6/6] Parsing PAML results and building tree for substitutions. ERROR: java.lang.NullPointerException

[Steven-Kemp]

Hi Asif and Ziheng,

I've been trying unsuccessfully to get this to run on either Linux (Ubuntu 1804 LTS) or MacOS catalina (10.15.1).

Seems that even with the example alignment in the treesub example folder, I keep getting the error at the last step:

6/6] Parsing PAML results and building tree for substitutions. ERROR: java.lang.NullPointerException

I can't figure out why. I've installed all dependencies, PAML seems to be running successfully, but it cannot parse the PAML results for some reason. Any advice at all please?

Thanks!

[virologist]

Dear ALL, I met the same error as well.

Successfully ran RAxML.

[4/6] Rooting tree by outgroup sequence.
Successfully rooted the tree.

[5/6] Running PAML application. Output from PAML:
BASEML in paml version 4.9j, October 2019
ns = 1514  	ls = 1693

**Error: option C?**.

Successfully ran PAML.

[6/6] Parsing PAML results and building tree for substitutions.
ERROR: java.lang.NullPointerException

Is there anyone have any clue about this?

Solved: https://github.com/tamuri/treesub/issues/10 The problem is ls = 1693. 1693/3=564.3333333..... Just trim your sequences so that it's an integer multiple of 3.