A flexible genome annotation pipeline combining funannotate and MAKER, snakemake and singularity

Prerequisites

• Access to a Linux based HPC cluster (local execution is possible but dicouraged)
• globally installed SLURM, SGE or TORQUE job management system.
• globally installed singularity 3.4.1+
• installed snakemake 6.0.2 (eg. in an anaconda environment)

IMPORTANT

Annocomba is still under developement. While everything generally works, it can also happen that you will run into problems.

Getting annocomba

Installing annocomba is simple. You need to clone the repository and you are good to go. While annocomba itself only has two dependencies (Singuilarity and Snakemake) there are a few additional dependencies which are required to unlock its full functionality.

$ git clone --recursive https://github.com/reslp/annocomba.git
$ cd annocomba
$ ./annocomba


			     Welcome to annocomba v0.1

Usage: annocomba <command> <arguments>
Commands:
	setup			Setup pipeline
	call-genes		De-novo gene-calling using different software
	annotate		Produce functional annotations for called genes

	util			Utilities
	-v, --version 		Print version
	-h, --help		Display help
Examples:
	To see options for the setup step:
	./annocomba setup -h

Rulegraph

Issues (inherited from smsi-funannotate):

• Sauron: There is a strange issue with RepeatMasker. For some reason it does not run. ReapearMasking with TanTan works fine.
• Sauron: I have had many jobs failing due to a singularity error: FATAL: container creation failed: failed to resolved session directory. This does not occur on VSC. From the extended message: Activating singularity image /cl_tmp/reslph/projects/xylographa_fun/.snakemake/singularity/195cc8bdbe1d3f304062822f8f4f06ce.simg FATAL: container creation failed: failed to resolved session directory /usertmp/singularity/mnt/session: lstat /tmp/singularity: no such file or directory I assume it has to do with the tmp directory not being present. I have seen this after the jobs have been in the queue for a week (and other jobs ran fine). Maybe the /tmp directory is automatically deleted from time to time which causes this error.