967        ctg len     18050  gap to next        -6 +- 1434
ScaffoldSanity()-- Contig 18560999 at    110972 +- 12401       to    111064
+- 12404        ctg len        92  gap to next        13 +- 1663
ScaffoldSanity()-- Contig 29685140 at    111076 +- 14067       to    116805
+- 14216        ctg len      5729  gap to next       166 +- 1291
ScaffoldSanity()-- Contig 29939427 at    116971 +- 15507       to    128743
+- 15813        ctg len     11772  gap to next       -12 +- 967
ScaffoldSanity()-- Contig 29630932 at    128732 +- 16780       to    136671
+- 16986        ctg len      7939
cgw: CIScaffoldT_CGW.C:1143: void ScaffoldSanity(ScaffoldGraphT*,
CIScaffoldT*): Assertion `hasProblems == 0' failed.

Failed with 'Aborted'

Backtrace (mangled):

/loginhome/cwischmeyer/cwischmeyer-home-ubuntu/source/wgs-8.3rc2/Linux-amd64/bin/cgw(_Z17AS_UTL_catchCrashiP9siginfo_tPv+0x2a)[0x41b56a]
/lib/x86_64-linux-gnu/libpthread.so.0(+0x10330)[0x7f3b66b99330]
/lib/x86_64-linux-gnu/libc.so.6(gsignal+0x37)[0x7f3b667fac37]
/lib/x86_64-linux-gnu/libc.so.6(abort+0x148)[0x7f3b667fe028]
/lib/x86_64-linux-gnu/libc.so.6(+0x2fbf6)[0x7f3b667f3bf6]
/lib/x86_64-linux-gnu/libc.so.6(+0x2fca2)[0x7f3b667f3ca2]
/loginhome/cwischmeyer/cwischmeyer-home-ubuntu/source/wgs-8.3rc2/Linux-amd64/bin/cgw(_Z14ScaffoldSanityP14ScaffoldGraphTP9NodeCGW_T+0x8f9)[0x446fc9]
/loginhome/cwischmeyer/cwischmeyer-home-ubuntu/source/wgs-8.3rc2/Linux-amd64/bin/cgw(main+0x181c)[0x419c9c]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5)[0x7f3b667e5f45]

/loginhome/cwischmeyer/cwischmeyer-home-ubuntu/source/wgs-8.3rc2/Linux-amd64/bin/cgw[0x41a5cd]