Panaroo error with GFF3 input TIP: include .gff in the file names and collection identifiers

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1

Hi,

I hope you are doing well.

I am trying to run Panaroo on Galaxy using a collection of GFF3 files, but I encounter the following error:

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I wanted to share a couple of observations that might help clarify the issue:

  • I encountered a very similar error when running Panaroo locally. In that case, the issue was resolved by using Biopython version 1.80 and ensuring the environment handled the input paths correctly.

  • In Galaxy, even after renaming files to “.gff” ,i still got the same error.

I was wondering if this could be related to the specific environment or dependency versions used by the Galaxy Panaroo tool .

Thank you very much for your time and help—I really appreciate it :).

Best regards,
Jana

2

Hi @Jana_Mohsen,

the short answer is that your input datasets need to have their names ending in .gff.

This topic: Panaroo & PanTA: sample recognition troubleshooting has more details including an example of how to change the names.

Sorry for the inconvenience,

Wolfgang