Search found 8 matches

by mehlan
Mon Jan 09, 2023 2:56 pm
Forum: Predicting Genes with AUGUSTUS
Topic: Filterbam error of segmentation fault
Replies: 3
Views: 6602

Re: Filterbam error of segmentation fault

As far as I can see, the problem is a segmentation fault in the execution of line filterBam --uniq --paired --in $outputDIR1/accepted_hits.s --out $outputDIR1/accepted_hits.sf.bam I don't know what is going wrong. You can try with filterBam --verbose --uniq --paired --in $outputDIR1/accepted_hits.s ...
by mehlan
Mon Dec 13, 2021 2:20 pm
Forum: WebAUGUSTUS
Topic: how to use webAUGUSTUS-derived parameters in local version
Replies: 2
Views: 7268

Re: how to use webAUGUSTUS-derived parameters in local version

download the "Species parameter archive" (parameters.tar.gz) from the webAUGUSTUS training page unpack parameters.tar.gz and place the contained folder into the local Augustus "Species" folder (probably in config/species) use the folder name as argument for the augustus --specie...
by mehlan
Thu Nov 18, 2021 2:42 pm
Forum: WebAUGUSTUS
Topic: URL error - FASTA format
Replies: 4
Views: 17667

Re: URL error - FASTA format

Please note the restrictions for the DNA fasta file format: https://bioinf.uni-greifswald.de/webaugustus/predictiontutorial#genome_file Reasons why the error message "The provided genome file "input.fasta" is not in DNA Fasta format" is displayed: the first line is not a header l...
by mehlan
Wed Aug 11, 2021 3:31 pm
Forum: AUGUSTUS Compilation/Installation
Topic: Error during installation
Replies: 1
Views: 7477

Re: Error during installation

Please read docs/INSTALL.md in case of installation problems
or try:
sudo apt-get install libmysql++-dev
by mehlan
Thu Mar 25, 2021 8:26 am
Forum: Training AUGUSTUS
Topic: Species File Failing in MAKER
Replies: 1
Views: 5696

Re: Species File Failing in MAKER

The line
Invalid nucleotide '�' encountered.
may show that not all input files are in ASCII format.
Please check this for all input files.
For example for the files in the species folder use:

Code: Select all

$ find species -type f -print0 | xargs -0 file 
by mehlan
Thu May 28, 2020 2:16 pm
Forum: WebAUGUSTUS
Topic: Trouble with prediction submission
Replies: 1
Views: 4715

Re: Trouble with prediction submission

WebAUGUSTUS retrieves large files from a public web link. This web link points directly to the file, e.g. https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/013/425/GCF_000013425.1_ASM1342v1/GCF_000013425.1_ASM1342v1_genomic.fna.gz or http://bioinf.uni-greifswald.de/webaugustus/examples/LG16.fa When p...
by mehlan
Mon Oct 14, 2019 2:26 pm
Forum: Training AUGUSTUS
Topic: Training Histomonas failed
Replies: 1
Views: 4701

Re: Training Histomonas failed

Sorry, we had a misconfiguration in our augustus training pipeline, which is now fixed.
Sorry for any inconvenience