Buffer limit issue with evolrates.run: "NOTE: wrapped lines before wrapping buffer contents!" corrupting Newick exports

[Alejandro Otero]

Hi everyone,

I am running the evolrates.run script (Pol & Ezcurra, 2025) to estimate evolutionary rates on a large dataset (90 x 423 chs). The script worked perfectly for my first attempt, but I am hitting a persistent buffer/word-wrap error when trying to process.

Because the script injects rate metadata into every node and branch (e.g., [max_branch_rate=...,avg_branch_rate=...]), the resulting Newick strings for my EW trees seems to be extremely long.

When the script attempts to export these trees using the quote command, TNT seems to hit a hard-coded horizontal character limit. It breaks the line and dumps its internal command logs directly into my output text files (_trees_for_R.txt).

The Newick format gets interrupted by lines like this:

COMMAND: LOG

COMMAND: LQUOTE

COMMAND: LQUOTE
NOTE: wrapped lines before wrapping buffer contents!

COMMAND: QUOTE

COMMAND: QUOTE
NOTE: wrapped lines before wrapping buffer contents!
(
COMMAND: LQUOTE

COMMAND: LQUOTE
NOTE: wrapped lines before wrapping buffer contents!

This corruption prevents R (ape package) from reading the tree files later. I know lquote is supposed to prevent this, and the script does use lquote=; and lquote-; correctly.

Here is what I have already tried to fix it natively in TNT:

1. Increased the script's internal macro memory limits to macro *2000 50000000;.

2. Expanded the text size using txtsize 150000; before running the script (it worked once, but not subsequently).

3. Completely avoided the GUI (wtnt.exe) and ran the analysis from a clean slate in the Windows command prompt (tnt.exe) to prevent visual console wrapping.

Despite all this, the string still forces a wrap and crashes the output format. (I am currently using a post-processing R script to delete the TNT error lines and stitch the Newick strings back together, which works, but I would love to solve the root cause). So, basically, the information is in the txt file but hidden.

so... Is there a hard-coded maximum line length for the quote buffer in TNT that overrides lquote? If so, is there a native TNT command or workaround to completely suppress this word-wrapping panic when exporting massive single-line strings?

Thank you in advance for any insights!

Ale.-

[Edward SIddall]

This needs escalation to Pablo

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[Alejandro Otero]

Hi everyone,

regarding the evolrates script output problem, I got the solution from PAG (thanks Pablo!).

The problem was caused by the ECHO command. I did run the script with the activated ECHO command, which causes the output masking, both in tnt console as well as in the output file (the same happens with other scripts).

So, it is recommended to deactivate the ECHO command before running any script.

IMPORTANT: if you run the script with the ECHO activated, the script runs anyway and the output information IS in the file, but masked. You can un-mask the info a posteriori with any custom R script, but it implies an extra step.

Alejandro.-