Re: [iqtree] Constrained tree search: problems with version 1.6.12 and 2.3.2

[Thomas Wong]

Hi Bastian,

Thanks for your message. Can you please try the version 2.3.4 at https://github.com/iqtree/iqtree2/releases?

Issues about the constrained tree have been resolved in version 2.3.4. Can you try it?

If there is still an error when using version 2.3.4, please send us the alignment file, the constrained tree, and the log file, and we will look into it.

Moreover, when you rerun the analysis, please use the option "-redo" as the program will not load the previous intermediate results. Thank you!

Cheers,

Thomas

On Tue, Apr 30, 2024 at 6:19 PM Bastian Heimburger <josef.k...@gmail.com> wrote:

Hello,

I've some issues concerning a constrained tree search. I've used both IQ-Tree 1.6.12 and 2.3.2, both of which show different error messages when I run the analysis. My constrained tree contains 339 species.

For 1.6.12: I get an error message indicating that an alignment sequence does not appear in the tree (e.g. "ERROR: Alignment sequence JQ000045_Afronothrus_sp_Trhypochthoniidae_Crotonioidea does not appear in the tree"), however this is clearly wrong, because this sequence is included in my constrained tree as well as in the alignment. I tried to switch the position of this sequence in the constrained tree file, but then I get another error message including a different sequence, which is nonetheless also included in both the alignment fasta file and constrained tree. I've double-checked my tree and alignment file and I cannot find any mistake.

For 2.3.2: Using the same alignment as well as constrained tree, I get following error: "---> START RUN NUMBER 1 (seed: 506818)
Creating fast initial parsimony tree by random order stepwise addition...
ERROR: phylotreepars.cpp:1245: virtual int PhyloTree::computeParsimonyTree(const char*, Alignment*, int*): Assertion `index == 4*leafNum-6' failed.
ERROR: STACK TRACE FOR DEBUGGING:
ERROR:
ERROR: *** IQ-TREE CRASHES WITH SIGNAL ABORTED
ERROR: *** For bug report please send to developers:
ERROR: ***    Log file: cl_om_gappy_constr.log
ERROR: ***    Alignment files (if possible)"

Here I used also the `-keep-ident` command, but without success.

If requested, I can give you the alignment file, the constrained tree, and all log files.

Any help is highly appreciated,

Cheers Bastian

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