ERROR: C:\Users\minh\Dropbox\iqtree-git\tree\phylotree.cpp:2652:

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Wu

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Jul 11, 2019, 11:07:55 PM7/11/19
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Hi Developers:
    I encounter one question. My data contains 422 protein sequences, then I run the iqtree with command:

    iqtree -s 422.phy -st AA -m WAG+G4+F -b 100 -nt AUTO

    But it doesn't work
ERROR: C:\Users\minh\Dropbox\iqtree-git\tree\phylotree.cpp:2652: virtual double PhyloTree::optimizeAllBranches(int, double, int): Assertion `fabs(new_tree_lh-tree_lh) < max_delta_lh' failed.
ERROR:
ERROR: *** IQ-TREE CRASHES WITH SIGNAL ABORTED
ERROR: *** For bug report please send to developers:
ERROR: ***    Log file: 422.phy.log
ERROR: ***    Alignment files (if possible)

while it works fine in the another computer win 7, using the same sequences file and command

I am not sure the reason, So can you help this?

Any help will be appreciated!

422.phy.log

Minh Bui

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Jul 14, 2019, 8:19:59 PM7/14/19
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Hi Wu,
THanks for the report. Can you please send the alignment file to my personal email, for further inspection?

Cheers,
Mih

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<422.phy.log>

Wu

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Jul 31, 2019, 10:59:07 AM7/31/19
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Hi Mih

I'm sorry, I didn't notice your reply before. After several attempts, it works without the "-nt AUTO" parameter, but what exactly caused it is not clear.

在 2019年7月15日星期一 UTC+8上午8:19:59,Minh Bui写道:
Hi Wu,
THanks for the report. Can you please send the alignment file to my personal email, for further inspection?

Cheers,
Mih

On 12 Jul 2019, at 1:07 pm, Wu <5547...@qq.com> wrote:

Hi Developers:
    I encounter one question. My data contains 422 protein sequences, then I run the iqtree with command:

    iqtree -s 422.phy -st AA -m WAG+G4+F -b 100 -nt AUTO

    But it doesn't work
ERROR: C:\Users\minh\Dropbox\iqtree-git\tree\phylotree.cpp:2652: virtual double PhyloTree::optimizeAllBranches(int, double, int): Assertion `fabs(new_tree_lh-tree_lh) < max_delta_lh' failed.
ERROR:
ERROR: *** IQ-TREE CRASHES WITH SIGNAL ABORTED
ERROR: *** For bug report please send to developers:
ERROR: ***    Log file: 422.phy.log
ERROR: ***    Alignment files (if possible)

while it works fine in the another computer win 7, using the same sequences file and command

I am not sure the reason, So can you help this?

Any help will be appreciated!


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To unsubscribe from this group and stop receiving emails from it, send an email to iqt...@googlegroups.com.

KATHERIN OTALORA

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Feb 22, 2023, 5:13:43 AM2/22/23
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Hello,

I have the same problem.

I am trying to run the following line, because I am looking for the .rootstrap : 

./iqtree2 -s rev_allsamples.varsites.phy -p partition_prueba2_rev_allsamples.best_scheme.nex --model-joint 12.12 -B 1000 -T AUTO -pre partition_prueba2_NOrev_allsamples

And I get an error:

ERROR: phylotree.cpp:2751: virtual double PhyloTree::optimizeAllBranches(int, double, int): assertion `fabs(new_tree_lh-tree_lh) < max_delta_lh' failed.

ERROR: STACK TRACE FOR DEBUGGING:
ERROR: 2 _sigtramp()
ERROR: 5 PhyloTree::optimizeAllBranches(int, double, int)
ERROR: 6 PhyloTree::testNumThreads()
ERROR: 7 PhyloTree::ensureNumberOfThreadsIsSet(Params*)
ERROR: 8 runTreeReconstruction(Params&, IQTree*&)
ERROR: 9 runPhyloAnalysis(Params&, Checkpoint*, IQTree*&, Alignment*&)
ERROR: 10 runPhyloAnalysis(Params&, Checkpoint*&)
ERROR 
ERROR: *** IQ-TREE CRASHES WITH ABORTED SIGNAL

ERROR: *** For bug report please send to developers:
ERROR: *** Log file: partition_test2_NOrev_allsamples.log

ERROR: *** Alignment files (if possible)
zsh: abort ./iqtree2 -s rev_allsamples.varsites.phy -p --model-joint 12.12 -B 1000 -T

I send the .log to see if you can help me.

I tried removing the -T AUTO but I get the same error

Thanks. 
partition_prueba2_NOrev_allsamples.log

KATHERIN OTALORA

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Feb 23, 2023, 5:32:39 AM2/23/23
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I solved this by deleting the -p partition_test2_rev_allsamples.best_scheme.nex as in my case I have SNPs and the model could be GTR+ASC

Thanks

Aline Silva

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Jan 24, 2024, 7:00:41 PMJan 24
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Hi, I'm trying to perform a maximum likelihood analysis IQTree, but after providing the concatenated data file (.phy) and the partition file .nex format, I'm encountering an error. IQTree returns: " WARNING: Estimated model parameters are at boundary that can cause numerical instability! Perform nearest neighbor interchange... Optimizing NNI: done in 0.72736 secs using 98.82% CPU Estimate model parameters (epsilon = 1.000) Initial log-likelihood: -27523.841 Current log-likelihood at step 1: -27522.667 Current log-likelihood at step 2: -27521.683 Partition-specific rates: 0.909 0.236 4.444 Parameters optimization took 1 rounds (0.595 sec) Time for fast ML tree search: 4.343 seconds ERROR: \Users\minh\Dropbox\iqtree2\tree\phylotree.cpp:475: virtual void PhyloTree::setRootNode(const char *, bool): Assertion `root' failed. ERROR: ERROR: *** IQ-TREE CRASHES WITH SIGNAL ABORTED ERROR: *** For bug report please send to developers: ERROR: *** Log file: particoes.nex.log ERROR: *** Alignment files (if possible)

C:\bin>pause

Here is my partition file (in .nex):

DNA,12S = 1-972

DNA,16S = 973-3544

DNA,COI_codon1 = 3546-4203\3

DNA,COI_codon2 = 3547-4203\3

DNA,COI_codon3 = 3545-4203\3

DNA,RAG1_codon1 = 4204-4659\3

DNA,RAG1_codon2 = 4205-4659\3

DNA,RAG1_codon3 = 4206-4659\3

And this is the command I run in IQTree:

iqtree2.exe -s Pseudopaludicola_Concat_RaxML.phy -p particoes.nex -m  MFP+MERGE -AICc -B 1000 -o Leptodactylus_latrans_MACN_38648 -nt AUTO -alrt 1000

 

pause

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