Segmentation fault with mixed protein+DNA partition

[iqtree]

Segmentation fault with mixed protein+DNA partition

[bqminh]

Sorry for the delay. Did you use version 2.1.2? Can you check if it works with version 2.1.0: https://github.com/iqtree/iqtree2/releases/tag/v2.1.0 <https://github.com/iqtree/iqtree2/releases/tag/v2.1.0> Minh

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On 15 Nov 2020, at 7:08 am, Zoltán Füssy ***@***.***> wrote: Hello, sorry to post here instead of Google groups but I cannot seem to join that. I am experiencing an apparently unreported segmentation fault on a rather small dataset of 8 proteins and 1 rDNA matrix (altogether ~4300 characters). After loading the input, IQ-TREE consumes 90GB RAM and crashes. This does not happen with version 1.6, or with protein and DNA partitions analyzed separately. Would you kindly advise me on this? I am attaching the log file. partition.nex.log <https://github.com/iqtree/iqtree2/files/5541394/partition.nex.log> Many thanks, kind regards Zoltan — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#12>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADRTPUY4ISXZTU2HYW2CBETSP3PS7ANCNFSM4TVXSLKA>.

[morpholino]

Dear Minh, I confirm that we have tried precompiled versions 2.0.8, 2.1.0 and 2.1.2 on servers with ubuntu 16.04.6 and 18.04.3LTS with the same result (we also tried locally on a computer with ubuntu 20.04LTS but in this case we quickly ran out of memory). We did not try compiling any of the earlier versions. Sorry we could not narrow down the problem more. Best Zoltan On Thu, 3 Dec 2020 at 15:34, Bui Quang Minh <[email protected]> wrote:

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Sorry for the delay. Did you use version 2.1.2? Can you check if it works with version 2.1.0: https://github.com/iqtree/iqtree2/releases/tag/v2.1.0 < https://github.com/iqtree/iqtree2/releases/tag/v2.1.0> Minh > On 15 Nov 2020, at 7:08 am, Zoltán Füssy ***@***.***> wrote: > > > Hello, > > sorry to post here instead of Google groups but I cannot seem to join that. I am experiencing an apparently unreported segmentation fault on a rather small dataset of 8 proteins and 1 rDNA matrix (altogether ~4300 characters). After loading the input, IQ-TREE consumes 90GB RAM and crashes. This does not happen with version 1.6, or with protein and DNA partitions analyzed separately. Would you kindly advise me on this? > I am attaching the log file. partition.nex.log < https://github.com/iqtree/iqtree2/files/5541394/partition.nex.log> > Many thanks, kind regards > > Zoltan > > — > You are receiving this because you are subscribed to this thread. > Reply to this email directly, view it on GitHub < #12>, or unsubscribe < https://github.com/notifications/unsubscribe-auth/ADRTPUY4ISXZTU2HYW2CBETSP3PS7ANCNFSM4TVXSLKA >. > — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#12 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AG6FNOBRFKZW2Y7F66GOTP3SS6OVXANCNFSM4TVXSLKA> .

[bqminh]

I don't see any Segmentation fault from the log file, thus it's hard to say without running IQ-TREE myself on your dataset. Moreover, there has been a lot of versions since then and thus I will close this issue now. However, please feel free to reopen it if you see that the latest version of IQ-TREE still crashes, and in that case pls send us the input data.