Augustus
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Gaius-Augustus
Genome annotation with AUGUSTUS
if augustus is compiled with -DDEBUG, a number of tests fail with errors such as: ``` Traceback (most recent call last): File "/hive/users/markd/compartiveGenomics/projs/cat/augustus/Augustus-master/tests/examples/testcases.py", line 339, in test_utr_on self.process([ File "/hive/users/markd/compartiveGenomics/projs/cat/augustus/Augustus-master/tests/examples/testcases.py",...
Debian runs the testsuite (`make test`) during the build process for its Augustus packages. While building packages for non-amd64 architectures (see list at https://buildd.debian.org/status/package.php?p=augustus), we noticed that builds were failing...
Hi all, I was wondering how augustus distinguishes between internal stop codons that represent 'true' pseudogenization as opposed to something going wrong with characterising the boundaries of genes? If, for...
Hi @KatharinaHoff While running the script I encountered this error Error in file /mnt/bin/augustus/augustus-3.3.3/scripts/fix_in_frame_stop_codon_genes.py at line 267: Return code of subprocess was 255['/bin/perl', '/mnt/bin/augustus/augustus-3.3.3/scripts/gtf2gff.pl', '--out=corrected_07092020.gff3', '--printExon', '--gff3']
Hello, I do not know the history for this, but for some reason the Debian package does not reditribute the tutorial2015 folder. Seems like I should bring it back in,...
Hi, I want to use this vrey good software to predict genes. But I meet a problem when I train the module. here is my code : $AUGUSTUS/scripts/new_species.pl --species=for_bad_genes_removing --AUGUSTUS_CONFIG_PATH=/ds3512/home/panyp/genome_assess/augustus-3.3.3/config...
These tests to measure the accuracy on large regions of the human genome are not optimized to the end: 1. `optimize_augustus.pl` should be run as well. 2. The default `/Constant/decomp_num_steps=1`...
I am running into an issue where, after building a hal file for 4 species using cactus, then splitting into mafs with hal2maf_split.pl , running augustus in comparative mode leads...
Hi there, I've noticed that there have been 480 commits already since the last release in September 2019. Are you planning on releasing a new version soon? Thanks in advance....
Dear developers, I am following the Hoff and Stanke 2018 paper "ALTERNATIVE PROTOCOL 4 - TRAINING AUGUSTUS FOR A NEW SPECIES". Everything seems fine until the step "augustus --species=bug test.gb...
