Version 1.5.5: Variant sites file not produced

[Angela McGaughran]

Hi,

I'm trying to run iq-tree (version 1.5.5) on a SNP dataset using the following code:

iqtree-omp -s input.fasta -m MFP+ASC -bb 10000 -nt AUTO -st DNA

The program initially warns that it detects a different sequence type than that specified (it thinks I'm using proteins due to ambiguity codes), but I think it is safe to ignore this as I am using -st DNA?

However, the model selection does not take place, with the output "Skipped since +ASC is not applicable".

I understand that this is due to the fact that I have constant sites in the alignment, and I was expecting a .varsites file to be produced as per p121 of the manual.  However, no such file is produced and I cannot proceed.

I attach an example input file and the output log files to this post.

Thanks in advance,

Angela

[Bui Quang Minh]

Hi Angela,

On Aug 23, 2017, at 6:48 AM, Angela McGaughran <ang.mcg...@gmail.com> wrote:

Hi,

I'm trying to run iq-tree (version 1.5.5) on a SNP dataset using the following code:

iqtree-omp -s input.fasta -m MFP+ASC -bb 10000 -nt AUTO -st DNA

The program initially warns that it detects a different sequence type than that specified (it thinks I'm using proteins due to ambiguity codes), but I think it is safe to ignore this as I am using -st DNA?

You are right - you can ignore this warning because IQ-TREE mis-detected the data type due to many ambiguity code.

However, the model selection does not take place, with the output "Skipped since +ASC is not applicable".

I understand that this is due to the fact that I have constant sites in the alignment, and I was expecting a .varsites file to be produced as per p121 of the manual.  However, no such file is produced and I cannot proceed.

I attach an example input file and the output log files to this post.

Please do -m GTR+ASC instead of -m MFP+ASC. It should then produce a .varsites.phy file and an error message like:

For your convenience alignment with variable sites printed to example.phy.varsites.phy

ERROR: Invalid use of +ASC because of 686 invariant sites in the alignment

The bottom line is that ModelFinder does not write this file, but giving a specific model name like GTR will do. We will change the behavior in later version.

Thanks, Minh

Thanks in advance,

Angela

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<2015-10-01_quail_lib.new.gvcf.filtered.snps.xmdp10.mmc7.mac3.Z.thin200000.recode.vcf.fasta><Zonly_thinned.log><Zonly_thinned.ckp.gz>

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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

[Angela McGaughran]

Thanks so much, that worked fine!

All the best,

Angela