FORUMCategory: BioinformaticsFiguring out how to run MAKER on Cedar
sjossey asked 1 month 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 Staff answered 4 weeks 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 Staff answered 4 weeks 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 4 weeks 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 Staff replied 4 weeks 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 4 weeks ago

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

    Eloi Mercier Staff replied 4 weeks 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 4 weeks ago

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

    sjossey answered 4 weeks 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