calculate ai output file empty

[mgarl-10]

Hello,

Thank you for such a nice program. I am preparing the input files and I tried to get the ai.out file from my blast searches and the groups.yaml, however the output file is empty. I get something like this:

query name donor ingroup AI HGTindex query hits number AHS outg_pct gene_1 :::: :::: 0.0 0 500 0 0 gene_2 :::: :::: 0.0 0 115 0 0 gene_3 :::: :::: 0.0 0 608 0 0 gene_4 :::: :::: 0.0 0 511 0 0 gene_5 :::: :::: 0.0 0 43 0 0

Do you know what might be wrong?

Thanks

[GDKO]

Hi @mgarl-10,

Can you attach the 2000 first lines of your blast file and the groups.yaml file here or send them to my email?

Cheers, Georgios

[mgarl-10]

Here they are:

groups.yaml.txt blast_similarity.txt

[GDKO]

You attached the output of calculate_ai.py instead of the output of blast :).

[mgarl-10]

My bad X) Here it is:

blast_similarity.txt

[GDKO]

I see no issues from my end. I run the command ~/software/AvP/aux_scripts/calculate_ai.py -i blast_similarity.txt -x groups.yaml.txt and I got the attached results blast_similarity_ai.txt

Do you get any errors when you run the script?

[mgarl-10]

Maybe there is something wrong with my installation but I did not get any errors.

[GDKO]

Can you test on the same test files you attached? Just in case there is an error with the full blast.

[mgarl-10]

Hello @GDKO I get a similar output as with the complete file.

[GDKO]

Before diving deeper, is it possible to test on a different environment or machine?

[mgarl-10]

It is working now! The taxadb had not been downloaded properly for some reason. Thank you @GDKO :)