ks result is empty

[ardy20]

Hello I prepared the total.conf as follows but the result is empty. Could you please guide?

[ks] cds_file = /scratch/project_mnt/S0030/wgdi/male-female/male.cds.fa pep_file = /scratch/project_mnt/S0030/wgdi/male-female/male.pep.fa align software = muscle pairs_file = /scratch/project_mnt/S0030/wgdi/male-female/collinearity_file ks_file = ks_result

the collinerarity file is from Improved collinearity step.

Also how to prepare files for two species?

[ardy20]

Header of collinearity file:

[SunPengChuan]

If two or more different species, cat them to one file. If the ks result is empty, delete it and run again.

[ardy20]

I run the Ks analysis several times but it is still empty. It only shows one line of Wgdi -ks analysis (its header). My conda environment uses python 11. Could this be a conda python issue?

[SunPengChuan]

Delete the file named 'pep' in this directory

[ardy20]

Hi I think I found the error. In ks documentation, in total.config file there is a missing underline, in which align software should be converted to align_software

I mean: align software > align_software