FORUMCategory: BioinformaticsFiguring out how to run MAKER on Cedar
sjossey asked 1 year 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/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/gcc5.4/blast+/2.6.0/bin/makeblastdb #location of NCBI+ makeblastdb executable
blastn=/cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/gcc5.4/blast+/2.6.0/bin/blastn #location of NCBI+ blastn executable
blastx=/cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/gcc5.4/blast+/2.6.0/bin/blastx #location of NCBI+ blastx executable
tblastx=/cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/gcc5.4/blast+/2.6.0/bin/tblastx #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/restricted.computecanada.ca/easybuild/software/2017/avx2/MPI/gcc5.4/openmpi2.1/maker/2.31.9/bin/../exe/RepeatMasker/RepeatMasker #location of RepeatMasker executable
exonerate=/cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/gcc5.4/exonerate/2.4.0/bin/exonerate #location of exonerate executable
#—–Ab-initio Gene Prediction Algorithms
snap=/cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/gcc5.4/snap/2013-11-29/bin/snap #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.
Thanks,
Sushma

3 Answers
Best Answer
Eloi Mercier answered 12 months 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/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/gcc5.4/repeatmasker/4-0-7/RepeatMasker #location of RepeatMasker executable

edit the following lines in maker_opt.ctl:
genome=/cvmfs/restricted.computecanada.ca/easybuild/software/2017/avx2/MPI/gcc5.4/openmpi2.1/maker/2.31.9/data/dpp_contig.fasta
est=/cvmfs/restricted.computecanada.ca/easybuild/software/2017/avx2/MPI/gcc5.4/openmpi2.1/maker/2.31.9/data/dpp_est.fasta
protein=/cvmfs/restricted.computecanada.ca/easybuild/software/2017/avx2/MPI/gcc5.4/openmpi2.1/maker/2.31.9/data/dpp_protein.fasta
est2genome=1

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

Eloi Mercier answered 12 months 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?
Thanks,
Eloi

sjossey replied 12 months 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/soft.computecanada.ca/easybuild/software/2017/Core/perl/5.22.4/lib/perl5/site_perl/5.22.4/x86_64-linux-thread-multi/forks.pm 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
Thanks,
Sushma

Eloi Mercier replied 12 months 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 (support@computecanada.ca) so they can configure it properly for all users.

Eloi

sjossey replied 12 months ago

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

Eloi Mercier replied 12 months ago

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

Eloi

sjossey replied 12 months ago

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

sjossey answered 12 months 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,
Sushma