PartitionFinder error in CIPRES: Exiting without processing (because of the -c/--check-only option ...

[Angie Tovar]

HI GUYS

I HAVE A PROBLEM IN CIPRES WHEN I RUN THE PARTITIONFINDER 2. I ATTACH MY CFG SCRIPT.

## ALIGNMENT FILE ##

alignment = CONCATENADO_GENESTOTALES_08_07_2020.phy;

## BRANCHLENGTHS: linked | unlinked ##

branchlengths = linked;

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

models = all;

# MODEL SELECCTION: AIC | AICc | BIC #

model_selection = aicc;

## DATA BLOCKS: see manual for how to define ##

[data_blocks]

12S = 1-731;

16S = 732-1268;

COI_pos1 = 1269-1843\3;

COI_pos2 = 1270-1843\3;

COI_pos3 = 1271-1843\3;

CYTB_pos1 = 1844-2508\3;

CYTB_pos2 = 1845-2508\3;

CYTB_pos3 = 1846-2508\3;

RAG1_pos1 = 2509-3075\3;

RAG1_pos2 = 2510-3075\3;

RAG1_pos3 = 2511-3075\3;

TYR_pos1 = 3076-3482\3;

TYR_pos2 = 3077-3482\3;

TYR_pos3 = 3078-3482\3;

## SCHEMES, search: all | user | greedy | rcluster | rclusterf | kmeans ##

[schemes]

search = greedy;

THE ERROR IN CIPRES :

THANKS 

[Rob Lanfear]

Hi There,

The cfg file is fine, so presumably this is an issue with CIPRES. However, without more details it's impossible to say. If you can post your command line, and the error you are getting, that would certainly help. It would also be worth contacting the CIPRES help.

Rob