error to protein models

[Andrea Nino]

Dear Robert,

Im trying run partitonFinder2 to aminoacides to evolutionary models in BEAST as my cfg file: 

## ALIGNMENT FILE ##
alignment = MSA4-cox-def.phy;

## BRANCHLENGTHS: linked | unlinked ##
branchlengths = linked;

## MODELS OF EVOLUTION: all | allx | mrbayes | beast | gamma | gammai | <list> ##
models = beast;

# MODEL SELECCTION: AIC | AICc | BIC #
model_selection = aic;

## DATA BLOCKS: see manual for how to define ##
[data_blocks]
Gene1 = 1-224;
Gene2 = 225-278;
Gene3 = 279-792;
Gene4 = 793-1020;

## SCHEMES, search: all | user | greedy | rcluster | rclusterf | kmeans ##
[schemes]
search = greedy;

**But the error is that partitionfinder identified my sequences as nucleotids.

INFO     | 2024-12-09 14:01:34,458 | ------------------------ BEGINNING NEW RUN -------------------------------...
INFO     | 2024-12-09 14:01:34,569 | Estimating Maximum Likelihood tree with RAxML fast experimental tree search for ./analysis/start_tree/filtered_source.phy
INFO     | 2024-12-09 14:01:34,570 | Using a separate GTR+G model for each data block
ERROR    | 2024-12-09 14:01:34,589 | Warning, you specified a working directory via "-w" Keep in mind that RAxML only accepts absolute path names, not relative ones! ERROR: Bad base (L) at site 5 of sequence 1 Printing error context: gulifera MMTNLFSTFDPSTNFNLPLNWMSTL Problem reading alignment file

**Bad base (L) at site 5 of sequence is in fact L aminoacide 

I tryed use  ## SPECIFYING THE DATA TYPE ## datatype = protein;  

but it say also error.

Thank you for the advises

Best regards,

Andres