maker2zff error on run
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2.5 years ago
jferrier • 0

Hello,

I am using the software package called maker designed for genome annotation. Firstly, however, I need to convert a preexisting annotation set into a zff formatted annotation set. Maker comes with a pipeline to do this called maker2zff however whenever I run maker2zff I get empty files (output is genome.ann and genome.dna).

Here is the code snippet, as it namely suggests, the augustus_gff_annotations is a gif formatted annotation set generated using augustus.

/nobackup/echinotol/maker/maker/bin/maker2zff -n ${AUGUSTUS_GFF_ANNOTATIONS}.gff

I have a file collecting stdout dialog, here is a snippet from that (the rest of the file basically says the same thing).

Odd number of elements in hash assignment at /nobackup/echinotol/maker/maker/bin/maker2zff line 129, <GFF> line 20. Odd number of elements in hash assignment at /nobackup/echinotol/maker/maker/bin/maker2zff line 129, <GFF> line 21. Use of uninitialized value in split at /nobackup/echinotol/maker/maker/bin/maker2zff line 145, <GFF> line 24. Use of uninitialized value in split at /nobackup/echinotol/maker/maker/bin/maker2zff line 145, <GFF> line 25. Odd number of elements in hash assignment at /nobackup/echinotol/maker/maker/bin/maker2zff line 129, <GFF> line 33. Odd number of elements in hash assignment at /nobackup/echinotol/maker/maker/bin/maker2zff line 129, <GFF> line 34. Use of uninitialized value in split at /nobackup/echinotol/maker/maker/bin/maker2zff line 145, <GFF> line 37. Use of uninitialized value in split at /nobackup/echinotol/maker/maker/bin/maker2zff line 145, <GFF> line 38. Odd number of elements in hash assignment at /nobackup/echinotol/maker/maker/bin/maker2zff line 129, <GFF> line 46.

If need be I will be happy to include my gff file if that would help and any other information. I have seen loads of other posts on various websites with others saying they keep getting blank output files as well however I have yet to see someone post the output dialog from maker. If anyone could shed some light on what the issue might be that would be great. Thank you in advance!

Cheers

maker • 1.1k views
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I'm using this script fairly often and never had any issue. Yes please provide a piece of your gff file. And check you are providing the proper file:

head -n 50 ${AUGUSTUS_GFF_ANNOTATIONS}.gff
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Entering edit mode

Hello,

I am also having a similar issue like jferrier. I generated gff file using gff2_merge. When I run maker2zff, I get genome.dna with just the headers in it and no sequences within. I used the command below:

maker2zff -n genome.all.gff

I get the following error:

Use of uninitialized value in print at /usr/local/maker/bin/maker2zff line 171, <gff> line 12516300.

Use of uninitialized value in print at /usr/local/maker/bin/maker2zff line 171, <gff> line 12516300.

Use of uninitialized value in print at /usr/local/maker/bin/maker2zff line 171, <gff> line 12516300.

Any help regarding this is appreciated. Thank you in advance.

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