Error message when running 'Convert' tool under 'Genome Diversity' option -- All Genome Diversity tools are now deprecated and should be avoided

usegalaxy.org support
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Hi,
I am getting the following error message when running ‘Convert’ tool under ‘Genome Diversity’ option for converting vcf file to gd_genotype format "a bytes-like object is required, not ‘str’ "

1 Like
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Hello @Vijay_Kumar

Tools from the Genome Diversity tool group are known to be problematic due to the recent Python 3 upgrade at most public Galaxy servers, including usegalaxy.org.

A potential solution is in progress to address handling legacy tools dependent on a Python 2 environment, but the work is not completed yet: https://github.com/galaxyproject/usegalaxy-playbook/issues/288

Thanks!

3

Hi there,

I experienced the same error when trying to convert vcf to pg_snp using booth “Convert” and “Make file” .
Any idea on when the bug would be fixed?

Keep up the great work guys

Andrinajoro

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@andrinajoro @Vijay_Kumar

All tools in the Genome Diversity tool group have now been deprecated.

Several have had ongoing technical issues for many years now (unrelated to the more recent Python2 issues). Any tool that is labeled as deprecated should be avoided – or expect problems. The tools may not even necessarily fail, just product incorrect results that can be difficult to detect and lead to incorrect scientific conclusions.

Tools in the MiModD group are an alternative for many who were previously using Genome Diversity or Cloudmap protocols (both now deprecated).

Resources:

Thanks!