Mario Stanke

In newer versions by default and in any case when `--softmasking=1` is specified, AUGUSTUS treats each masked region as a little more likely to be not in an exon. Predicted...

In the current code we have the default ```genbank.hh:#define GBMAXLINELEN 40000``` If a single line in a Genbank file has more characters than that then you must use line breaks....

Please double check whether none of the lines is longer that the maximum. If so increase the max or simply introduce line breaks in the file. Usually GenBank files have...

The error message that included the maximal line length was also shown when the (implicit) maximal input file size was exceeded. This was about 2.1 Gb on many machines. I...

Apparently this is not completely solved, at least when predictions are requested on the complete chromosome in one run (rather than using `--predictionStart` and `--predictionEnd`) ``` $AUGUSTUS --species=rice --softmasking=0 --protein=on...

Yes. As the coordinates will be different, you have to use alignments. If the strains are very close, I suggest a nucleotide alignment:, a spliced alignment of the reference mRNAs...

The combination of singlestrand and intronless is not implemented. I recommend to not use the singlestrand in this case and rather ignore the predicted genes on the other strand.

Thanks for asking. I have no such plan.

What you are looking for is called *functional* annotation. This is usually done after *structural* annotation (finding genes and their coordinates and protein sequences) and independently of it. Many perform...

This appears to be an error in AUGUSTUS. If you could upload the input files to the command that crashes: /app/redhat6/augustus/augustus-20220316/bin/etraining --species=Sp_1 --AUGUSTUS_CONFIG_PATH=/app/redhat6/augustus/augustus-20220316/config /ddn/work/cjh/test/braker-20220128/tests/test1/train.f.gb and I can reproduce the segmentation...