Missing component to detect ORFs?

[piosierra]

Hello,

I am running TE-Aid with the default options, but it doesn't seem to find any ORF in any of my consensus sequences. On the exit I see these messages (indented by me). Do they mean that I am missing some requirement? I have (to the best of my knowledge) emboss installed. Is there a particular component I might be missing?

Thanks.

TE -> genome blastn e-value:   10e-8
full length min ratio:         0.9
hits transparency:             0.3
full length hits transparency: 0.9
        grep: plots/TE.orfs: No such file or directory
        no ORF detected, skipping blastp...
[1] "R: ploting genome blastn results and computing coverage..."
[1] "consensus length:  7271 bp"
[1] "R: ploting self dot-plot and orf/protein hits..."
        [1] "no orf to plot..."
        Warning message:
        In file(file, "rt") :
            cannot open file 'plots/orftetable': No such file or directory
null device 
          1 
Done! The graph (.pdf) can be found in the output folder: plots

[clemgoub]

Hello @piosierra !

From your output message it looks like it did not find ORF (default is >= 300bp (100AA)). If emboss was missing or not accessible, I think you would have a specific error message. You can lower the ORF size for detection with -m (in bp).

Alternatively, you can check your sequences with ORF finder. If you find ORFs not found by TE-Aid, let me know, I will look into it!

Cheers,

Clément

[piosierra]

Hello Cément,

I did some debugging and the problem was in the wrapper script I used to batch call TE-Aid on the HPC. Due to it the call to getorf was not working as expected, and no result was produced. I modified it and now it is working properly.

Thanks a lot for your support and the tool.

[clemgoub]

No problem! Glad you found a solution!

Cheers,

Clément