cannot import a large tree into TNT

[Satoshi Aoki]

Hello,

I am having trouble importing a tree into TNT, even after reducing all taxon names to short unique IDs.

Environment:

* TNT version: 1.6 for Linux
* OS: Ubuntu 24.04 on wsl2 in Windows11

I prepared two files:

* `tnt_ready_short.tnt`
* `fixedTree_short.tre`
Stored at https://drive.google.com/drive/folders/16s3cvlW8v_FnneC9I7u2a330UhCjU5-F?usp=drive_link

These files appear to match exactly:

* number of taxa in the TNT matrix: 31749
* number of tips in the tree: 31749
* taxon names are short unique IDs (`T00001` ... `T31749`)
* no obvious problematic symbols remain in tip names

Commands used:
mxram 4000;
proc tnt_ready_short.tnt;
taxname = ;
shortread fixedTree_short.tre;

Result:
Tree file fixedTree_short.tre is not for 31749 taxa

I also tried:
tread fixedTree_short.tre;
Result:
Unidentified taxon name: fixedTree_short.tre

And:
tread "fixedTree_short.tre";
Result:
Taxon -1 repeated

Earlier I also tested:

* replacing long names with short IDs
* rewriting the tree file in wrapped form

But the same error persists.

At this point I suspect either:

1. a specific formatting requirement of TNT tree import that I am missing, or
2. a bug / limitation in `shortread` for this case.

Could you please advise what exact tree format `shortread` expects here, and whether there is a recommended way to import a matching Newick/Hennig86-style tree from file?

Thank you.

Best regards,
Satoshi Aoki

[Santiago Catalano]

Hi Satoshi, 

The tree file was in the wrong format. Please find the corrected file attached. In addition, be sure that you are working with a TNT version that can handle large datasets (mac version, cywin version, windows version with no taxon limit ).

bests,

Santi

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Dr. Santiago A. Catalano

Investigador Independiente CONICET

Unidad Ejecutora Lillo (UEL FML-CONICET)

FCNeIML-UNT

SM Tucumán - Tucumán
Argentina

[Satoshi Aoki]

Thank you Martin. Referencing your file, I removed apostrophes in taxon names in the tnt file, conbined the tnt file and tree file into one, and proc the combined file. Then, I could successfully import the tree!

Best,

Satoshi Aoki

2026年3月17日火曜日 20:49:40 UTC+9 santiago: