error1: attempt to add partition...when that name already exists; error2: Failed to run models...not sure why

[bela arora]

Hi everyone,

Anyone came across these two errors yet ?

error1: attempt to add partition...when that name already exists; (PF version 1)

error2: Failed to run models...not sure why (PF version 2)

INFO     | 2022-04-13 14:11:08,700 | ------------- Configuring Parameters -------------
INFO     | 2022-04-13 14:11:08,701 | Setting datatype to 'DNA'
INFO     | 2022-04-13 14:11:08,703 | Setting phylogeny program to 'phyml'
INFO     | 2022-04-13 14:11:08,703 | Program path is here C:\Users\frp726\OneDrive - K°benhavns Universitet\CMEC\PhD\PhD chapters\chapters\chapter 1\R\tree stuff\PartitionFinderV1.1.1_Windows\programs
INFO     | 2022-04-13 14:11:08,703 | Setting rcluster-percent to 10.00
INFO     | 2022-04-13 14:11:08,704 | Setting working folder to: 'C:\Users\frp726\OneDrive - K°benhavns Universitet\CMEC\PhD\PhD chapters\chapters\chapter 1\R\tree stuff\PartitionFinderV1.1.1_Windows\CMEC genera\luscinia'
INFO     | 2022-04-13 14:11:08,706 | Loading configuration at '.\partition_finder.cfg'
INFO     | 2022-04-13 14:11:08,716 | Setting 'alignment' to 'luscinia.phy'
INFO     | 2022-04-13 14:11:08,716 | Setting 'branchlengths' to 'linked'
INFO     | 2022-04-13 14:11:08,717 | Setting 'models' to 'all'
INFO     | 2022-04-13 14:11:08,719 | The models included in this analysis are: K81+I, GTR+I, F81+I+G, GTR+G, TrN+G, F81, K81+G, F81+G, TIM, TIM+I+G, TVM+G, JC+I+G, TVMef+G, TVMef+I, TVM+I, TrNef+I, F81+I, JC, TIMef+G, HKY, K81uf+I, TVMef, K81uf+G, K81+I+G, TIMef+I, TVM, SYM+I, K81uf, JC+I, K80, K81, K80+I+G, K80+I, SYM+G, K81uf+I+G, K80+G, TrN+I, GTR+I+G, GTR, TIM+G, HKY+I+G, TIMef, TIM+I, TVMef+I+G, TVM+I+G, HKY+G, SYM+I+G, TrN, HKY+I, SYM, TIMef+I+G, JC+G, TrNef, TrNef+G, TrNef+I+G, TrN+I+G
INFO     | 2022-04-13 14:11:08,720 | Setting datatype to 'DNA'
INFO     | 2022-04-13 14:11:08,724 | Setting 'model_selection' to 'bic'
ERROR    | 2022-04-13 14:11:08,730 | Attempt to add Partition(ldh, 2536-3244\3) when that name already exists
ERROR    | 2022-04-13 14:11:08,732 | Error in 'ldh' can be found at line:26, column:9
ERROR    | 2022-04-13 14:11:08,733 | Failed to run. See previous errors.

Why is it making that attempt to begin with?

My cfg file is - 

## ALIGNMENT FILE ##
alignment = luscinia.phy;

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

## MODELS OF EVOLUTION for PartitionFinder: all | raxml | mrbayes | beast | <list> ##
##              for PartitionFinderProtein: all_protein | <list> ##
models = all;

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

## DATA BLOCKS: see manual for how to define ##
[data_blocks]
    cytb_1st = 1-1088\3;
    cytb_2nd = 2-1088\3;
    cytb_3rd = 3-1088\3;
    odc_1st = 1089-1906\3;
    odc_2nd = 1090-1906\3;
    odc_3rd = 1091-1906\3;
    myo_1st = 1907-2534\3;
    myo_2nd = 1908-2534\3;
    myo_3rd = 1909-2534\3;
    ldh = 2535-3244\3;
    ldh = 2536-3244\3;
    ldh = 2537-3244\3;
   
## SCHEMES, search: all | greedy | rcluster | hcluster | user ##
[schemes]
search = greedy;

#user schemes go here if search=user. See manual for how to define.#

After updating Partition Finder to version 2, the same files give the following error - 

INFO     | 2022-04-13 14:12:50,539 | ------------- PartitionFinder 2.1.1 -----------------
INFO     | 2022-04-13 14:12:50,540 | You have Python version 2.7
INFO     | 2022-04-13 14:12:50,540 | Command-line arguments used: C:\Users\frp726\OneDrive - K°benhavns Universitet\CMEC\PhD\PhD chapters\chapters\chapter 1\R\tree stuff\PartitionFinderV1.1.1_Windows\partitionfinder-2.1.1\partitionfinder-2.1.1\PartitionFinder.py C:\Users\frp726\OneDrive - K°benhavns Universitet\CMEC\PhD\PhD chapters\chapters\chapter 1\R\tree stuff\PartitionFinderV1.1.1_Windows\partitionfinder-2.1.1\partitionfinder-2.1.1\CMEC genera\luscinia\partition_finder.cfg
INFO     | 2022-04-13 14:12:50,540 | ------------- Configuring Parameters -------------
INFO     | 2022-04-13 14:12:50,542 | Setting datatype to 'DNA'
INFO     | 2022-04-13 14:12:50,542 | Setting phylogeny program to 'phyml'
INFO     | 2022-04-13 14:12:50,542 | Program path is here C:\Users\frp726\OneDrive - K°benhavns Universitet\CMEC\PhD\PhD chapters\chapters\chapter 1\R\tree stuff\PartitionFinderV1.1.1_Windows\partitionfinder-2.1.1\partitionfinder-2.1.1\programs
INFO     | 2022-04-13 14:12:50,543 | Setting working folder to: 'C:\Users\frp726\OneDrive - K°benhavns Universitet\CMEC\PhD\PhD chapters\chapters\chapter 1\R\tree stuff\PartitionFinderV1.1.1_Windows\partitionfinder-2.1.1\partitionfinder-2.1.1\CMEC genera\luscinia'
INFO     | 2022-04-13 14:12:50,545 | Loading configuration at '.\partition_finder.cfg'
INFO     | 2022-04-13 14:12:50,551 | Setting 'alignment' to 'luscinia.phy'
INFO     | 2022-04-13 14:12:50,552 | Setting 'branchlengths' to 'linked'
INFO     | 2022-04-13 14:12:50,552 | You set 'models' to: all
INFO     | 2022-04-13 14:12:50,569 | This analysis will use the following 56 models of molecular evolution
INFO     | 2022-04-13 14:12:50,569 | JC, K80, TRNEF, K81, TVMEF, TIMEF, SYM, F81, HKY, TRN, K81UF, TVM, TIM, GTR, JC+G, K80+G, TRNEF+G, K81+G, TVMEF+G, TIMEF+G, SYM+G, F81+G, HKY+G, TRN+G, K81UF+G, TVM+G, TIM+G, GTR+G, JC+I, K80+I, TRNEF+I, K81+I, TVMEF+I, TIMEF+I, SYM+I, F81+I, HKY+I, TRN+I, K81UF+I, TVM+I, TIM+I, GTR+I, JC+I+G, K80+I+G, TRNEF+I+G, K81+I+G, TVMEF+I+G, TIMEF+I+G, SYM+I+G, F81+I+G, HKY+I+G, TRN+I+G, K81UF+I+G, TVM+I+G, TIM+I+G, GTR+I+G
INFO     | 2022-04-13 14:12:50,569 | Setting 'model_selection' to 'bic'
INFO     | 2022-04-13 14:12:50,575 | Setting 'search' to 'greedy'
INFO     | 2022-04-13 14:12:50,575 | ------------------------ BEGINNING NEW RUN -------------------------------
INFO     | 2022-04-13 14:12:50,578 | Looking for alignment file '.\luscinia.phy'...
INFO     | 2022-04-13 14:12:50,579 | Using 8 cpus
INFO     | 2022-04-13 14:12:50,581 | Beginning Analysis
INFO     | 2022-04-13 14:12:50,618 | Reading alignment file '.\luscinia.phy'
INFO     | 2022-04-13 14:12:50,635 | Reading alignment file '.\analysis\start_tree\source.phy'
INFO     | 2022-04-13 14:12:50,664 | Starting tree file found.
INFO     | 2022-04-13 14:12:50,665 | Performing Greedy Analysis
INFO     | 2022-04-13 14:12:50,667 |    *** Analysing starting scheme ***
ERROR    | 2022-04-13 14:18:14,216 |       Failed to run models K81+I, GTR+I, F81+I+G, K81UF+I+G, GTR+G, F81, K81+G, F81+G, TIM, TIM+I+G, TVM+G, JC+I+G, TVMEF, TRNEF, TVM+I, TRNEF+I+G, F81+I, JC, TIMEF+G, HKY, TRN+I+G, K81+I+G, TIMEF+I, TVMEF+I+G, TVM, TRN+G, K80, K81, SYM+I+G, K80+I, HKY+I+G, SYM+G, TRN, SYM+I, K80+G, GTR, TIM+G, TVMEF+G, TVMEF+I, TIMEF, TIM+I, K80+I+G, TVM+I+G, HKY+G, K81UF+I, K81UF+G, HKY+I, SYM, TIMEF+I+G, TRN+I, K81UF, TRNEF+G, JC+G, GTR+I+G, JC+I, TRNEF+I; not sure why
ERROR    | 2022-04-13 14:18:14,220 | Failed to run. See previous errors.

How did you fix it?

Looking forward to a solution.

Cheers,

Bela

[Rob Lanfear]

Hi Bela,

This is happening because you have three partitions with the same name 'ldh'.

All you need to do is change them to somethign like:

ldh_1stpos

ldh_2ndpos

ldh_3rdpos

Any names will work, as long as they're all different.

Rob