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Automated genome annotation pipeline combining MAKER and funannotate with singularity and snakemake

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reslp/annocomba

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

Prerequisites

  • A Linux cluster
  • globally installed SLURM 18.08.7.1
  • globally installed singularity 3.4.1+
  • installed snakemake 5.19.3 (eg. in an anaconda environment)

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.

Setup annocomba

$ git clone [email protected]:reslp/annocomba.git
$ ./annocomba --setup

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Automated genome annotation pipeline combining MAKER and funannotate with singularity and snakemake

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