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Rinoahu / SwiftOrtho

A high performance tool to identify orthologs and paralogs across genomes.
GNU General Public License v3.0
27 stars 11 forks source link

Not getting results #4

Closed ESDeutekom closed 4 years ago

ESDeutekom commented 4 years ago

Hi,

I am really curious to use SwiftOrtho and tried it on a small subset of my own species vs. species files. However, I am not getting any results and I cannot seem to find the cause. The test ran successfully btw.

So my input file looks like a standard m8 tabular output with the 11th column containing the e-value and 12th bit score:

107_0 10_9279 23.313 163 80 10 90 225 172 316 7.51e-04 40.8 107_0 10_9279 25.926 135 68 8 74 193 199 316 0.002 39.7

Although I have no two last columns with sequences lengths.

I used example code: python ~/eva2/Programs/SwiftOrtho/bin/find_orth.py -i Downloads/bigBlast -c 0.5 -y 0 > blast.orth

But all the output files are empty. So is it even possible to use my own blast outputs? And is that the reason it is going wrong, or something else? Kind regards, Eva

ESDeutekom commented 4 years ago

PS: sorry, I forgot to say that my file now looks like (I substituted the underscores with pipes):

107|2 100|6827 30.769 52 33 2 11 62 350 398 1.7 25.4 107|2 100|16251 25.862 58 28 1 22 64 588 645 1.7 25.4 107|2 100|11834 25.862 58 28 1 22 64 611 668 1.7 25.4