Trouble with prediction submission

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efcoak
Posts: 1
Joined: Thu May 21, 2020 12:45 am

Trouble with prediction submission

Post by efcoak » Thu May 21, 2020 1:20 am

I am a newcomer to Augustus. I have been trying to do a prediction submission for an insect genome (1.2 Bbp). My genome file in .fasta.gz format is 0.4 GB, and my cDNA file is about 15 MB. I have tried using BOX and also Google drive, but at first I kept getting the error "could not access the genome file." My latest is that the file is not in fasta format.

Any suggestions on how to circumvent theses obstacles would be appreciated.

mehlan
Site Admin
Posts: 2
Joined: Mon Oct 14, 2019 2:24 pm

Re: Trouble with prediction submission

Post by mehlan » Thu May 28, 2020 2:16 pm

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/al ... mic.fna.gz
or
http://bioinf.uni-greifswald.de/webaugu ... es/LG16.fa
When putting this links into a browser, you will either
asked to download this files (like in the first example, as it is quite pointless to show a zipped file in the browser)
or
the browser shows you the file content and nothing but the content.

In contrast, if you put links to Google drive, Dropbox, BOX, ... into your browser,
you will see a webpage (sometimes with the file content embedded in this page) with a download button somewhere.
And only after you have pressed this button, the download will start.

WebAUGUSTUS don't "see" this download button and can't start the download.
For this reason WebAUGUSTUS don't support links to BOX, Google drive, Dropbox, ...

Maybe you can ask your administrator for a way to provide a web link.
If your genome file contains multiple fasta entries (e.g. one for each chromosome), you could split your fasta file into multiple files, each meeting the size limit of WebAUGUSTUS.

Please ask augustus-web@uni-greifswald.de if you have a file that is larger than the allowed limit and there is no possibility to create a download link.

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