MAKER command maker2zff .ann and .dna files are empty

Question

[mks002]

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

[GenoMax]

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?

[mks002]

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

[Chris Fields]

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.

[jblommaert92]

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

[jblommaert92]

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

[mks002]

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.

[von_klatka]

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

Answer 1

[956120746]

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

[mks002]

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

Answer 2

[Juke34]

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