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MAKER command maker2zff .ann and .dna files are empty

Hi All,

I tried using MAKER but the output files generated is empty, below is my command

   /data1/ngs/programs/maker/src/bin/maker2zff -n ../genome.all.gff

-n option is used for no filter , still output files .ann and .dna are empty. How to fix this issue.

Awaiting for kind replies

genome next-gen maker software error sequencing
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updated by Juke34 Juke34 • written by mks002 mks002

There is not enough information in this post to help diagnose. Were there any errors did the program crash? Have you tested maker install with a test dataset (generally should be included with the software) to confirm that the installation is working as expected?

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written by GenoMax GenoMax

Thank you for your reply.

Before I started working on this tools I check the installation which showed fine,

Same issue was seen before in other forum and the post link is below

https://groups.google.com/forum/#!topic/maker-devel/lWuqHGugRNw

Below are my commands 

 /data1/ngs/programs/Maker/maker/bin/maker -CTL
 /data1/ngs/programs/Maker/maker/bin/maker maker_opts.ctl maker_bopts.ctl maker_exe.ctl
/data1/ngs/programs/Maker/maker/bin/gff3_merge -d genome.maker.output/genome_master_datastore_index.log
/data1/ngs/programs/maker/src/bin/maker2zff -n ../genome.all.gff
or
/data1/ngs/programs/Maker/maker/bin/maker2zff -d ../genome.maker.output/genome_master_datastore_index.log

I have check all the intermediate file are present and the final *index.log shows successful completed maker run.

gff3_merge command is working fine and the final gff output is obtained.

Now the issue is the maker2zff gives two output .ann and .dna which is empty. Since i tried both the option in maker2zff still the output is empty.

I would be thankful to you for your kind reply

• 1 views • link
written by mks002 mks002

Have you tried any of the recommendations Carson suggested in that thread? Also, if you don't get a reply here it may be worth posting something to the MAKER list linking back to this post . In general Carson and Daniel Ence are both pretty responsive to questions.

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written by Chris Fields Chris Fields

Hi, I'm having the same issue and I'd like to know if anyone has found a solution to this? My MAKER run went well, and the gff3_merge command worked well, but then when I call maker2zff, it produces and empty .ann and an empty .dna file

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written by jblommaert92 jblommaert92

I'll add that I tried both maker2zff with and without the -n option, both produced empty files and no error

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written by jblommaert92 jblommaert92

You can try alternate method . Use the following command

To merge the gff

maker/bin/gff3_merge -d Bcon_rnd1_master_datastore_index.log -o bcon_genome.all.gff -g

To get the protein sequences and then transcripts sequences

Maker/maker/bin/fasta_merge -d Bcon_rnd1_master_datastore_index.log

Hope u get the desired result.

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written by mks002 mks002

you have to be in the .maker.output dir for all of it (see gff3/fasta_merge -h) to work.

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written by von_klatka • von_klatka

2 answers

Hi, I'm having the same issue, anyone has found a solution to this?

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written by 956120746 • 956120746

Hi, Check the alternative which I've given in this thread.

• 0 views • link
written by mks002 mks002

You need the FASTA sequence embedded in the GFF file. That might be the problem.

Check if the sequence is present tail annotation.gff.

If no sequence:

echo “##FASTA” >> annotation.gff
cat genome.fa >> annotation.gff
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written by Juke34 Juke34

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