What does that means for "zoeNewFeature illegal feature"?

[LuffyLouis]

I got the errors in the forge process according to your training protocol. And so what does that means and how do I handle with the error? I will appreciate for your answer!

ZOE WARNING (from ~/miniconda3/envs/snakemake/share/snap/bin/forge): zoeVerifyFeature: coordinate not positive
ZOE WARNING (from ~/miniconda3/envs/snakemake/share/snap/bin/forge): zoeVerifyFeature: undefined coordinates
Acceptor	0	0	+	.	.	.	.
ZOE ERROR (from ~/miniconda3/envs/snakemake/share/snap/bin/forge): zoeNewFeature illegal feature
ZOE library version 2013-02-16

[iankorf]

There's probably something wrong with your data file.

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On Oct 3, 2022, at 5:31 AM, LuffyLouis ***@***.***> wrote: I got the errors in the forge process according to your training protocol. And so what does that means and how do I handle with the error? I will appreciate for your answer! ZOE WARNING (from ~/miniconda3/envs/snakemake/share/snap/bin/forge): zoeVerifyFeature: coordinate not positive ZOE WARNING (from ~/miniconda3/envs/snakemake/share/snap/bin/forge): zoeVerifyFeature: undefined coordinates Acceptor 0 0 + . . . . ZOE ERROR (from ~/miniconda3/envs/snakemake/share/snap/bin/forge): zoeNewFeature illegal feature ZOE library version 2013-02-16 — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.

[musaqa]

I had the same problem tried everything reformating the gff and subsequent zff files as well as fasta file(shortening header lines, exon names, adding semicolons to the end of each line (which my gff and zff files didn't have while training files did), removing exons with NNNs, shortening genome fasta to contain only features from gff). In the end omitting -plus flag in fathom -export command did the trick. So i am wondering what does the -plus flag do?