Augustus

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chromosomes longer than 2.1 GB lead to crash

2

Apparently, this is a result of 4Byte `int` not allowing for positions that are 2^31 or larger. Error message ``` examining piece 1..-1928087540 (-1928087540 bp) terminate called after throwing an...

MarioStanke

PP::ProfileReadError while using `fastBlockSearch` and `augustus --proteinprofile`

3

Hi, I encountered an error when I provide a protein profile to the program. Running `fastBlockSearch ` gives this message: ``` terminate called after throwing an instance of 'PP::ProfileReadError' what():...

endixk

Genbank input file appears to have fewer records than expected.

3

Dear Augustus team, I wanted to retrain an Augustus model with following command using Augustus 3.3.3 (yes, not the latest version but as far as I could see this doesn't...

schellt

Dear Author I had a problem when I went augustus with commond `augustus --species=h1tg000001l training.new.gb.test > test.2.CRF.out`. The error information is in fig below.How could I solve it ? ...

YuChrming

PanSN is incompatible with gff2gbSmallDNA.pl

1

Hello, In a pangenome project in A. thaliana we have adopted @ekg's [PanSN contig naming scheme](https://github.com/pangenome/PanSN-spec). Specifically, we name contigs like `${INDIVIDUAL}#${HAPLOTYPE_N}#${CONTIG_OR_CHROM}`, e.g. `at9900#1#chr1`. However, gff2gbSmallDNA.pl [line 106](https://github.com/Gaius-Augustus/Augustus/blob/master/scripts/gff2gbSmallDNA.pl#L106) removes anything...

kdm9

This is how I fixed #348 locally. There may be more places where such logic is used, and would also need correction.

kdm9

augustus: symbol lookup error: /home/yue/anaconda3/envs/funannotate/bin/../lib/libgsl.so.25: undefined symbol: cblas_ctrmv

4

Hi The following problems occurred when I used Augustus. when I installed it with conda: ``` conda install augustus=3.3.3 augustus --species=help ``` The following error occurs：(The version of gsl is...

Midreancgle

Hi, I submitted a genome file and protein file for annotation training on Augustus web and get this error: **GBProcessor::getGeneList(): Stop codon out of sequence bounds. Ignoring sequence. Encountered error...

Andi16

GBProcessor::getGeneList(): Could not read the following line in Genbank file.

6

@KatharinaHoff, Hi, I'am using augustus etraining training a very large genome, approxiate ~10Gb. my training set is select from transdecoder result. my gene model is very long. longer than 1Mbp....

YuntaoTan

"Fatal error: can't create gtest-all.o: Read-only file system" while building the Singularity container

2

Hi I'm using singularity version 3.8.7-1.el8 and creating the Singularity container fails with ``` INFO: Adding help info INFO: Adding environment to container INFO: Adding testscript INFO: Running testscript cd...

ttys42