Augustus output

Question

[kirillkirilenko]

I decided to annotate genome using AUGUSTUS. Previously I used AUGUSTUS web-interface, but it allow you to upload files less then 8 mb in size, so I installed AUGUSTUS via conda and ran this augustus --strand=both --species=aedes genome.fa. But it didn't create any output files, why? It returned stdout but it is not what I expected (.gff, .gtf or .bed). I can't find information in documentation about outfiles, any suggestions?

[Juke34]

Some hints how to use Augustus can be found here: https://github.com/NBISweden/workshop-genome_annotation_elixir/blob/master/labs/augustus.md

[lieven.sterck]

what kind of output did you then get?

[kirillkirilenko]

There was no files. stdout looked like :

....
# start gene g97
2R  AUGUSTUS    gene    752955  758230  0.1 -   .   g97
2R  AUGUSTUS    transcript  752955  758230  0.1 -   .   g97.t1
....
2R  AUGUSTUS    CDS 758157  758230  0.46    -   0   transcript_id "g97.t1"; gene_id "g97";
2R  AUGUSTUS    start_codon 758228  758230  .   -   0   transcript_id "g97.t1"; gene_id "g97";
# protein sequence = [MPQTRPWEVTSVAGKRYQCSHLSSHPYGEGVTASTLWLAGWLAVRFSGLCGVSVVAYNLDEHLFTESATLELLQIRWH
# PASPTDSHLLALLSDNSIRVYDVDSLRHVWRIGPTPTPQPVVIGSGSGVGGGCKHGPSASFVGSPGTAAASPGVTSKLAYLNSLGDTAVDFDIAPPRV
....

I can extract the data manually, but I don't understand why the output didn't split to separate files.

[lieven.sterck]

Augustus only outputs to STDOUT so you'll need to capture that to get a GFF file (what it writes to stdout is actually most gff like you can get from augustus.)

To get for instance fasta files from that you can run one of the auxiliary scripts that come with Augustus. (eg getAnnoFasta.pl)

[kirillkirilenko]

Ok, I didn't know it, thank you