"IQ-TREE CRASHES WITH SIGNAL SEGMENTATION FAULT", ASR anlysis with codon model

[Gabriel DUPRE]

Hi,

I launched an ASR job and received the following error message:

Optimal log-likelihood: -78003.192

Nonsynonymous/synonymous ratio (omega): 0.117
Transition/transversion ratio (kappa): 1.000
Site proportion and rates:  (0.036,0.143) (0.138,0.326) (0.225,0.598) (0.373,0.952) (0.174,1.625) (0.053,3.092) (0.002,7.859)
Parameters optimization took 38 rounds (20224.067 sec)
BEST SCORE FOUND : -78003.192
ERROR: STACK TRACE FOR DEBUGGING:
ERROR:
ERROR: *** IQ-TREE CRASHES WITH SIGNAL SEGMENTATION FAULT
ERROR: *** For bug report please send to developers:
ERROR: ***    Log file: /home/gdupre/work/HA_phylo/muscleAlign/ancestors/with_codons_models/with_dnatreefile/ali_dna_HA5_ntCDSlist.trim.aln.log
ERROR: ***    Alignment files (if possible)

/bin/bash: line 1: 47554 Segmentation fault      iqtree -s /home/gdupre/work/HA_phylo/muscleAlign/ancestors/with_codons_models/with_dnatreefile/ali_dna_HA5_ntCDSlist.trim.aln -m MG+F1X4+R7 -st CODON -te ali_dna_HA5_ntCDSlist.trim.aln.contree -asr

With another data set (alignment which is very similar to the previous one, above), I also tried to perform an ASR analysis with the same command, but without specifying any user-provided tree, and I received the same error message:

                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -87225.673
2. Current log-likelihood: -87225.637
3. Current log-likelihood: -87225.621
Optimal log-likelihood: -87225.615
Nonsynonymous/synonymous ratio (omega): 0.099
Transition/transversion ratio (kappa): 1.000
Site proportion and rates:  (0.020,0.084) (0.144,0.353) (0.353,0.650) (0.257,1.039) (0.173,1.677) (0.052,3.083)
Parameters optimization took 3 rounds (1701.168 sec)
BEST SCORE FOUND : -87225.615
ERROR: STACK TRACE FOR DEBUGGING:
ERROR:
ERROR: *** IQ-TREE CRASHES WITH SIGNAL SEGMENTATION FAULT
ERROR: *** For bug report please send to developers:
ERROR: ***    Log file: /home/gdupre/work/HA_phylo/muscleAlign/ancestors/with_codons_models/without_treefile/ali_dna_HA7_ntCDSlist.trim.aln.log
ERROR: ***    Alignment files (if possible)

I do not understand where the problem is. How can I fix this issue?

The logfiles of these jobs are attached to this post.

Best regards

Gabriel

[Minh Bui]

It looks like some problem with codon models when combined with free-rate model [+R].

Olga has also recently found this issue.

So can you please avoid using the free rate model, and just use Gamma model [+G]. Before we have time to look into the issue. Note that this is specific to codon models.

If the problem still persists, let me know.

Thanks

Minh

--
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 view this discussion on the web visit https://groups.google.com/d/msgid/iqtree/16a00ba2-683d-4f8e-8e27-c63424676f41o%40googlegroups.com.
<ali_dna_HA5_ntCDSlist.trim.aln.log><ali_dna_HA7_ntCDSlist.trim.aln.log>

[Gabriel DUPRE]

Hi,

Thank you very much for your response.

I'll keep you informed.

Best regards,

Gabriel

[Janice Valencia]

Hi,

I got the same error message using the command "-T AUTO", "-T 15", "-T 10",... So, I just removed it and it run. But it takes a while to finish.

I had the same issue with IQTree 1 and looks like this hasn't been solved.

:/

Best,

Janice

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.114 seconds

Generating 1000 samples for ultrafast bootstrap (seed: 373364)...

NOTE: 165 MB RAM (0 GB) is required!

Measuring multi-threading efficiency up to 16 CPU cores

Increase to 10 rounds for branch lengths

10 trees examined

Threads: 1 / Time: 17.756 sec / Speedup: 1.000 / Efficiency: 100% / LogL: -142912

Threads: 2 / Time: 10.464 sec / Speedup: 1.697 / Efficiency: 85% / LogL: -142912

Threads: 3 / Time: 8.468 sec / Speedup: 2.097 / Efficiency: 70% / LogL: -142912

Threads: 4 / Time: 8.217 sec / Speedup: 2.161 / Efficiency: 54% / LogL: -142912

ERROR: 

ERROR: *** IQ-TREE CRASHES WITH SIGNAL SEGMENTATION FAULT

ERROR: *** For bug report please send to developers

:*** IQ-TREE CRASHES WITH SIGNAL SEGMENTATION FAULT

ERROR: 

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

ERROR: ***    Alignment files (if possible)

ERROR: ***    Log file: concat.log

ERROR: ***    Alignment files (if possible)

Segmentation fault: 11

[Lee Grismer]

Hi everyone,

Is anyone else having problems? I can't get my files to load. They just hang on "waiting".

--

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 view this discussion on the web visit https://groups.google.com/d/msgid/iqtree/9f3e3f1c-f5a1-4888-89c2-9464288ed5f3o%40googlegroups.com.

--

L. Lee Grismer, Director of Research

Herpetology Laboratory

Department of Biology, La Sierra University
4500 Riverwalk Parkway
Riverside, CA 92515-8247, USA
Tel. 951-785-2345

"A risk free world is a very dull world, one from which we are apt to learn little of consequence."  - Geerat Vermeij

"If people are good only because they fear punishment, and hope for reward, then we are a sorry lot indeed." - Albert Einstein

[Minh Bui]

Hi Lee, Janice,

Can you please send me the data and the log file per my personal email?

While this same crash message occurs, the issue may be actually different… so I can only say something once having a look at individual cases.

Thanks

Minh

To view this discussion on the web visit https://groups.google.com/d/msgid/iqtree/CAMe9Yo9WSQWKC7tUhu8Xk78oekE3d7d2zW10aaD9CAOdc2Ln8Q%40mail.gmail.com.

[Gabriel DUPRE]

Hi Minh,

As you said in your previous email on this issue, I tried to redo my ASR analysis for some of my data sets with another codon model (without the free-rate model, when it was possible).
ASR analysis with a provided-DNA-tree worked well, but the same analysis without any provided tree failed (with the following error message: "IQtree crashes with signal aborted").

Have you got any update on this problem?
I cannot change the codon model with my other data sets (alignments) as the likelihood, AIC, and BIC scores are too far from the best-estimated codon-model.

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

[Minh Bui]

Hi Gabriel,

I suggest that you avoid doing codon models for tree reconstruction for your dataset:

Alignment has 1928 sequences with 597 columns, 595 distinct patterns

558 parsimony-informative, 18 singleton sites, 21 constant sites

This is rather short for a full analysis with complex codon models.

So I’d better (as you did) reconstruct a tree with DNA model, and then use the DNA tree as input for codon models for the ASR reconstruction.

This is the same when people use PAML - users typically input a tree inferred by another software for PAML codon analysis.

Cheers

Minh

To unsubscribe from this group and stop receiving emails from it, send an email to iqtree+un...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/iqtree/9d6fbdb9-66f1-423c-a51f-29c048642775o%40googlegroups.com.