ERROR: permutation ids

[ardy20]

Hi

I am trying to run Ragout using a .maf alignment file created with SibeliaZ. But I get the following error:

ERROR: An error occured while running Ragout:
ERROR: permutation ids in /ragout/results/maf-workdir/100/blocks_coords.txt do not follow naming convention: 'genome.chromosome'

Could you please explain which file should I change and how? Is there any script for that?

Regards
Ardy

[sajjadasaf]

I have faced the same issue by using maf alignment created with SibeliaZ.

[mikolmogorov]

Hi,

For the maf workflow, you need to have your fasta sequence names in a form genome.chromosome, where genome is the same name you are using in the recipe file, and chromosome is any unique identifier.

Mikhail

[ardy20]

Thanks Mikhaeil My fasta file has 250 contigs. Is there any tool or script that can do this? Regards Ardy

On Tue, 15 Dec 2020 at 3:41 am, Mikhail Kolmogorov ***@***.***> wrote: Hi, For the maf workflow, you need to have your fasta sequence names in a form genome.chromosome, where genome is the same name you are using in the recipe file, and chromosome is any unique identifier. Mikhail — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#71 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/APA35LY4RZSOED3A4EV2HE3SUZE3FANCNFSM4UV6NWUA> .

-- Regards Ardy Kharabian-Masouleh (PhD) Email: kharabian1@gmail.com a.kharabianmasouleh@uq.edu.au Mobile: +61405134478

[mikolmogorov]

I'm not aware of any scripts, unfortunately.

[sajjadasaf]

Dear Mikhaeil,
You can do it by using awk with following command
awk '/^>/{print ">genome.chromosome" ++i; next}{print}' < file.fasta > output.fasta