Newbler de novo assembly

[moinul]

Hi all!
I'm very new to de novo assembly. I tried to assemble 454 cDNA shotgun reads using Newbler 2.5.3. By adding reads to a new project, I tried to run the project with default parameters, but got the following error at the end-

"Error: An internal error has occurred in the computation.
Assertion: pos >= 1 && pos <= getLength()
Location: 'int Sequence::getCafieScore(int)' [Sequence.cpp:259]
Please report this error to your customer support representative."

Can anyone help me how to resolve this? And also let me know what to do exactly if want to assemble reads at once (i.e. one step assembly)?

Moinul

[RCJK]

Hi moinul,

I had the same error a week or two ago(below) and have been trying to get an answer from Roche.
In the generating output phase:

Call Stack:
8: safeAssert(char const*, char const*, unsigned int, char const*)
7: Sequence::getCafieScore(int)
6: Alignment::setSnpMode(int)
5: Alignment::set(ChordMatrix*, std::vector<ChordRegion, std::allocator<ChordRegion> > const&, bool, int)
4: OutputPhase::setupAlignmentObject(ScaffoldIterJob*)
3: OutputPhaseWorkerThread::run()
2: Thread::_dispatch(void*)
1: /lib64/libpthread.so.0 [0x324ff0683c]

Error: An internal error has occurred in the computation.
Assertion: pos >= 1 && pos <= getLength()
Location: 'int Sequence::getCafieScore(int)' [Sequence.cpp:259]
Please report this error to your customer support representative.


The best thought they've had so far is that perhaps there is too much depth in a part of the assembly and it is causing problems w/ Newbler. I can assemble the first region fine and it goes rather quickly, but when I try adding the file for the other half of the plate, it goes for days and days and eventually stops responding.

Anybody have any thoughts? Any idea how to look for areas of high coverage (what's too high?) and how to exclude some of those reads from and assembly to see if it'll finish. Would running newbler on something more powerful (more cpus/ram) than the titanium cluster help?

[moinul]

thanks RCJK..............

[mccallumj]

Newbler fail reproduced!

Im having the same issues with re-assembling a plate of Titanium cDNA reads.
Will inspect for depth issues, contact my customer support representative and maybe look at another assembler to be on the safe side!

Regards
John

>>>>>>>>>>>>>>>>>

Call Stack:
8: safeAssert(char const*, char const*, unsigned int, char const*)
7: Sequence::getCafieScore(int)
6: Alignment::setSnpMode(int)
5: Alignment::set(ChordMatrix*, std::vector<ChordRegion, std::allocator<ChordRegion> > const&, bool, int)
4: OutputPhase::setupAlignmentObject(ScaffoldIterJob*)
3: OutputPhaseWorkerThread::run()
2: Thread::_dispatch(void*)
1: /lib64/libpthread.so.0 [0x3b3f60673d]

Error: An internal error has occurred in the computation.
Assertion: pos >= 1 && pos <= getLength()
Location: 'int Sequence::getCafieScore(int)' [Sequence.cpp:259]