failed to unitig and segmentation fault

[evansbenj]

Hello Aleksey,

I am using masurca v. 4.1.0 to do a de novo assembly of a large (~3.4 Gb) vertebrate genome using a combination of short(100-150 bp) inward and matepair sequences and also low coverage PacBio sequences. My run failed due to a segmentation fault and 'failed to unitig' (log attached). However, the maximum memory used in the run was less (~335Gb) than the total allocated (740Gb).

My systems admin thinks this may be a bug..? I would be grateful for any insights please.

Thank you,
Ben
CA.mr.97.17.15.0.02.log

[M-Johansen]

Hi I'm struggling with the same problem, did you find a solution to this?

[evansbenj]

Hi Maggie, I found that masurca ran fine on one of our networks but not another. So there was some issue/incompatibility that is related to the architecture of each system, but I am not sure what it is. I hope this helps! Ben Ben Evans Biology Department McMaster University Life Sciences Building room 328 1280 Main Street West Hamilton, Ontario L8S4K1 Canada phone (office/lab) : 905-525-9140 x 26973 <905-525-9140;26973>/27261 fax: 905-522-6066 Lab Website: http://benevanslab.wordpress.com/

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On Fri, Aug 18, 2023 at 9:31 AM MaggieJoh ***@***.***> wrote: Hi I'm struggling with the same problem, did you find a solution to this? — Reply to this email directly, view it on GitHub <#320 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AC6WYOOY3U2RLVHL7BJHX3DXV5VDPANCNFSM6AAAAAAXLIWOQ4> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[vidsvur]

Hi, I'm using the latest version (4.1.1), and I'm also struggling with this. Do you recommend just restarting the assembly, @evansbenj?