FORUMCategory: BioinformaticsFiguring out how to run MAKER on Cedar
sjossey asked 2 years ago

I am planning to run maker so started out with
$ maker -CTL
makes some files
$ ls
_Inline maker_bopts.ctl maker_exe.ctl maker_opts.ctl
So the file maker_exe.ctl  is supposed to have paths to all the different programs/executable it calls but some of the paths/locations of the executable are not there so how should I go from here. There is quite a few of them that needs to be added I hope I don’t have to install all the missing once
$ cat maker_exe.ctl

#—–Location of Executables Used by MAKER/EVALUATOR
makeblastdb=/cvmfs/ #location of NCBI+ makeblastdb executable
blastn=/cvmfs/ #location of NCBI+ blastn executable
blastx=/cvmfs/ #location of NCBI+ blastx executable
tblastx=/cvmfs/ #location of NCBI+ tblastx executable
formatdb= #location of NCBI formatdb executable
blastall= #location of NCBI blastall executable
xdformat= #location of WUBLAST xdformat executable
blasta= #location of WUBLAST blasta executable
RepeatMasker=/cvmfs/ #location of RepeatMasker executable
exonerate=/cvmfs/ #location of exonerate executable
#—–Ab-initio Gene Prediction Algorithms
snap=/cvmfs/ #location of snap executable
gmhmme3= #location of eukaryotic genemark executable
gmhmmp= #location of prokaryotic genemark executable
augustus= #location of augustus executable
fgenesh= #location of fgenesh executable
tRNAscan-SE= #location of trnascan executable
snoscan= #location of snoscan executable
#—–Other Algorithms
probuild= #location of probuild executable (required for genemark)
Hope you can help me with this.

3 Answers
Best Answer
Eloi Mercier answered 2 years ago

So it seems that despite the warning “Argument “2.53_02” isn’t numeric in numeric”, maker is working.
I ran it on the test data provided by maker and it run without error.

Here is what I did:

Load the modules:
module load nixpkgs/16.09 gcc/5.4.0 openmpi/2.1.1 maker/2.31.9

Create the config files:
maker -CTL

edit the following line in maker_exe.ctl:
RepeatMasker=/cvmfs/ #location of RepeatMasker executable

edit the following lines in maker_opt.ctl:

Run maker:
Let me know if this works for you!

Eloi Mercier answered 2 years ago

Hi Sushma,
could you tell me how you are running it? Are you on your local computer or on one of the Compute Canada server?

sjossey replied 2 years ago

I am trying to figure it out on Cedar (Compute Canada)…. On the login node.. scratch folder. I loaded the Maker module

$ module load nixpkgs/16.09 gcc/5.4.0 openmpi/2.1.1 maker/2.31.9
$ maker -CTL
Argument “2.53_02” isn’t numeric in numeric ge (>=) at /cvmfs/ line 1570.

and makes 4 files and the above error
_Inline maker_bopts.ctl maker_exe.ctl maker_opts.ctl

After that I am trying find the path for all of the executable that are there in compute canada in the file maker_exe.ctl as many are blank. The modules for tRNAscan-SE and augustus is there but it is still blank and I am not sure if the rest are there or not

Eloi Mercier replied 2 years ago

It looks like an issue similar to what you had with BUSCO. The tool has been installed but not properly configured.
While I could find a similar workaround, it would be preferable to contact Compute Canada ( so they can configure it properly for all users.


sjossey replied 2 years ago

I will surely send an email to Compute Canada and hope it gets properly configured

Eloi Mercier replied 2 years ago

I’ve seen you haven’t had an answer from CC yet. That’s unfortunate.
I’ll see what I can do.


sjossey replied 2 years ago

I have not heard from CC indeed. Thank you very much for checking.

sjossey answered 2 years ago

Great! That worked for me too…so apparently I don’t need to configure it just pulls up what it requires.
Thank you very much,