Open casteljade opened 4 years ago
@Mataivic Do you have an idea? Jade is in Phd in ABICE (DYDIV)
At first look, possibly a problem with the regex in the format_transdecoder_headers.sh
script; I'll check that as soon as possible.
@casteljade Can you share your Galaxy history with me please ? (vmataigne@sb-rocoff.fr)
Normally it's shared. Tell me if this is not the case. Thank you so much. Jade
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@casteljade https://github.com/casteljade Can you share your Galaxy history with me please ? (vmataigne@sb-rocoff.fr)
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@casteljade Apparently it didn't work, I don't see it in my shared histories.
Anyway, I checked and this is indeed a problem with the regex : the OrthoFinder version which has been used does not write the genes headers as expected by the script.
There are unexpected characters, like _+_
and ORF type_internal
which make the file incompatible. I'll see what I can do.
Hello, If I remove these 2 strings, it should work? Thanks, Jade
@casteljade I need to access all your data to be sure, but I still can't see your Galaxy's history. Did you use OrthoFinder within Galaxy or externally and then sent the files into Galaxy ?
If I'm correct, the OrthoFinder version (2.1.2) used by Galaxy is not supposed to return Orthogroups written like that. Also I don't understand why genes' names appear several time in the orthogroups (haven't used OrthoFinder since version 2.1.2).
Bonjour, J'ai un problème à l'étape Orthogroup tool et je ne comprend pas le message d'erreur.
Mes fichiers d'entrées sont les suivant : Orthogroups. txt qui est sous la forme suivante :
et Filter Assemblies Output où les fichiers sont sous ce format:
Merci d'avance de votre aide, Castel Jade