[wgs-assembler-users] Contig consensus failure

[Ole K. T. <o.k...@bi...>]

Hi,
I'm having some problems while doing some low coverage sequencing
assembly testing. I've tried to assemble about 10x coverage of 150 nt
paired Illumina reads of 500 bp fragment size. These are from the
parrot used in the Assemblathon 2
(http://assemblathon.org/pages/download-data). Everything seems to run
fine, until contig consensus, where 1 partition just don't succeed. It
seems to run for quite some time (20 hours or something) before
failing. These are the last 20 lines from the output of the ctgcns
partition that fails:
Alignment params: 297 333 200 200 0  0.12 1e-06 30 1
 -- e/l = 7/112 =  6.25%
  A -----+------+---->  []
  B  332 -------> 40    []
GetAlignmentTrace()-- Overlap ACCEPTED!  accept=1000.000000
lScore=0.026087 (112 vs 115) aScore=0.160000 (332 vs 316)
bScore=0.150000 (-42 vs -27).  (CONTIGF)
GetAlignmentTrace()-- Overlap found between 1076523 (U) and 25763657
(R) expected hangs: a=316 b=-27 erate=0.060000 aligner=Local_Overlap
GetAlignmentTrace()-- Overlap ACCEPTED!  accept=1000.000000
lScore=0.026087 (112 vs 115) aScore=0.160000 (332 vs 316)
bScore=0.150000 (-42 vs -27).  (CONTIGF)
Local_Overlap_AS_forCNS found overlap between 1076523 (U) and 25763657
(R) ahang: 332, bhang: -42 (expected hang was 316)
Alignment params: 298 334 200 200 0  0.12 1e-06 30 1
 -- e/l = 6/112 =  5.36%
  A -----+------+---->  []
  B  332 -------> 42    []
GetAlignmentTrace()-- Overlap ACCEPTED!  accept=1000.000000
lScore=0.009009 (110 vs 111) aScore=0.140000 (332 vs 318)
bScore=0.130000 (-42 vs -29).  (CONTIGF)
GetAlignmentTrace()-- Overlap found between 1076523 (U) and 57537697
(R) expected hangs: a=318 b=-29 erate=0.060000 aligner=Local_Overlap
GetAlignmentTrace()-- Overlap ACCEPTED!  accept=1000.000000
lScore=0.009009 (110 vs 111) aScore=0.140000 (332 vs 318)
bScore=0.130000 (-42 vs -29).  (CONTIGF)
Local_Overlap_AS_forCNS found overlap between 1076523 (U) and 57537697
(R) ahang: 332, bhang: -42 (expected hang was 318)
Alignment params: 300 336 200 200 0  0.12 1e-06 30 1
 -- e/l = 6/110 =  5.45%
  A -----+------+---->  []
  B  332 -------> 42    []

This is the error message:
 at /usit/titan/u1/olekto/src/wgs-7.0/Linux-amd64/bin/runCA line 1237
	main::caFailure('1 consensusAfterScaffolder jobs failed; remove
8-consensus/co...', undef) called at
/usit/titan/u1/olekto/src/wgs-7.0/Linux-amd64/bin/runCA line 5142
	main::postScaffolderConsensus() called at
/usit/titan/u1/olekto/src/wgs-7.0/Linux-amd64/bin/runCA line 5885

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

1 consensusAfterScaffolder jobs failed; remove
8-consensus/consensus.sh to try again

I've tried removing consensus.sh and running again, but get the same error.

This is the spec file:
utgErrorRate=0.03
utgErrorLimit=2.5
ovlErrorRate=0.06
cnsErrorRate=0.06
cgwErrorRate=0.10
merSize = 22
overlapper=ovl
unitigger = bogart
merylMemory   = 128000
merylThreads = 16
merOverlapperThreads = 2
merOverlapperExtendConcurrency = 8
merOverlapperSeedConcurrency = 8
ovlThreads = 2
mbtThreads = 2
mbtConcurrency = 8
ovlConcurrency = 8
ovlCorrConcurrency = 16
ovlRefBlockSize  = 32000000
ovlHashBits = 24
ovlHashBlockLength = 800000000
ovlStoreMemory = 128000
frgCorrThreads    = 2
frgCorrConcurrency = 8
ovlCorrBatchSize  = 1000000
ovlCorrConcurrency = 16
cnsConcurrency   = 16
doExtendClearRanges = 0

I don't need to have that unitig (1076523 (U)) in my finished
assembly, so it's possible to just remove it as long as I get a
finished assembly. I've also tried to just create the .success file,
but then terminator fails.

Does anyone have any ideas of what I might do different? Can I just
remove that unitig and proceed? How do I do that?

Sincerely,
Ole Kristian Tørresen
PhD student
University of Oslo