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Error training snap for genome annotation with MAKER 2.31.8

I have been trying to use the “-l 50 -x 0.5” parameter in maker2zff commands to specify gene models while training snap.

Here's the command;

maker2zff -l 50 -x 0.5 T_tenax.all.gff

And I get this error

Use of uninitialized value $annot in split at /mnt/storage/apps/eb/software/MAKER/2.31.8-foss-2017b-Perl-5.26.0-RMBlast/bin/maker2zff line 126, <GFF> line 35217843.
Use of uninitialized value $annot in split at /mnt/storage/apps/eb/software/MAKER/2.31.8-foss-2017b-Perl-5.26.0-RMBlast/bin/maker2zff line 126, <GFF> line 35224618.
Odd number of elements in hash assignment at /mnt/storage/apps/eb/software/MAKER/2.31.8-foss-2017b-Perl-5.26.0-RMBlast/bin/maker2zff line 126, <GFF> line 38299426.
Use of uninitialized value $annot in split at /mnt/storage/apps/eb/software/MAKER/2.31.8-foss-2017b-Perl-5.26.0-RMBlast/bin/maker2zff line 126, <GFF> line 38539398.
Use of uninitialized value $annot in split at /mnt/storage/apps/eb/software/MAKER/2.31.8-foss-2017b-Perl-5.26.0-RMBlast/bin/maker2zff line 126, <GFF> line 38705794.
Use of uninitialized value $tag in string eq at /mnt/storage/apps/eb/software/MAKER/2.31.8-foss-2017b-Perl-5.26.0-RMBlast/bin/maker2zff line 127, <GFF> line 38705794.
Use of uninitialized value $tag in string eq at /mnt/storage/apps/eb/software/MAKER/2.31.8-foss-2017b-Perl-5.26.0-R*MBlast/bin/maker2zff line 141, <GFF> line 38705794.

I can't seem to figure out what I am doing wrong. Help please :(

maker maker2zff annotation
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updated by kfletcher • kfletcher • written by shinasplitzo • shinasplitzo

I'm facing same issue. Did you manage to resolve it?

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written by aylward.megan • aylward.megan

Hi @aylward.megan

Not yet. Did you find a solution?

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written by shinasplitzo • shinasplitzo

These are just Perl warnings, not errors, if the process works and produces output it is possibly fine anyway.

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written by Michael Dondrup Michael Dondrup

1 answer

Did you have the ##FASTA line before the FASTA sequences in your file? I got similar errors when this was not present. Were there only FASTA headers in your genome.dna output file?

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written by kfletcher • kfletcher

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