CREx: "missing header" error

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1

Hi,

i try to use CREx and CREx2 but I get the “missing header” error. As an input file, I use the file in gene order FASTA format as stated in the readme file on GitHub.

>Species1 Name1
nad2 cox1 nad6 ...
>Species2 Name2
nad2 nad6 cox1 ...

I tried: with or without space after “>”, different species names, gene names with capital letters. But I always get “missing header” error.

How could I solve the problem?

Thank you

2

Welcome, @Polina_Apel

Here is an example file

> genome1
A B C D
> genome2
A C B D
> genome3
A -C -B D
> genome4
A -C B D

As a guess, having two words on the > line was likely the problem. I guess you could create a compound word with the >species-name if you want to track that part.

This is a test history with an example → https://usegalaxy.eu/u/jenj/h/test-crex. Maybe check to see if this is the result you are looking for?

The tool author happens to be a part of the Galaxy community, and follows this forum. Let’s see if they have more to add. Hi @bernt-matthias – can you help? And I’m wondering if we could put an example of the input file directly on the tool form Help as a reference? Thanks!

3

Hi @Polina_Apel,

can you please share dataset or the history? Would be cool to make CREx more flexible wrt the input.

And I’m wondering if we could put an example of the input file directly on the tool form Help as a reference?

Great idea.

Best,
Matthias

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4

Dear @jennaj and @bernt-matthias,
it works now. My problem was not only with heading line but also the file format was considered as .txt (not .fasta).
Thank you!

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5

Thanks for the notification. Still it would be great if you could share the original data. I would really like to try to make the import more robust.

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