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

[Wu]

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!

[Minh Bui]

Hi Wu,

THanks for the report. Can you please send the alignment file to my personal email, for further inspection?

Cheers,

Mih

--
You received this message because you are subscribed to the Google Groups "IQ-TREE" group.
To unsubscribe from this group and stop receiving emails from it, send an email to iqtree+un...@googlegroups.com.
To post to this group, send email to iqt...@googlegroups.com.
Visit this group at https://groups.google.com/group/iqtree.
To view this discussion on the web visit https://groups.google.com/d/msgid/iqtree/520d66e3-823e-4a23-b648-bdd1efc8f77d%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.
<422.phy.log>

[Wu]

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!

--
You received this message because you are subscribed to the Google Groups "IQ-TREE" group.

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

[KATHERIN OTALORA]

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. 

[KATHERIN OTALORA]

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]

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