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

18 views
Skip to first unread message

Angie Tovar

unread,
Jul 19, 2020, 7:39:32 PM7/19/20
to PartitionFinder
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

unread,
Jul 19, 2020, 7:50:10 PM7/19/20
to PartitionFinder
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

Reply all
Reply to author
Forward
0 new messages