Maker: Combining Annotations for Large Genomes
Hi everyone,
I'm interested in using Maker3 to annotate a rather large genome by dividing it into smaller parts (each containing 1 or 2 contigs per file) and running the analysis in parallel. I'd like to know if there's a way to merge the results of multiple annotations.
I've read in several forums that Maker should resume if the job is interrupted due to a computational time limit, as long as the options haven't changed. However, it seems not to be working for me. I've tried relaunching it, but the annotation restarted from scratch. Is there a way to restart Maker after it's been interrupted?
Thank you in advance for any insights or guidance you can provide!
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
ERROR: The system limits on the number of files a process can open is too low.
written by Neel •
-
Orthofinder returning error max file limit reached.
written by basusudipto92 •
-
Error in The system limits on the number of files in the Orthofinder
written by K.Gee •
-
Get sequences for all genes in a GTF file
written by madzayasodara •
-
Resume Blast search
written by sd.gamboa.t •
-
Subread average running time
written by Jarretinha
-
Converting to fasta from .bam
written by zgayk •
-
Snakemake: set cluster cores per rule
written by samesense •
-
Tool to unmark duplicates
written by Mark Ebbert
-
How To Think In Parallel In Bioinformatics
written by Andrea_Bio •
Are the contigs non-redundant? You could use something from AGAT toolkit to deal with the annotations. One tool that comes to mind: https://agat.readthedocs.io/en/latest/tools/agat_sp_merge_annotations.html
Thank you for your comment @GenoMax.
When you refer about "contigs non-reduntant" do you mean that every contigs have a unique ID?
Every contig has unique sequence. Contigs are not wholly contained in other contigs.
I checked and yes, it is non-redundant.
Why did you delete the post, Edoardo ?
Hi @Ram. I apologize, I deleted the post without realizing. Thank you for restoring it as I have other questions regarding this.
I managed to restart maker after the command was interrupted due to timeout.
Anyway, I would like to try annotating in parallel by dividing the genome into fasta files containing some scaffold. I would like to know if anyone has experience with merging outputs from different maker annotations performed on a genome that is divided in this way.
Thanks for the help
That was not an invitation for follow up questions, Edoardo - please ask those either as a reply to someone who helped you earlier (if it's a minor follow up question) or as a new question if it branches off of the answer your received already. Please do not delete posts that have received feedback.