Maker Annotation pipeline Output error

Question

[ashaneev07]

Hiii.....I'm ruuning maker annotation pipeline for the first time. It is given that in the maker tutorial the output folder contains number of files and a directory.

ie, contig-dpp-500-500.gff
contig-dpp-500-500.maker.proteins.fasta
contig-dpp-500-500.maker.transcripts.fasta
run.log
theVoid.contig-dpp-500-500

But my output folder contains only the following files. why didn't generate the protein and transcript sequence files?

contig-dpp-500-500.gff
run.log
theVoid.contig-dpp-500-500

Please help...thankyou.

[Tm]

For us, it was possible to run MAKER only after reffering this link written by darencard.

He has explained each step in very nice manner. I think it will be useful to you too.

Answer 1

[Philipp Bayer]

Have you run the MAKER scripts fasta_merge to create the protein/transcript fasta files and gff3_merge to create the final gff file?

[ashaneev07]

Not yet..could u please mention the syntax for the same.

[jean.elbers]

./fasta_merge


Synopsis:

fasta_merge -d maker_datastore_index.log
fasta_merge -o genome.all -i <fasta1> <fasta2> ...

Descriptions:

This script will take a MAKER datastore index log file, extract all
the relevant fasta files and create fasta files with relevant
categories of sequence (i.e. transcript, protein, GeneMark protien,
etc.).  For this to work properly you need to be in the same directory
as the datastore index.

Options:

  -d The location of the MAKER datastore index log.
  -o Alternate base name for the output files.
  -i A optional list of files to process along with or instead of the
     datastore.

./gff3_merge


Synopsis:

gff3_merge -d maker_datastore_index.log
gff3_merge -o genome.all.gff <gff3_file1> <gff3_file2> ...

Descriptions:

This script will take a MAKER datastore index log file, extract all
the relevant GFF3 files and combined GFF3 file.  The script can also
combine other correctly formated GFF3 files.  For this to work
properly you need to be in the same directory as the datastore index.

Options:

  -d The location of the MAKER datastore index log file.
  -o Alternate base name for the output files.
  -s Use STDOUT for output.
  -g Only write MAKER gene models to the file, and ignore evidence.
  -n Do not print fasta sequence in footer
  -l Merge legacy annotation sets (ignores already having seen
     features more than once for the same contig)

[ashaneev07]

i ran the below command but nothing was generated.Do you have any advices ? Thanks for your help

fasta_merge -d dpp_contig_master_datastore_index.log

[jean.elbers]

Is the datastore index still present (i.e., was it accidentally removed)?

[ashaneev07]

No..it is there..

contig-dpp-500-500  dpp_contig_datastore/05/1F/contig-dpp-500-500/  STARTED
contig-dpp-500-500  dpp_contig_datastore/05/1F/contig-dpp-500-500/  FINISHED

[jean.elbers]

Is the directory dpp_contig_datastore still there, not the file dpp_contig_master_datastore_index.log

[ashaneev07]

yes..it is there.

dpp_contig_datastore  dpp_contig_master_datastore_index.log  maker_exe.log   mpi_blastdb
dpp_contig.db         maker_bopts.log                        maker_opts.log  seen.dbm

[jean.elbers]

Sorry, not sure why fasta_merge -d dpp_contig_master_datastore_index.log produces no output then unless the directory dpp_contig_datastore/05/1F/contig-dpp-500-500/ is missing or the .fa or .gff files are missing from that sub-directory.

[ashaneev07]

Hii...Maker didn't generate the protein and transcript sequence files even after fasta_merge program. Do you have any advices ? Could u please help me..Thank you.

[jean.elbers]

Sorry, I don't know what the problem is. Can you point us to your tutorial you are using and the commands you entered on your computer? Also, did MAKER generate .fa and .gff files in the sub-directory dpp_contig_datastore/05/1F/contig-dpp-500-500/?

[ashaneev07]

Hereby attached the link of the tutorial that i followed for the installation and running of maker. The contig-dpp-500-500 contains the theVoid.contig-dpp-500-500 directory and contig-dpp-500-500.gff, run.log files.

http://gmod.org/wiki/MAKER_Tutorial_2013#Installation

[jean.elbers]

The example from above works on my computer and produces the following output. Note the deep levels of sub-directories. I am using MAKER 2.31.10

working directory /genetics/elbers/test/
ls /genetics/elbers/test/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500
contig-dpp-500-500.gff  contig-dpp-500-500.maker.proteins.fasta  contig-dpp-500-500.maker.transcripts.fasta  run.log  theVoid.contig-dpp-500-500

[ashaneev07]

K..Thanks. Did u make changes in the maker_opts.ctl file? i'm also using the same version.

[jean.elbers]

Yes,

genome=/genetics/elbers/maker-2.31.10/data/dpp_contig.fasta #genome sequence (fasta file or fasta embeded in GFF3 file)
est=/genetics/elbers/maker-2.31.10/data/dpp_est.fasta #set of ESTs or assembled mRNA-seq in fasta format
protein=/genetics/elbers/maker-2.31.10/data/dpp_protein.fasta  #protein sequence file in fasta format (i.e. from mutiple oransisms)
repeat_protein=/genetics/elbers/maker-2.31.10/data/te_proteins.fasta

note that dpp_est.fasta and dpp_protein.fasta are named differently in new versions of MAKER than the version of MAKER used in the tutorial

[ashaneev07]

Yes.I did the same. But still protein and transcript files are missing. did u train the gene prediction tools before running?

[jean.elbers]

Running MAKER on this example produces some very extensive logs that are outputted to standard out and perhaps standard error. Have you checked to see if there are perhaps some errors in these logs? Maybe there is a tool that was not installed properly?

[ashaneev07]

Thank you so much for the support and advice. Solved it..
got the protein and transcript files. :-)

[jean.elbers]

Great! May I ask what the problem was?

[ashaneev07]

Actually the problem was in the opts.ctl file. I didn't make a new maker_opts.ctl. i edited the maker generated opt.ctl which includes other configurations. That made the mistake.

[Barsha]

Could you please let me know, what exactly did you change in maker_opts.ctl file to get the fasta output. I am getting the same error but I am not able to figure out the cause.

[ashaneev07]

Created a new opts.ctl file which contains only genome,est,protein,est2genome files.

[anahi.canedotx]

I have the same issue, so I would like to know, what exactly did you change. I wonder if can I see your maker_opts.clt file?