#286 consensusAfterScaffolder error

[Alycia Lau]

Hi,

I am trying to assemble a plant genome (~2Gb) with error-corrected PacBio reads and Illumina contigs that are shredded into pseudo-reads using wgs-8.1. At the consensusAfterScaffolder stage, 1 partition doesn’t succeed contig consensus. These are the lines from the output of the ctgcns partition that fails:

GetAlignmentTrace()-- Overlap ACCEPTED! accept=1000.000000 lScore=0.052288 (1771 vs 1683) aScore=0.160000 (2310 vs 2326) bScore=0.110000 (-12447 vs -12458). (CONTIGF)
GetAlignmentTrace()-- Overlap found between 5324820 (U) and 28194323 (R) expected hangs: a=2326 b=-12458 erate=0.060000 aligner=DP_Compare
GetAlignmentTrace()-- Overlap ACCEPTED! accept=1000.000000 lScore=0.052288 (1771 vs 1683) aScore=0.160000 (2310 vs 2326) bScore=0.110000 (-12447 vs -12458). (CONTIGF)
DP_Compare found overlap between 5324820 (U) and 28194323 (R) ahang: 2310, bhang: -12447 (expected hang was 2326)
Alignment params: 2308 2344 200 200 0 0.12 1e-06 30 1
-- e/l = 133/1771 = 7.51%
A -----+------+----> []
B 2310 -------> 12447 []
ctgcns: ApplyAlignment.C:439: void ApplyAlignment(int32, int32, beadIdx, int32, int32, int32): Assertion `lasta == GetBead(beadStore, aindex[apos])->prev' failed.

Failed with 'Aborted'

Backtrace (mangled):

/home/nyoksean/wgs-8.1/Linux-amd64/bin/ctgcns(_Z17AS_UTL_catchCrashiP7siginfoPv+0x27)[0x40bb87]
/lib64/libpthread.so.0[0x3ffc20f500]
/lib64/libc.so.6(gsignal+0x35)[0x3ffbe328e5]
/lib64/libc.so.6(abort+0x175)[0x3ffbe340c5]
/lib64/libc.so.6[0x3ffbe2ba0e]
/lib64/libc.so.6(assert_perror_fail+0x0)[0x3ffbe2bad0]
/home/nyoksean/wgs-8.1/Linux-amd64/bin/ctgcns(_Z14ApplyAlignmentiiP7beadIdxiiPi+0xef9)[0x43d3d9]
/home/nyoksean/wgs-8.1/Linux-amd64/bin/ctgcns[0x42806e]
/home/nyoksean/wgs-8.1/Linux-amd64/bin/ctgcns(_Z16MultiAlignContigP11MultiAlignTP7gkStoreP11CNS_Options+0x8e1)[0x4289f1]
/home/nyoksean/wgs-8.1/Linux-amd64/bin/ctgcns(main+0x4ea)[0x40911a]
/lib64/libc.so.6(libc_start_main+0xfd)[0x3ffbe1ecdd]
/home/nyoksean/wgs-8.1/Linux-amd64/bin/ctgcns[0x408929]

Backtrace (demangled):

[0] /home/nyoksean/wgs-8.1/Linux-amd64/bin/ctgcns::AS_UTL_catchCrash(int, siginfo, void) + 0x27 [0x40bb87]
[1] /lib64/libpthread.so.0() [0x3ffc20f500]
[2] /lib64/libc.so.6::(null) + 0x35 [0x3ffbe328e5]
[3] /lib64/libc.so.6::(null) + 0x175 [0x3ffbe340c5]
[4] /lib64/libc.so.6() [0x3ffbe2ba0e]
[5] /lib64/libc.so.6::(null) + 0 [0x3ffbe2bad0]
[6] /home/nyoksean/wgs-8.1/Linux-amd64/bin/ctgcns::ApplyAlignment(int, int, beadIdx, int, int, int) + 0xef9 [0x43d3d9]
[7] /home/nyoksean/wgs-8.1/Linux-amd64/bin/ctgcns() [0x42806e]
[8] /home/nyoksean/wgs-8.1/Linux-amd64/bin/ctgcns::MultiAlignContig(MultiAlignT, gkStore, CNS_Options*) + 0x8e1 [0x4289f1]
[9] /home/nyoksean/wgs-8.1/Linux-amd64/bin/ctgcns::(null) + 0x4ea [0x40911a]
[10] /lib64/libc.so.6::(null) + 0xfd [0x3ffbe1ecdd]
[11] /home/nyoksean/wgs-8.1/Linux-amd64/bin/ctgcns() [0x408929]

GDB:

Can you advise on how to fix the problem?

[Brian Walenz]

Yikes, this one fell through the cracks. Sorry.

These errors are impossible to fix without access to the data, however, since this is a contig with exactly one unitig, you can reuse the unitig sequence for the contig.

If you're still interested, I can walk you through the steps, hopefully without a three month delay.

In a nutshell, you want to dump the layout of this contig, then the layout of the unitig, paste the unitig consensus sequence into the contig, and add the contig back to the store. All of this can be done with the tigStore command, but getting the parameters correct is a bit tricky.

http://wgs-assembler.sourceforge.net/wiki/index.php/TigStore