Syntax issue in snakemake

a-ludi / dentist

Close assembly gaps using long-reads at high accuracy.

https://a-ludi.github.io/dentist/

MIT License

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Syntax issue in snakemake #4

Closed harish0201 closed 4 years ago

harish0201 commented 4 years ago

Hi,

Apologies that I'm pasting screenshots here, in unable to login through my workstation.

The following are the versions that I'm using: Snakemake: 3.13.3 dentist v1.0.0-beta.1 (commit 9e049a98751bee89de49546e1138c18f009a77fe)

Issue:

The second is the location of the same with respect to the Snakemake file: 1590057598372_image

I'd appreciate any help regarding the same

a-ludi commented 4 years ago

Hi, you will need to use a newer version of snakemake. I recommend at least >=5.10.0. Best use the latest version as of now.

harish0201 commented 4 years ago

Hi, thanks for the suggestion. I have installed snakemake from bioconda and the version is 5.3.0

The error remains the same.

a-ludi commented 4 years ago

The reason that you get the syntax error is that your version of snakemake does not know about checkpoints. The feature has been introduced in version 5.4.0.

So, your version is still not recent enough. There are newer versions available on biocaonda, so please update using conda update snakemake.

Note: I recommend a version >=5.10.0 because I encountered several bugs in the checkpoints feature in older versions. I am using 5.10.0 right now and there are no issues anymore.