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ABySS-Explorer cannot find my adj file

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

abyss assembly
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updated by Ram Ram • written by ljw53 • ljw53

1 answer

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

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updated by Ram Ram • written by Shaun Jackman Shaun Jackman

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