Question: MAKER command maker2zff .ann and .dna files are empty
0
gravatar for mks002
3.3 years ago by
mks002190
Bangalore. India
mks002190 wrote:

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

ADD COMMENTlink modified 18 days ago by Juke-343.1k • written 3.3 years ago by mks002190

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?

ADD REPLYlink modified 3.3 years ago • written 3.3 years ago by genomax75k

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

ADD REPLYlink written 3.3 years ago by mks002190

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.

ADD REPLYlink written 3.3 years ago by Chris Fields2.1k

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

ADD REPLYlink written 15 months ago by jblommaert9270

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

ADD REPLYlink written 15 months ago by jblommaert9270

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.

ADD REPLYlink written 15 months ago by mks002190

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

ADD REPLYlink written 11 months ago by von_klatka0
0
gravatar for 956120746
18 days ago by
9561207460
9561207460 wrote:

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

ADD COMMENTlink written 18 days ago by 9561207460

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

ADD REPLYlink written 2 days ago by mks002190
0
gravatar for Juke-34
18 days ago by
Juke-343.1k
Sweden
Juke-343.1k wrote:

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
ADD COMMENTlink written 18 days ago by Juke-343.1k
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