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shilpagarg / pstools

MIT License
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Segmentation fault #4

Closed iggyB closed 3 years ago

iggyB commented 3 years ago

Hi,

It is a very interesting concept you present in pstools. I would be very curious to see phasing performance for particular genome. Unfortunately, resolve_haplotypes consistently fails at a same point:

...
Start get Sequence: utg019112l to utg023847l
Finish get Sequence: utg014729l to utg016802l
Finish get Sequence: utg014646l to utg016393l
Finish get Sequence: utg016785l to utg023311l
Finish get Sequence: utg007839l to utg014248l
Finish get Sequence: utg006195l to utg004256l
Finish get Sequence: utg009564l to utg014552l
Finish get Sequence: utg008379l to utg012250l
Finish get Sequence: utg007720l to utg008464l
Finish get Sequence: utg013148l to utg023083l
Finish get Sequence: utg008626l to utg019008l
Finish get Sequence: utg019112l to utg023847l
Finish get Sequence: utg005218l to utg009287l
Finish get Sequence: utg002365l to utg006658l
Finish get Sequence: utg007585l to utg008971l
Finish get Sequence: utg012274l to utg015527l
Finish get Sequence: utg015688l to utg017541l
Finish get Sequence: utg017089l to utg021840l
Finish get Sequence: utg003477l to utg005574l
Finish get Sequence: utg010467l to utg021432l
Finish get Sequence: utg012512l to utg016870l
Finish get Sequence: utg005659l to utg016905l
Finish get Sequence: utg015729l to utg027229l
Finish get Sequence: utg010244l to utg013714l
All above 10M: 0
All above 1.5M: 6
Segmentation fault (core dumped)

Since there is very little/none information reported it is difficult to trace the reason.

I can give more background on data, assembly, hardware and etc, but perhaps that "Segmentation fault" error rings the bell immediately?

Cheers, Iggy

shilpagarg commented 3 years ago

Please see https://github.com/shilpagarg/DipAsm/issues/16. Hope this helps!