iqtree crashes when using ultrafast bootstraps and tree topology contraint

[Max Schön]

Hej,

I just played around a little bit with constrainig my topology using a newick file, and experienced a series of crashes... after a while i switched from ultrafast bootstraps to normal (from -bb to -b) and now its running.... The error message i received was

IQ-TREE multicore version 1.5.3 for Linux 64-bit built Jan 15 2017
Copyright (c) 2011-2016 Nguyen Lam Tung, Olga Chernomor, Arndt von Haeseler and Bui Quang Minh.

Host:    molev-32-72 (AVX2, FMA3, 125 GB RAM)
Command: iqtree-omp -s SRR3987482-86.trim.aln -g COG0086.tree -bb 1000 -nt 40 -pre SRR3987482-86.trim.iqtree -v
Seed:    523557 (Using SPRNG - Scalable Parallel Random Number Generator)

64 bit Linear Congruential Generator with Prime Addend

        seed = 523557, stream_number = 0        parameter = 0

Time:    Fri May  5 08:49:37 2017
Kernel:  AVX+FMA - 40 threads(48 CPU cores detected)

Reading alignment file SRR3987482-86.trim.aln ... Fasta format detected
.
.
.
For your convenience alignment with unique sequences printed to SRR3987482-86.trim.iqtree.uniqueseq.phy
Creating fast SIMD initial parsimony tree by random order stepwise addition...
iqtree-omp: /home/CIBIV/minh/Dropbox/iqtree-git/phylotreepars.cpp:378: int PhyloTree::computeParsimonyTree(const char*, Alignment*): Assertion `taxon_order.size() == constraintTree.leafNum' failed.
STACK TRACE FOR DEBUGGING:

*** IQ-TREE CRASHES WITH SIGNAL ABORTED
*** For bug report please send to developers:
***    Log file: SRR3987482-86.trim.iqtree.log
***    Alignment files (if possible)

and no problems  running
iqtree-omp -s SRR3987482-86.trim.aln -g COG0086.tree -b 100 -nt 40 -pre SRR3987482-86.trim.iqtree -v

cheers,
Max

[Bui Quang Minh]

Hi Max, thanks for the report. Can you send me the alignment and constraint tree via personal email?

For constrained standard bootstrap, please use version 1.5.4 because of an important change:

• Combining standard bootstrap (-b) and constraint tree option (-g) will impose the constraint on bootstrap trees (previously not). Thanks to Matthew Prebus for discussions.

Cheers, 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 post to this group, send email to iqt...@googlegroups.com.
Visit this group at https://groups.google.com/group/iqtree.
For more options, visit https://groups.google.com/d/optout.

--

Bui Quang Minh

Center for Integrative Bioinformatics Vienna (CIBIV)

Campus Vienna Biocenter 5, VBC5, Ebene 1

A-1030 Vienna, Austria

Phone: ++43 1 4277 74326

Email: minh.bui (AT) univie.ac.at

[teo...@gmail.com]

Hi Minh,

The same error message appears with iqtree-opm 1.5.5 (downloaded today) when running a tree search under a topological constraint (-g) with identical sequences in the dataset. It appears that the duplicate taxa are removed from the alignment, but they are not pruned from the constraint tree. Using a constraint with these duplicates removed, fixes the issue.

Here are last few lines of the log file:

Reading constraint tree con.tree...
NOTE: Entomoneis_pseudoduplex_ROS_AF18 is identical to Entomoneis_pseudoduplex_ROS_KD19 but kept for subsequent analysis
NOTE: 2 identical sequences (see below) will be ignored for subsequent analysis
NOTE: Entomoneis_pseudoduplex__ROS_AF18_ (identical to Entomoneis_pseudoduplex_ROS_KD19) is ignored but added at the end
NOTE: Entomoneis_pseudoduplex_ROS_KD16 (identical to Entomoneis_pseudoduplex_ROS_KD19) is ignored but added at the end

For your convenience alignment with unique sequences printed to xx.uniqueseq.phy
Creating fast initial parsimony tree by random order stepwise addition...
iqtree-omp: /home/minh/Dropbox/iqtree-git/phylotreepars.cpp:378: int PhyloTree::computeParsimonyTree(const char *, Alignment *): Assertion `taxon_order.size() == constraintTree.leafNum' failed.

Dropping Entomoneis_pseudoduplex__ROS_AF18_ and Entomoneis_pseudoduplex_ROS_KD16 from the constraint tree (these sequences are not in xx.uniqueseq.phy) fixes the problem.

Regards

[Heiko Schmidt]

Dear Max,

Another way to achieve this is to state the option “-keep-ident” on the command line.
This tells IQ-Tree not to prune identical sequences.

Best wishes,
Heiko

-----------------------------------------------------------------------------
Heiko Schmidt

Center for Integrative Bioinformatics Vienna (CIBIV)

http://www.cibiv.at/
-----------------------------------------------------------------------------

[swat...@uohyd.ac.in]

Hi Max,

I am experiencing a similar problem. Did you get any solution of this problem.

Cheers,

Swati

[Minh Bui]

Dear Swati,

I believe such “old" problem has been resolved. So before we can provide further help, please explain the problem you encountered explicitly, e.g. what is the command line? Did you see any warning or error messages in the log? 

Cheers

Minh