ABySS-Explorer cannot find my adj file

Question

[ljw53]

I am running into the same error when I try to load an assembly: ERROR: Cannot find adjacency graph in <PATH>. However, the adj file is in every assembly directory that I am working with.

Here's an example of one of my assembly directories, k64:

coverage.hist   ecoil100x-1.adj   ecoil100x-1.fa   ecoil100x-2.adj  ecoil100x-2.fa  ecoil100x-3.adj  ecoil100x-3.fa  ecoil100x-bubbles  ecoil100x-indel  ecoil100x-unitigs  nohup.out

I believe that I have everything set up correctly. Could this error be due to the fact that my assembler is ABySS version 1.5.2 and I am using ABySS-Explorer 1.3.4? Is there a way to fix it?

Thank you very much,
Louisa

Answer 1

[Shaun Jackman]

Hi, Louisa. The default is to load the contigs adjacency file, ecoil100x-6.adj, but your assembly stopped at unitigs, ecoil100x-3.adj. To load the unitigs adjacency file:

1. Click the arrow to the right of "Stats/Plots" to display "Navigator"
2. Click the radio button "unitigs"
3. Click the button "Navigator" beside "Statistics" and "Plots"

Cheers,
Shaun