BUG: iqtree 1.7-beta7 Concordance Factors - Assertion `!aln->ordered_pattern.empty()' failed

[Bradley Martin]

Hello,

I am trying to use the new concordance factor feature in iqtree 1.7-beta7. I am using Linux (CentOS 6.10).

When I try to run the analysis, it throws errors when creating "initial parsimony tree by phylogenetic likelihood library (PLL)".

ERROR: phylotreepars.cpp:63: void PhyloTree::computePartialParsimonyFast(PhyloNeighbor *, PhyloNode *): Assertion `!aln->ordered_pattern.empty()' 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: concat.log
ERROR: ***    Alignment files (if possible)

I have tried using a directory of NEXUS files as input, and I have also tried with a concatenated NEXUS file with NEXUS CHARSET partitions specified as the partitions file. Both give the same errors.I have also tried withboth UFBoot and standard non-parametric bootstraps.

Here are the commands I have tried to run the analysis with:

iqtree_beta77 -s $ALN_FILE -p $ALN_FILE --prefix concat -bb 1000 -nt 32

iqtree_beta77  -p $ALN_DIR --prefix concat -bb 1000 -nt 32

iqtree_beta77 -s $ALN_FILE -p $ALN_FILE --prefix concat -b 100 -nt 32

iqtree_beta77 -s $ALN_FILE -p $ALN_FILE --prefix concat -B 1000 -nt 32

I have attached a file with all WARNINGS and ERRORS from the log file.

Could you please look into this?

Thank you for your time.

-Bradley Martin

[Bradley Martin]

Looks like the problem is fixed with version 1.7-beta8. Just saw that you pushed the new beta earlier today. Ran it with the new version and it got past the point where v. 1.7-beta7 would throw errrors.

Sorry about that.

[Minh Bui]

Hi Bradley,

No worries, good that you realised the new version which just fixed this issue.

Moreover, I’m not sure if this is a bug or a feature. The assertion occurs when there is at least one gene with no variant sites, i.e. all sequences within this gene are identical, which is even less than parsimony-informative. So this gene tree will be essentially “random” and will reduce the concordance factor. One can either be happy with that or can remove such genes from the analysis. In the beta8 version IQ-TREE will print a warning:

WARNING: No variant sites in partition ...

So that you know what to remove in the latter case.

Cheers

Minh

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[Bradley Martin]

Hello,

Thank you for your insight and prompt reply. I will probably filter out the non-informative loci.

I did encounter another error that occurred during model selection and that I want to ask you about:

7995 JC           269.016     BOX_6219  0h:41m:14s (0h:27m:6s left)
7996 F81+F+I      281.284     BOX_12239 0h:41m:15s (0h:27m:6s left)
7997 K2P+R2       565.220     BOX_6888  0h:41m:15s (0h:27m:5s left)
7998 K3P+R2       415.668     BOX_9997  0h:41m:15s (0h:27m:5s left)
ERROR: modelmarkov.cpp:1246: virtual void ModelMarkov::decomposeRateMatrix(): Assertion `(Q - Q.transpose()).cwiseAbs().maxCoeff() < 1e-4 && "transformed Q is symmetric"' failed.

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

(END)

In addition, there were multiple warnings that said: WARNING: ABNORMAL_TERMINATION_IN_LNSRCH

I have attached another .txt file with all the warnings.

Sorry to bother you again about this, but I wanted to ask you about it in case it might be something that can be fixed in the code.

It might also be because I had a bunch of invariant and non-informative loci, so I will try pre-filtering those and re-running model selection in the meantime.