IQtree 1.7.b9, MF+MERGE with -p creates best_scheme.nex file with __NA__

[Mese]

Dear Minh,

I have been playing around with IQtree 1.7.b9 (unix version on a Rocks cluster) and really like the -p option where a directory with individual alignment files can be specified, instead of a concatenated alignment. Model selection and likelihood searches have been running fine. Then I tried using MF+MERGE as shown below either for nucleotides or amino acids. This finished without any error message, but the resulting best_scheme.nex file in both cases contains __NA__ instead of pointing to the filenames of the loci in the partition, and the corresponding best_scheme file just has a row of commas with spaces in between. The file name only appears for partitions consisting of a single locus, as also shown in the example below. Would it be possible to fix this, or should I rather use -s and a concatenated file when using +MERGE?

./iqtree_17b9 -p ../NT_CODON_3 -m MF+MERGE -rclusterf 10 -rcluster-max 10000 -cmax 4  -pre NTC3 -nt 10

./iqtree_17b9 -p ../AA -m MF+MERGE -rclusterf 10 -rcluster-max 10000 -cmax 4 -mset BLOSUM62,Dayhoff,DCMut,JTT,JTTDCMut,LG,WAG -madd LG4M,LG4X -pre AA -nt 10

First few partitions in best_scheme.nex:

#nexus

begin sets;

  charset DPOGS200021_PA_5_7_mafft.trimmed.ALICUT_codon_3rd.fas_DPOGS205054_PA_3_5_mafft.trimmed.ALICUT_codon_3rd.fas_DPOGS209799_PA_17_29_mafft.trimmed.ALICUT_codon_3rd.fas_DPOGS209930_PA_3_11_mafft.trimmed.ALICUT_codon_3rd.fas_DPOGS211783_PA_10_45_mafft.trimmed.ALICUT_codon_3rd.fas_DPOGS212039_PA_2_2_mafft.trimmed.ALICUT_codon_3rd.fas_DPOGS214262_PA_4_4_mafft.trimmed.ALICUT_codon_3rd.fas_DPOGS215600_PA_1_9_mafft.trimmed.ALICUT_codon_3rd.fas = __NA__:               ;

charset DPOGS208056_PA_3_3_mafft.trimmed.ALICUT_codon_3rd.fas_DPOGS211134_PA_3_4_mafft.trimmed.ALICUT_codon_3rd.fas_DPOGS213170_PA_3_3_mafft.trimmed.ALICUT_codon_3rd.fas_DPOGS213297_PA_14_15_mafft.trimmed.ALICUT_codon_3rd.fas_DPOGS213796_PA_3_14_mafft.trimmed.ALICUT_codon_3rd.fas_DPOGS214696_PA_12_14_mafft.trimmed.ALICUT_codon_3rd.fas_DPOGS216067_PA_3_3_mafft.trimmed.ALICUT_codon_3rd.fas = __NA__:             ;

  charset DPOGS208823_PA_24_35_mafft.trimmed.ALICUT_codon_3rd.fas = ../NT_CODON_3/DPOGS208823_PA_24_35_mafft.trimmed.ALICUT_codon_3rd.fas: ;

  charset DPOGS209957_PA_2_2_mafft.trimmed.ALICUT_codon_3rd.fas_DPOGS211215_PA_3_5_mafft.trimmed.ALICUT_codon_3rd.fas_DPOGS214287_PA_6_18_mafft.trimmed.ALICUT_codon_3rd.fas = __NA__:     ;

 

Best wishes,

Marianne

[Minh Bui]

Hi Marianne,

This is because when merging two partitions, each is an alignment file in your case, the merged file name does not exist. That’s why IQ-TREE writes __NA__. We don’t have a solution for this yet, so you can’t use the best_scheme output file right now. if you want to use this best_scheme file, then do the option you suggested, i.e., using the concatenated alignment file. IQ-TREE can help you generate such a file, let me know if you need...

Cheers,

Minh

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[Minh Bui]

Hi Marianne,

There is now a new option --out-alignment in the latest beta11 version: 

https://github.com/Cibiv/IQ-TREE/releases/tag/v1.7-beta11

iqtree -p ALN_DIR --out-alignment CONCAT

will print two files: the concatenated alignment (CONCAT) and partition file (CONCAT.nex) for all alignments in the directory.

Cheers,

Minh

On 26 Apr 2019, at 5:19 pm, Marianne Espeland <marianne...@gmail.com> wrote:

Thanks, Minh. 

I have a python script for generating concatenated files and the partition file, but would still be interested in learning how to do this in IQ-tree.  Couldn't find any documentation on this, so it would be great if you could show me how this is done. I, however, very much like the possibility of giving a directory with individual alignments as input, since by not concatenating there is one less step to do, and thus one less step that can go wrong... 

Best wishes,

Marianne

______________________________

 

Marianne Espeland, PhD

Curator, Head of Lepidoptera Section

Zoological Research Museum Alexander Koenig

Adenauer Allee 160

53113 Bonn

Germany

email: marianne...@gmail.com

or m.esp...@leibniz-zfmk.de

phone: +49 228 9122-220