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amkozlov / raxml-ng

RAxML Next Generation: faster, easier-to-use and more flexible
GNU Affero General Public License v3.0
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Error: assertion failed #161

Open greektash opened 1 year ago

greektash commented 1 year ago

Hi there, I'm using raxml-ng version 1.2.0 on a Macbook M1. I keep getting a variety of errors (log attached) - either "Assertion failed" error or "libc++abi: terminating due to uncaught exception". These persist despite adding blopt nr_safe, removing identical sequences, uninstalling & reinstalling raxml-ng, and recreating the input file to ensure all okay... Nothing's worked so far! Weirdly, after the attempt aborts, I can often get it started again, and it'll manage a few more bootstraps (picking up from where it left off last time) and then abort again. Any ideas?! Thanks in advance :-)

raxlog.txt

amkozlov commented 1 year ago

Thanks for reporting!

Could you please:

  1. Check if you get the same error in x86 emulation mode (rosetta)
  2. Send me your input files
greektash commented 1 year ago

Hi there, Thanks for that. Yes, I’ve re-run it with Rosetta2 and still getting errors (below). Input file and most recent log attached. Thanks in advance for your help, and best wishes,

libc++abi: terminating due to uncaught exception of type std::runtime_error: ERROR in SPR round (LIBPLL-2240): BL opt converged to a worse likelihood score by -14.658877165522426 units

zsh: abort raxml-ng --all --msa clean.full.noref.fasta --model GTR+G --prefix Nlac --see

From: Alexey Kozlov @.> Date: Tuesday, 18 July 2023 at 17:37 To: amkozlov/raxml-ng @.> Cc: Anastasia Theodosiou @.>, Author @.> Subject: Re: [amkozlov/raxml-ng] Error: assertion failed (Issue #161) This email was sent to you by someone outside the University. You should only click on links or attachments if you are certain that the email is genuine and the content is safe.

Thanks for reporting!

Could you please:

  1. Check if you get the same error in x86 emulation mode (rosetta)
  2. Send me your input files

— Reply to this email directly, view it on GitHubhttps://github.com/amkozlov/raxml-ng/issues/161#issuecomment-1640564131, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A4GIC2K4ZU5M57QGZI7SZWTXQ23TJANCNFSM6AAAAAA2H3HNNI. You are receiving this because you authored the thread.Message ID: @.***>

The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th’ ann an Oilthigh Dhùn Èideann, clàraichte an Alba, àireamh clàraidh SC005336.

amkozlov commented 1 year ago

sorry but I don't see the attachment

greektash commented 1 year ago

Hiya, I’ve tried resending, but I get a mail delivery notification saying the attachment is too large (I think this is an issue on your end, as it’s within the size limits for me to send). Is there another email address I can send to?

From: Alexey Kozlov @.> Date: Monday, 24 July 2023 at 12:05 To: amkozlov/raxml-ng @.> Cc: Anastasia Theodosiou @.>, Author @.> Subject: Re: [amkozlov/raxml-ng] Error: assertion failed (Issue #161) This email was sent to you by someone outside the University. You should only click on links or attachments if you are certain that the email is genuine and the content is safe.

sorry but I don't see the attachment

— Reply to this email directly, view it on GitHubhttps://github.com/amkozlov/raxml-ng/issues/161#issuecomment-1647698037, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A4GIC2M63RKDHJ7THZIULK3XRZJF3ANCNFSM6AAAAAA2H3HNNI. You are receiving this because you authored the thread.Message ID: @.***>

The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th’ ann an Oilthigh Dhùn Èideann, clàraichte an Alba, àireamh clàraidh SC005336.

amkozlov commented 1 year ago

please try alexey.kozlov (at) h-its (dot) com

or just share it via google drive or similar

greektash commented 1 year ago

I've shared an item with you:

clean.full.noref.fasta.gz https://drive.google.com/file/d/1lv8Pm98FpI65XUChrgMFTdBSq-ZzugX_/view?usp=sharing&invite=CJiuzqUL&ts=64c7ae52

It's not an attachment -- it's stored online. To open this item, just click
the link above.

greektash commented 1 year ago

Hi there, I’ve just received another delivery failure notification from the email I sent you last week with the zipped input file. I’ve now sent this to you again as a Google drive link from my gmail account, hope that works! Here is the link: https://drive.google.com/file/d/1lv8Pm98FpI65XUChrgMFTdBSq-ZzugX_/view?usp=drive_link

From: Alexey Kozlov @.> Date: Monday, 24 July 2023 at 12:36 To: amkozlov/raxml-ng @.> Cc: Anastasia Theodosiou @.>, Author @.> Subject: Re: [amkozlov/raxml-ng] Error: assertion failed (Issue #161) This email was sent to you by someone outside the University. You should only click on links or attachments if you are certain that the email is genuine and the content is safe.

please try alexey.kozlov (at) h-its (dot) com

or just share it via google drive or similar

— Reply to this email directly, view it on GitHubhttps://github.com/amkozlov/raxml-ng/issues/161#issuecomment-1647741912, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A4GIC2PGDUQS3OGROFQ5OS3XRZM5HANCNFSM6AAAAAA2H3HNNI. You are receiving this because you authored the thread.Message ID: @.***>

The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th’ ann an Oilthigh Dhùn Èideann, clàraichte an Alba, àireamh clàraidh SC005336.

amkozlov commented 1 year ago

Hi, thanks for the file!

I now can reproduce the problem, but.don't have a fix yet.

So for the time being, please try x86 mac version which seems to work fine on this dataset:

https://github.com/amkozlov/raxml-ng/releases/download/1.2.0/raxml-ng_v1.2.0_macos_x86_64.zip

greektash commented 1 year ago

Thanks, I've installed the x86 version and run with Rosetta and it worked fine! Appreciate your help, Best wishes,

Sent from Outlook for Androidhttps://aka.ms/AAb9ysg

From: Alexey Kozlov @.> Sent: Tuesday, August 1, 2023 4:42:31 PM To: amkozlov/raxml-ng @.> Cc: Anastasia Theodosiou @.>; Author @.> Subject: Re: [amkozlov/raxml-ng] Error: assertion failed (Issue #161)

This email was sent to you by someone outside the University. You should only click on links or attachments if you are certain that the email is genuine and the content is safe.

Hi, thanks for the file!

I now can reproduce the problem, but.don't have a fix yet.

So for the time being, please try x86 mac version which seems to work fine on this dataset:

https://github.com/amkozlov/raxml-ng/releases/download/1.2.0/raxml-ng_v1.2.0_macos_x86_64.zip

— Reply to this email directly, view it on GitHubhttps://github.com/amkozlov/raxml-ng/issues/161#issuecomment-1660583081, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A4GIC2IYI7K535UN72QIIVDXTEPWPANCNFSM6AAAAAA2H3HNNI. You are receiving this because you authored the thread.Message ID: @.***>

The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th’ ann an Oilthigh Dhùn Èideann, clàraichte an Alba, àireamh clàraidh SC005336.