[maker-devel] MAKER Commercial User -- Install and run issues

Tue Sep 26 08:22:28 MDT 2023

Hi Carson,

Thought I should report back that this worked! Now I am just dealing with
4/32 of my contigs failing. It looks like they are failing on the repeat
masking step. I am a bit confused as to why just a handful would fail here.
Any suggestions on how to overcome this (hopefully final) obstacle?

Thanks,

Hayley

On Wed, Sep 13, 2023 at 11:20 AM Carson Hinton Holt <
carson.holt at genetics.utah.edu> wrote:

> The seg fault is being thrown by MPI itself. That is why MAKER can run on
> its own.
>
> There are several things you can check (or just do them all as a sort of
> nuclear option):
> *First make sure you are not using conda or miniconda environments. This
> can create subtle conflicts between executables and libraries as
> condo/minicanda will try to override some paths.
> *Next you may need to install OpenMPI or MPICH yourself (i.e. don’t use
> apt-get or other package install managers).
> https://www.mpich.org/downloads/.
> *Lastly you can also install your own perl and override the system perl.
> Depends on your system configuration, i.e. if using CentOS 7, your perl is
> very out of date with other libraries that may have been updated on the
> system.
>
> After compiling everything and installing, you will want to reinstall
> MAKER (the new MPI install must recompile it’s bindings to the application
> bering run).
>
>
> Here is a step by step (comments marked with ‘#'):
> #create a directory to prep install
> mkdir $HOME/install_prep
>
> #install MPICH
> cd $HOME/install_prep
> wget https://www.mpich.org/static/downloads/4.1.2/mpich-4.1.2.tar.gz
> tar -zxvf mpich-4.1.2.tar.gz
> cd mpich-4.1.2/
> ./configure --prefix=$HOME/opt/mpich
> make
> make install
> echo 'export PATH=$HOME/opt/mpich/bin:$PATH' >> ~/.bash_profile
> source ~/.bash_profile
>
> #install a new Perl
> cd $HOME/install_prep
> wget https://www.cpan.org/src/5.0/perl-5.38.0.tar.gz
> --no-check-certificate
> tar -zxvf perl-5.38.0.tar.gz
> cd perl-5.38.0
> ./Configure -d -Dprefix=$HOME/opt/perl5
> make
> make install
> echo 'export PATH=$HOME/opt/perl5/bin:$PATH' >> ~/.bash_profile
> source ~/.bash_profile
>
> #install MAKER with MPI support
> cd $HOME/opt
> wget
> http://weatherby.genetics.utah.edu/maker_downloads/AD6E/A1B0/C2B7/558563CFD35E343BA1B888148294/maker-3.01.04.tgz
> tar -zxvf maker-3.01.04.tgz
> rm -rf maker-3.01.04.tgz
> cd maker/src
> perl Build.PL ##say yes to MPI question
> ./Build installdeps ##just hit 'enter' to accept any defaults
> ### if you get errors mentioning '--no-check-certificate', run the command
> 'cpan' in your terminal.
> ### If it asks to set up everything automatically, say 'yes'.
> ### Next, whil einside cpan, run the command 'o conf init pushy_https'.
> ### Say 'no' to the question it asks, and then run 'o conf commit' to save
> changes and 'q' to exit.
> ### Then retry the './Build installdeps' command
> ./Build installexes
> ./Build install
> echo 'export PATH=$HOME/opt/maker/bin:$PATH' >> ~/.bash_profile
> source ~/.bash_profile
>
> #test MAKER
> cd $HOME/install_prep
> mpiexec -n 10 maker --help ##should print a single help message
> cp -R $HOME/opt/maker/data ./test
> cd test
> maker -CTL
> mpiexec -n 10 maker --protein dpp_protein.fasta --genome dpp_contig.fasta
> --est dpp_est.fasta ##should run MAKER under MPI
>
>
>
> —Carson
>
>
> On Sep 12, 2023, at 2:22 PM, Hayley Mangelson <hayley at phasegenomics.com>
> wrote:
>
> Hi Carson,
>
> I have tried installing MPICH and OpenMPI various ways now and am still
> having issues. MAKER appears to be running when I am not using MPI, but I
> am attaching the maker output (with -debug flag) and here is the error I
> get when trying to multithread.
>
>
> ===================================================================================
> =   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
> =   PID 35952 RUNNING AT ip-172-31-12-194
> =   EXIT CODE: 9
> =   CLEANING UP REMAINING PROCESSES
> =   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
>
> ===================================================================================
> YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault
> (signal 11)
> This typically refers to a problem with your application.
> Please see the FAQ page for debugging suggestions
>
> On Thu, Aug 24, 2023 at 6:26 PM Carson Holt <carsonhh at gmail.com> wrote:
>
>> Once you install MPICH or OpenMPI you must launch MAKER through mpiexec
>> and speciffy the CPU count to MPI. On a single instance you just give the
>> CPU count off that instance, but you can also go across instances using
>> Amazon’s Parallel Cluster.
>>
>> Here is an example —>
>> https://efish.integrativebiology.msu.edu/2015/02/10/annotate.html
>> That example uses StarCluster which is now deprecated, but the MPI
>> install and MAKER run still apply.
>>
>> Here is another example of using MPi —>
>> https://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_WGS_Assembly_and_Annotation_Winter_School_2018#MPI_Support
>>
>> Note that for OpenMPI you have to set the LD_PRELOAD environmental
>> variable before launch.
>> export LD_PRELOAD=/usr/lib64/openmpi-1.10/lib/libmpi.so
>>
>> —Carson
>>
>>
>> On Aug 18, 2023, at 2:53 PM, Hayley Mangelson <hayley at phasegenomics.com>
>> wrote:
>>
>> I am working on an AWS EC2 instance that runs Amazon Linux, and I have
>> tried a couple of installs (MPICH and Open MPI), neither of which worked. I
>> don't have any installed on my current instance.
>>
>> On Tue, Aug 15, 2023 at 5:08 PM Carson Holt <carsonhh at gmail.com> wrote:
>>
>>> Do you already have MPI installed on your system, and if so which MPI
>>> and what version (i.e. MPICH, MVAPICH2, Intel MPI, Open MPI, etc)?
>>>
>>> —Carson
>>>
>>>
>>> On Aug 15, 2023, at 9:34 AM, Hayley Mangelson <hayley at phasegenomics.com>
>>> wrote:
>>>
>>> Hi Carson,
>>>
>>> Excellent, thanks so much! I have that part working. The multithreading
>>> is still eluding me. Do you have a recommended method of installing a
>>> compatible version of MPI?
>>>
>>> Thanks,
>>>
>>> Hayley
>>>
>>> On Fri, Aug 11, 2023 at 4:04 PM Carson Holt <carsonhh at gmail.com> wrote:
>>>
>>>> The error is coming from Augustus. There is a problem with the species
>>>> file you selected. Or you put it in the wrong place.
>>>>
>>>> This is the error —>
>>>> Could not find the config file
>>>> /home/ec2-user/MAKERTOOLS/maker/exe/augustus/config/species/BUSCO_evans_trout_hap1/BUSCO_evans_trout_hap1_parameters.cfg
>>>>
>>>> The species info must exist under this base directory by default (it’s
>>>> where you let MAKER install Augustus) —>
>>>>  /home/ec2-user/MAKERTOOLS/maker/exe/augustus/config/species/
>>>>
>>>> You can also place the species files somewhere else but you need to set
>>>> the AUGUSTUS_CONFIG_PATH so Augustus knows where to look.
>>>>
>>>> Example (in your ~/.bash_profile):
>>>> export AUGUSTUS_CONFIG_PATH=$HOME/muy_augustus_species
>>>>
>>>> Thanks,
>>>> Carson
>>>>
>>>>
>>>>
>>>> On Aug 11, 2023, at 7:20 AM, Hayley Mangelson <hayley at phasegenomics.com>
>>>> wrote:
>>>>
>>>> Hi Carson,
>>>>
>>>> Sure thing! Sorry for the delay, I was on vacation. I reran with just a
>>>> single scaffold. Here is the STDERR.
>>>>
>>>> On Mon, Jul 31, 2023 at 12:06 PM Carson Holt <carsonhh at gmail.com>
>>>> wrote:
>>>>
>>>>> Can you send me the STDERR from the maker run? If you don’t have it,
>>>>> run maker again with the output from the screen redirected to a file.
>>>>> Example —> maker &> all_output.txt
>>>>>
>>>>> --Carson
>>>>>
>>>>> Sent from my iPhone
>>>>>
>>>>> On Jul 31, 2023, at 10:04 AM, Hayley Mangelson <
>>>>> hayley at phasegenomics.com> wrote:
>>>>>
>>>>> 
>>>>> Hi!
>>>>>
>>>>> I am trying to get a fresh install of MAKER to work for me and am
>>>>> having a few issues.
>>>>>
>>>>> 1. I got MAKER installed (I thought) and now the log is saying all
>>>>> contigs failed. See attached log.
>>>>> 2. Having tried several versions and methods of installation, I cannot
>>>>> get multithreading to work.
>>>>>
>>>>> Could you help me work through these issues?
>>>>> Thanks,
>>>>>
>>>>> Hayley
>>>>> --
>>>>> Hayley Mangelson
>>>>> Senior Bioinformatics Lead
>>>>> Phase Genomics, Inc
>>>>> www.phasegenomics.com
>>>>>
>>>>> <PGA_assembly_hap1_master_datastore_index.log>
>>>>> _______________________________________________
>>>>> maker-devel mailing list
>>>>> maker-devel at yandell-lab.org
>>>>> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org
>>>>>
>>>>>
>>>>
>>>> --
>>>> Hayley Mangelson
>>>> Senior Bioinformatics Lead
>>>> Phase Genomics, Inc
>>>> www.phasegenomics.com
>>>>
>>>> <all_output.txt>
>>>>
>>>>
>>>>
>>>
>>> --
>>> Hayley Mangelson
>>> Senior Bioinformatics Lead
>>> Phase Genomics, Inc
>>> www.phasegenomics.com
>>>
>>>
>>>
>>
>> --
>> Hayley Mangelson
>> Senior Bioinformatics Lead
>> Phase Genomics, Inc
>> www.phasegenomics.com
>>
>>
>>
>
> --
> Hayley Mangelson
> Senior Bioinformatics Lead
> Phase Genomics, Inc
> www.phasegenomics.com
>
> <all_output.txt>
>
>
>

-- 
Hayley Mangelson
Senior Bioinformatics Lead
Phase Genomics, Inc
www.phasegenomics.com
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