Segmentation fault for large datasets

[Shubhangi1397]

Hey,
I ran multiple sequence alignments on protein sequences of length 7096 for largedatasets (1000's, 100,000's) on clustalO and kalign. I had cleaned the datasets i.e. removed sequences having BJOUXZ characters and duplicate sequences. Running MSA for 15,000 sequences and above gave me segmentation fault for building guide tree on kalign whereas, clustalO ran just fine.
[2022-03-10 11:55:18] : LOG : Building guide tree.
Segmentation fault

[TimoLassmann]

Could you share the sequences with me so I can reproduce the problem? Thanks

[Shubhangi1397]

Hey Timo, Thanks for your email. I am currently working on SARS-CoV-2 ORF1ab protein sequences. I have removed the sequences consisting of ambiguous characters (BJOUXZ) and duplicate sequences. Here is the dataset. link: https://drive.google.com/file/d/1fBgjKxpmDXm7gfOYF8JhYIEr8GcF-VpE/view?usp=sharing I have been getting segmentation faults for sequences above 13k. Your input would be valuable. Many thanks Shubhangi Kandwal

[TimoLassmann]

Thanks! I think I identified the problem; working on a solution. This may take a few days.

[TimoLassmann]

Dear Shubhangi Kandwal,
I fixed the problem in the latest release (3.3.2). Let me know if this works on your end.
Thanks for bringing this to me attention!
T

[Shubhangi1397]

Thank you so much Timo. I will let you know how it goes. Regards Shubhangi

…

On Mon, 21 Mar 2022 at 05:52, TimoLassmann ***@***.***> wrote: Dear Shubhangi Kandwal, I fixed the problem in the latest release (3.3.2). Let me know if this works on your end. Thanks for bringing this to me attention! T — Reply to this email directly, view it on GitHub <#30 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AYFGVFRGKKSHSJLVWTWKLRLVBAFCPANCNFSM5QM65I5A> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you authored the thread.Message ID: ***@***.***>

-- Shubhangi Kandwal PhD Student in Biochemistry, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute (TBSI), Trinity College Dublin, University of Dublin email: ***@***.***

[Shubhangi1397]

Hey Timo, Thanks for the fix. Kalign is working fine now :) Regards Shubhangi

…

On Mon, 21 Mar 2022 at 12:08, Shubhangi Kandwal ***@***.***> wrote: Thank you so much Timo. I will let you know how it goes. Regards Shubhangi On Mon, 21 Mar 2022 at 05:52, TimoLassmann ***@***.***> wrote: > Dear Shubhangi Kandwal, > I fixed the problem in the latest release (3.3.2). Let me know if this > works on your end. > Thanks for bringing this to me attention! > T > > — > Reply to this email directly, view it on GitHub > <#30 (comment)>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/AYFGVFRGKKSHSJLVWTWKLRLVBAFCPANCNFSM5QM65I5A> > . > Triage notifications on the go with GitHub Mobile for iOS > <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> > or Android > <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. > > You are receiving this because you authored the thread.Message ID: > ***@***.***> > -- Shubhangi Kandwal PhD Student in Biochemistry, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute (TBSI), Trinity College Dublin, University of Dublin email: ***@***.***

-- Shubhangi Kandwal PhD Student in Biochemistry, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute (TBSI), Trinity College Dublin, University of Dublin email: ***@***.***

[TimoLassmann]

Great. Any other issues let me know!