Error: Could not find the dependency pandas
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Danon Cardoso
Apr 21, 2020, 9:39:14 PM4/21/20
to PartitionFinder
I have installed Anaconda 2.7 to run PF2, but I got de fooling error:
**** ERROR ****
Could not find the dependency pandas, please check that you have followed the installation instructions in the manual and try again.
PartitionFinder 2 (unlike PartitionFinder 1) requires a few other Python packages to work. All of these can be installed very easily, in a single click, by installing the Python 2.7.x version of the Anaconda Python distrubition, which you can find here (remember to get the 2.7 version!):
https://www.continuum.io/downloads
Further instructions are in the installation section of the manual, which points out a number of other differences between PartitionFinder 1 and PartitionFinder 2 too.
***************
Traceback (most recent call last):
File "/Applications/partitionfinder2/PartitionFinder.py", line 20, in <module>
from partfinder import dependencies
File "/Applications/partitionfinder2/partfinder/dependencies.py", line 43, in <module>
raise ImportError
ImportError
danonclemescardoso@MBP-de-Danon ~ %
I have also tried in another computer, and also on windows e regularly I am getting the same error.
I look in anaconda environment and pandas package is installed.
Someone can help?
Best,
Danon.
Danon Cardoso
Apr 21, 2020, 10:17:17 PM4/21/20
to PartitionFinder
I finally find-out how to solve the problem, I just write the entire directory of python2.7.
It start to run, but finish in error:
INFO | 2020-04-21 22:54:40,244 | config | Loading configuration at './partition_finder.cfg'
INFO | 2020-04-21 22:54:40,249 | config | Setting 'alignment' to 'test.phy'
INFO | 2020-04-21 22:54:40,249 | config | Setting 'branchlengths' to 'linked'
INFO | 2020-04-21 22:54:40,250 | parser | You set 'models' to: GTR, GTR+G, GTR+I+G
INFO | 2020-04-21 22:54:40,263 | model_load | This analysis will use the following 3 models of molecular evolution
INFO | 2020-04-21 22:54:40,263 | model_load | GTR, GTR+G, GTR+I+G
INFO | 2020-04-21 22:54:40,264 | config | Setting 'model_selection' to 'aicc'
INFO | 2020-04-21 22:54:40,268 | config | Setting 'search' to 'greedy'
INFO | 2020-04-21 22:54:40,268 | config | ------------------------ BEGINNING NEW RUN -------------------------------
INFO | 2020-04-21 22:54:40,269 | config | Looking for alignment file './test.phy'...
INFO | 2020-04-21 22:54:40,274 | threadpool | Using 12 cpus
INFO | 2020-04-21 22:54:40,274 | analysis | Beginning Analysis
INFO | 2020-04-21 22:54:40,288 | alignment | Reading alignment file './test.phy'
INFO | 2020-04-21 22:54:40,290 | analysis | Starting tree will be estimated from the data.
INFO | 2020-04-21 22:54:40,290 | raxml | Estimating Maximum Likelihood tree with RAxML fast experimental tree search for ./analysis/start_tree/filtered_source.phy
INFO | 2020-04-21 22:54:40,291 | raxml | Using a separate GTR+G model for each data block
ERROR | 2020-04-21 22:55:05,437 | main | A program that Partitionfinder uses failed. Output follows, in case it's helpful for finding the problem
ERROR | 2020-04-21 22:55:05,437 | main |
ERROR | 2020-04-21 22:55:05,437 | main |
INFO | 2020-04-21 22:55:32,443 | config | Loading configuration at './partition_finder.cfg'
INFO | 2020-04-21 22:55:32,447 | config | Setting 'alignment' to 'test.phy'
INFO | 2020-04-21 22:55:32,447 | config | Setting 'branchlengths' to 'linked'
INFO | 2020-04-21 22:55:32,447 | parser | You set 'models' to: GTR, GTR+G, GTR+I+G
INFO | 2020-04-21 22:55:32,457 | model_load | This analysis will use the following 3 models of molecular evolution
INFO | 2020-04-21 22:55:32,457 | model_load | GTR, GTR+G, GTR+I+G
INFO | 2020-04-21 22:55:32,457 | config | Setting 'model_selection' to 'aicc'
INFO | 2020-04-21 22:55:32,460 | config | Setting 'search' to 'greedy'
INFO | 2020-04-21 22:55:32,461 | config | ------------------------ BEGINNING NEW RUN -------------------------------
INFO | 2020-04-21 22:55:32,461 | config | Looking for alignment file './test.phy'...
INFO | 2020-04-21 22:55:32,464 | threadpool | Using 12 cpus
INFO | 2020-04-21 22:55:32,464 | analysis | Beginning Analysis
INFO | 2020-04-21 22:55:32,483 | alignment | Reading alignment file './test.phy'
INFO | 2020-04-21 22:55:32,484 | alignment | Reading alignment file './analysis/start_tree/source.phy'
INFO | 2020-04-21 22:55:32,485 | analysis | Starting tree will be estimated from the data.
INFO | 2020-04-21 22:55:32,486 | raxml | Estimating Maximum Likelihood tree with RAxML fast experimental tree search for ./analysis/start_tree/filtered_source.phy
INFO | 2020-04-21 22:55:32,486 | raxml | Using a separate GTR+G model for each data block
ERROR | 2020-04-21 22:55:32,487 | util | No such file: '/Applications/partitionfinder2/programs/raxml_pthreads'
ERROR | 2020-04-21 22:55:32,488 | main | Failed to run. See previous errors.
INFO | 2020-04-21 22:58:31,336 | config | Loading configuration at './partition_finder.cfg'
INFO | 2020-04-21 22:58:31,339 | config | Setting 'alignment' to 'test.phy'
INFO | 2020-04-21 22:58:31,339 | config | Setting 'branchlengths' to 'linked'
INFO | 2020-04-21 22:58:31,340 | parser | You set 'models' to: GTR, GTR+G, GTR+I+G
INFO | 2020-04-21 22:58:31,349 | model_load | This analysis will use the following 3 models of molecular evolution
INFO | 2020-04-21 22:58:31,349 | model_load | GTR, GTR+G, GTR+I+G
INFO | 2020-04-21 22:58:31,349 | config | Setting 'model_selection' to 'aicc'
INFO | 2020-04-21 22:58:31,353 | config | Setting 'search' to 'greedy'
INFO | 2020-04-21 22:58:31,353 | config | ------------------------ BEGINNING NEW RUN -------------------------------
INFO | 2020-04-21 22:58:31,353 | config | Looking for alignment file './test.phy'...
INFO | 2020-04-21 22:58:31,357 | threadpool | Using 12 cpus
INFO | 2020-04-21 22:58:31,357 | analysis | Beginning Analysis
INFO | 2020-04-21 22:58:31,376 | alignment | Reading alignment file './test.phy'
INFO | 2020-04-21 22:58:31,376 | alignment | Reading alignment file './analysis/start_tree/source.phy'
INFO | 2020-04-21 22:58:31,378 | analysis | Starting tree will be estimated from the data.
INFO | 2020-04-21 22:58:31,379 | raxml | Estimating Maximum Likelihood tree with RAxML fast experimental tree search for ./analysis/start_tree/filtered_source.phy
INFO | 2020-04-21 22:58:31,379 | raxml | Using a separate GTR+G model for each data block
ERROR | 2020-04-21 22:58:31,379 | util | No such file: '/Applications/partitionfinder2/programs/raxml_pthreads'
ERROR | 2020-04-21 22:58:31,380 | main | Failed to run. See previous errors.
-----
Best,
Danon
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