ImportError: Can't determine version for tables

[Siacm]

Hi,

I used sistr a few months ago with this command line:

sistr -i /path/to/contigs.fa genome_name -f csv -o output.csv

and now, its not working and I get this error: ImportError: Can't determine version for tables

Have I deleted a required module or something? I'm using sistr_cmd 1.0.2.

[peterk87]

Hi @Siacm It sounds like PyTables, one of the dependencies for sistr changed.

You could try to pip install tables and see if that fixes your issue.

Or you could try installing sistr using Conda from the BioConda channel with:

conda install -c bioconda sistr

With Conda it might be a good idea to install sistr into its own Conda environment so it doesn't have any conflicts with any other programs you might have installed:

conda create -n sistr_cmd-v1.0.2 -y sistr_cmd=1.0.2
# after your Conda env is created, activate it
conda activate sistr_cmd-v1.0.2
# run sistr
sistr --help

See:

• https://anaconda.org/bioconda/sistr_cmd
• https://bioconda.github.io/recipes/sistr_cmd/README.html

There's also a Singularity image for sistr. See https://github.com/phgenomics-singularity/sistr for more info.

Hope that helps you get sistr up and running again!

[Siacm]

Ah, makes sense. Thanks Peter!