[maker-devel] Maker not installing

[Emmanuel Nnadi]

Hello all,

I downloaded Maker and tried to install it. I succeeded in installing all prerequisites however running maker ./build install, it showed that maker installed.

However trying to run maker it wouldn't run.

Please how do I install maker to run on local computer?

Thanks

Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications

   

[Ence,daniel]

Hi Emmanuel, In order for anyone to help you, you need post to the mailing list the command and output (including errors) of the step that didn’t work. 

Thanks,

Daniel Ence

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[Ence,daniel]

Hi, It looks like MAKER installed ok. What is the command that you used to try to run MAKER? Can you show the result of running “MAKER -ctl”? 

Thanks,

Daniel Ence

On Aug 28, 2017, at 9:24 AM, Emmanuel Nnadi <een...@gmail.com> wrote:

Hi Ence,

Thanks for your reply,

This is the step and error received

emmannamekasMBP:src emmannaemeka$ ./build install
Installing MAKER...
Building MAKER
Skip /Users/emmannaemeka/desktop/Gpm/maker/src/../perl/config-darwin-thread-multi-2level-5.018002 (unchanged)

The build status is

=============================================================================
STATUS MAKER v2.31.9
==============================================================================
PERL Dependencies:  VERIFIED
External Programs:  VERIFIED
External C Libraries:   VERIFIED
MPI SUPPORT:        DISABLED
MWAS Web Interface: DISABLED
MAKER PACKAGE:      CONFIGURATION OK

Nnadi Nnaemeka Emmanuel

Department of Microbiology,

Faculty of Natural and Applied Science,

Plateau State University, Bokkos, Plateau State, Nigeria.

Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications

[Ence,daniel]

Sorry I should have typed “maker -CTL”. If that doesn’t work, what is the result of “which maker”? 

On Aug 28, 2017, at 10:00 AM, Emmanuel Nnadi <een...@gmail.com> wrote:

Hi Daniel

The reply is 

emmannamekasMBP:maker emmannaemeka$ MAKER -ctl

-bash: MAKER: command not found

Nnadi Nnaemeka Emmanuel

Department of Microbiology,

Faculty of Natural and Applied Science,

Plateau State University, Bokkos, Plateau State, Nigeria.

Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications

[Emmanuel Nnadi]

Hi Ence,

Thanks for your reply,

This is the step and error received

emmannamekasMBP:src emmannaemeka$ ./build install
Installing MAKER...
Building MAKER
Skip /Users/emmannaemeka/desktop/Gpm/maker/src/../perl/config-darwin-thread-multi-2level-5.018002 (unchanged)

The build status is

=============================================================================
STATUS MAKER v2.31.9
==============================================================================
PERL Dependencies:  VERIFIED
External Programs:  VERIFIED
External C Libraries:   VERIFIED
MPI SUPPORT:        DISABLED
MWAS Web Interface: DISABLED
MAKER PACKAGE:      CONFIGURATION OK

Nnadi Nnaemeka Emmanuel

Department of Microbiology,

Faculty of Natural and Applied Science,

Plateau State University, Bokkos, Plateau State, Nigeria.

Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications

On Mon, Aug 28, 2017 at 2:00 PM, Ence,daniel <d.e...@ufl.edu> wrote:

[Emmanuel Nnadi]

Hi Daniel

The reply is 

emmannamekasMBP:maker emmannaemeka$ MAKER -ctl

-bash: MAKER: command not found

Nnadi Nnaemeka Emmanuel

Department of Microbiology,

Faculty of Natural and Applied Science,

Plateau State University, Bokkos, Plateau State, Nigeria.

Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications

On Mon, Aug 28, 2017 at 2:57 PM, Ence,daniel <d.e...@ufl.edu> wrote:

[Carson Holt]

After install the executables will be in the …/maker/bin directory. Example (if you did the install in your home directory) —> ~/maker/bin/maker

You need to add the …/maker/bin directory to your PATH for it to be found just by typing ‘maker'

Explanation of the Linux PATH —> http://www.linfo.org/path_env_var.html

—Carson

[Emmanuel Nnadi]

Thanks 

I tried to export PATH

running 

echo $PATH in the maker directory this returned

/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/emmannaemeka/Desktop/Gpm/maker/bin/maker

1. Does it mean that PATH has been exported?

secondly,

I tried to run

the command maker -h, which maker, maker -CTL

nothing returned.

2. how do i start up maker?

3. Do I need to be in maker directory to start maker?

Thanks

Nnadi Nnaemeka Emmanuel

Department of Microbiology,

Faculty of Natural and Applied Science,

Plateau State University, Bokkos, Plateau State, Nigeria.

Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications

[Carson Holt]

Path needs to be a list of directories to search (you specified an executable location).

So not this —> /Users/emmannaemeka/Desktop/Gpm/maker/bin/maker

Instead it needs to be this —> /Users/emmannaemeka/Desktop/Gpm/maker/bin

—Carson

On Aug 28, 2017, at 11:32 AM, Emmanuel Nnadi <een...@gmail.com>

[Emmanuel Nnadi]

Hello all,

Please how can I determine the following in maker:

1. The total number of chromosomes

2. The size of my genome

Thanks

Nnadi Nnaemeka Emmanuel

Department of Microbiology,

Faculty of Natural and Applied Science,

Plateau State University, Bokkos, Plateau State, Nigeria.

Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications

On Fri, Sep 1, 2017 at 10:52 PM, Emmanuel Nnadi <een...@gmail.com> wrote:

Ok, thanks. 

Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications

   

On Sep 1, 2017 10:50 PM, "Carson Holt" <cars...@gmail.com> wrote:

It would need to be a new run. You won't be able to use the updated contig names with the old run. 

--Carson

Sent from my iPhone

On Sep 1, 2017, at 3:41 PM, Emmanuel Nnadi <een...@gmail.com> wrote:

Hi carson

Thanks for the tip

perl -ane 's/1_S7_R1_001_\(paired\)_trimmed_\(paired\)_//g; print' genome.fasta

It worked well however, when i ran it, it removed 1_S7_R1_001_\(paired\)_trimmed_\(paired\)_, 

I have ran maker with 1_S7_R1_001_\(paired\)_trimmed_\(paired\)_, 

1. How can I effect the change when maker has produced some files from the the old sequence?

I have spent more than 24 hours running maker and it has produced some folders already.

How can I make this change?

Thanks

Nnadi Nnaemeka Emmanuel

Department of Microbiology,

Faculty of Natural and Applied Science,

Plateau State University, Bokkos, Plateau State, Nigeria.

Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications

On Fri, Sep 1, 2017 at 4:54 PM, Carson Holt <cars...@gmail.com> wrote:

BLAST which is used by MAKER can not handle really long contig names. MAKER tries to get around this by adding a secondary tag to the fasta header when long names are detected. Even then it would be better to change the IDs of your contigs to avoid downstream failures.

I would recommend removing '1_S7_R1_001_(paired)_trimmed_(paired)_’ from each contig name.

Example command to do that —> 

perl -ane 's/1_S7_R1_001_\(paired\)_trimmed_\(paired\)_//g; print' genome.fasta

—Carson

On Aug 30, 2017, at 3:54 PM, Emmanuel Nnadi <een...@gmail.com> wrote:

Hi Carson

Thanks for your response its been helpful

Please bear with me as I work through this

1. Please how do I generate EST for my novel sequences?

2. I am currently running maker without EST and protein sequences is it wrong? Can it predict properly?

3. One error in the contig just returned this value

FastaDB::_cleanIndexAndCompact(): Fasta file contains a sequence identifier which is too long ( max id length = 50 )

 at /usr/local/bin/RepeatMasker line 1464.

FastaDB::_cleanIndexAndCompact(): Fasta file contains a sequence identifier which is too long ( max id length = 50 )

 at /usr/local/bin/RepeatMasker line 1464.

FastaDB::_cleanIndexAndCompact(): Fasta file contains a sequence identifier which is too long ( max id length = 50 )

 at /usr/local/bin/RepeatMasker line 1464.

ERROR: RepeatMasker failed

--> rank=NA, hostname=emmannaemekas-MacBook-Pro.local

ERROR: Failed while doing repeat masking

ERROR: Chunk failed at level:0, tier_type:1

FAILED CONTIG:1_S7_R1_001_(paired)_trimmed_(paired)_contig_2

ERROR: Chunk failed at level:2, tier_type:0

FAILED CONTIG:1_S7_R1_001_(paired)_trimmed_(paired)_contig_2

examining contents of the fasta file and run log

Nnadi Nnaemeka Emmanuel

Department of Microbiology,

Faculty of Natural and Applied Science,

Plateau State University, Bokkos, Plateau State, Nigeria.

Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications

On Wed, Aug 30, 2017 at 4:12 PM, Carson Holt <cars...@gmail.com> wrote:

You can query valid species names using the queryTaxonomyDatabase.pl script that comes with RepeatMasker. Try not to be too specific. In general you should use the genus rather than the species for example (or even use all of RepBase).

Example —>

perl …/RepeatMasker/util/queryTaxonomyDatabase.pl -species “drosophila"

—Carson

On Aug 30, 2017, at 9:05 AM, Emmanuel Nnadi <een...@gmail.com> wrote:

Hi Carson,

 Thanks

I was able to start using maker.

However I am working with a plant Genome novel. I had set the repeatmasking to 

1. Dcotrep a names from the repbase release but maker returned it back as not known to repeat masker

How can I use specific known genomes for repeat masking

Thanks

Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications

   

On Aug 29, 2017 4:26 PM, "Carson Holt" <cars...@gmail.com> wrote:

MAKER will read the genome= options from the maker_opts.ctl file in your current directory or the maker_opts.ctl you specified on the command line. The error means you have left the value empty. Perhaps you did not save the changes you made or you did not specify the location of the maker_opts.ctl file to use.

You can check the contents of the file using cat. Example —> cat maker_opts.ctl

—Carson

On Aug 29, 2017, at 5:11 AM, Emmanuel Nnadi <een...@gmail.com> wrote:

Hi Carson,

Thanks a lot for yesterday. I was able to resolve the issue of running maker and i followed the commands in the tutorial.

I however encountered another problem

when I ran the command nano -c maker_opts.ctl

It gave the following 1_S7_assembly.fa I specified the name of the genome but when I ran maker in another tab it gave 

#-----Genome (these are always required)

genome=1_S7_assembly.fa #genome sequence (fasta file or fasta embeded in GFF3 file)

organism_type=eukaryotic #eukaryotic or prokaryotic. Default is eukaryotic

#-----Re-annotation Using MAKER Derived GFF3

maker_gff= #MAKER derived GFF3 file

est_pass=0 #use ESTs in maker_gff: 1 = yes, 0 = no

altest_pass=0 #use alternate organism ESTs in maker_gff: 1 = yes, 0 = no

protein_pass=0 #use protein alignments in maker_gff: 1 = yes, 0 = no

rm_pass=0 #use repeats in maker_gff: 1 = yes, 0 = no

model_pass=0 #use gene models in maker_gff: 1 = yes, 0 = no

pred_pass=0 #use ab-initio predictions in maker_gff: 1 = yes, 0 = no

other_pass=0 #passthrough anyything else in maker_gff: 1 = yes, 0 = no

#-----EST Evidence (for best results provide a file for at least one)

est= #set of ESTs or assembled mRNA-seq in fasta format

altest= #EST/cDNA sequence file in fasta format from an alternate organism

est_gff= #aligned ESTs or mRNA-seq from an external GFF3 file

altest_gff= #aligned ESTs from a closly relate species in GFF3 format

#-----Protein Homology Evidence (for best results provide a file for at least one)

protein=  #protein sequence file in fasta format (i.e. from mutiple oransisms)

protein_gff=  #aligned protein homology evidence from an external GFF3 file

#-----Repeat Masking (leave values blank to skip repeat masking)

model_org=all #select a model organism for RepBase masking in RepeatMasker

rmlib= #provide an organism specific repeat library in fasta format for RepeatMasker

repeat_protein=/Users/emmannaemeka/Desktop/Gpm/maker/data/te_proteins.fasta #provide a fasta file of transposable element proteins for RepeatRunner

rm_gff= #pre-identified repeat elements from an external GFF3 file

prok_rm=0 #forces MAKER to repeatmask prokaryotes (no reason to change this), 1 = yes, 0 = no

softmask=1 #use soft-masking rather than hard-masking in BLAST (i.e. seg and dust filtering)

I ran maker command on another tab and it returned the following

STATUS: Parsing control files...

ERROR: You have failed to provide a value for 'genome' in the control files.

--> rank=NA, hostname=emmannamekasMBP

Questions

1. Specifying the genome location, do I need to run maker on the same tab or open another bash tab?

2. My genome is novel and do not have proteins, how do I generate protein fast for the de novo sequence and EST?

Thanks

Nnadi Nnaemeka Emmanuel

Department of Microbiology,

Faculty of Natural and Applied Science,

Plateau State University, Bokkos, Plateau State, Nigeria.

Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications

On Mon, Aug 28, 2017 at 6:47 PM, Carson Holt <cars...@gmail.com> wrote:

Here is a class on how to use MAKER taught a couple of years back —> http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_GMOD_Online_Training_2014

There is also a linked video as well as an amazon image of the class material where you can run the image in the cloud and follow along.

Thanks,

Carson

On Aug 28, 2017, at 11:43 AM, Emmanuel Nnadi <een...@gmail.com> wrote:

Hi Carson,

Thanks a lot 

I ran this command maker -h it returned the following

The last thing I wish to ask you, how can I load my genome fine and being annotation?

Thanks

emmannamekasMBP:maker emmannaemeka$ maker -h

MAKER version 2.31.9

Usage:

     maker [options] <maker_opts> <maker_bopts> <maker_exe>

Description:

     MAKER is a program that produces gene annotations in GFF3 format using

     evidence such as EST alignments and protein homology. MAKER can be used to

     produce gene annotations for new genomes as well as update annotations

     from existing genome databases.

     The three input arguments are control files that specify how MAKER should

     behave. All options for MAKER should be set in the control files, but a

     few can also be set on the command line. Command line options provide a

     convenient machanism to override commonly altered control file values.

     MAKER will automatically search for the control files in the current

     working directory if they are not specified on the command line.

     Input files listed in the control options files must be in fasta format

     unless otherwise specified. Please see MAKER documentation to learn more

     about control file  configuration.  MAKER will automatically try and

     locate the user control files in the current working directory if these

     arguments are not supplied when initializing MAKER.

     It is important to note that MAKER does not try and recalculated data that

     it has already calculated.  For example, if you run an analysis twice on

     the same dataset you will notice that MAKER does not rerun any of the

     BLAST analyses, but instead uses the blast analyses stored from the

     previous run. To force MAKER to rerun all analyses, use the -f flag.

     MAKER also supports parallelization via MPI on computer clusters. Just

     launch MAKER via mpiexec (i.e. mpiexec -n 40 maker). MPI support must be

     configured during the MAKER installation process for this to work though

     

Options:

     -genome|g <file>    Overrides the genome file path in the control files

     -RM_off|R           Turns all repeat masking options off.

     -datastore/         Forcably turn on/off MAKER's two deep directory

      nodatastore        structure for output.  Always on by default.

     -old_struct         Use the old directory styles (MAKER 2.26 and lower)

     -base    <string>   Set the base name MAKER uses to save output files.

                         MAKER uses the input genome file name by default.

     -tries|t <integer>  Run contigs up to the specified number of tries.

     -cpus|c  <integer>  Tells how many cpus to use for BLAST analysis.

                         Note: this is for BLAST and not for MPI!

     -force|f            Forces MAKER to delete old files before running again.

This will require all blast analyses to be rerun.

     -again|a            recaculate all annotations and output files even if no

settings have changed. Does not delete old analyses.

     -quiet|q            Regular quiet. Only a handlful of status messages.

     -qq                 Even more quiet. There are no status messages.

     -dsindex            Quickly generate datastore index file. Note that this

                         will not check if run settings have changed on contigs

     -nolock             Turn off file locks. May be usful on some file systems,

                         but can cause race conditions if running in parallel.

     -TMP                Specify temporary directory to use.

     -CTL                Generate empty control files in the current directory.

     -OPTS               Generates just the maker_opts.ctl file.

     -BOPTS              Generates just the maker_bopts.ctl file.

     -EXE                Generates just the maker_exe.ctl file.

     -MWAS    <option>   Easy way to control mwas_server for web-based GUI

                              options:  STOP

                                        START

                                        RESTART

     -version            Prints the MAKER version.

     -help|?             Prints this usage statement.

[Carson Holt]

MAKER can’t give you those details. All MAKER does is try and identify gene models against the assembly you provide.

—Carson

[Emmanuel Nnadi]

Hello,

Good day,

I am trying to assign putative gene function to the maker generated fasta. I am using NCBI

I keep getting this error

  Command line argument error: Argument "query". File is not accessible:  `muc1_genome_snap2.all.maker.snap_masked.proteins.fasta'

What do I do?

can I use blast2go in place of ncbi command line software?

Nnadi Nnaemeka Emmanuel

Department of Microbiology,

Faculty of Natural and Applied Science,

Plateau State University, Bokkos, Plateau State, Nigeria.

Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications

On Mon, Aug 28, 2017 at 2:00 PM, Ence,daniel <d.e...@ufl.edu> wrote:

[Carson Holt]

I’m not sure what you mean by NCBI. Do you mean BLAST? If so, you probably did not format and index your input database before running BLAST. See BLAST documentation.

Also the file you are using —> muc1_genome_snap2.all.maker.snap_masked.proteins.fasta

That is not the maker result file. That is a reference fasta of raw SNAP results. The MAKER result file will have a name like this (see maker documentation) —> muc1_genome_snap2.all.maker.proteins.fasta

—Carson

[Fields, Christopher J]

Emmanuel,

 

Look for anything that will help calculate basic assembly metrics, such as N50, NG50, L50, etc.; these almost always give overall assembly size, and total scaffolds/contigs.  For instance I’ve used this:

 

http://korflab.ucdavis.edu/datasets/Assemblathon/Assemblathon2/Basic_metrics/assemblathon_stats.pl

 

(it requires FALite, which is here: http://korflab.ucdavis.edu/Unix_and_Perl/FAlite.pm )

 

The Broad also has GAEMR (http://software.broadinstitute.org/software/gaemr/ ), but I haven’t tested it myself (I’ve heard it’s a bit finicky).

 

Also, see this: https://www.biostars.org/p/237591/ , which has a few more options.

 

chris