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<p class="MsoNormal"><span style="font-size:11.0pt">Are you able to give me the specific errors for those contigs when run in isolation (i.e. redirect STDERR to a file)?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">--Carson<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><b><span style="font-size:12.0pt;color:black">From:
</span></b><span style="font-size:12.0pt;color:black">Hayley Mangelson <hayley@phasegenomics.com><br>
<b>Date: </b>Monday, November 6, 2023 at 9:03 AM<br>
<b>To: </b>Carson Hinton Holt <carson.holt@genetics.utah.edu><br>
<b>Cc: </b>AARON A DUFFY <Aaron.Duffy@tvc.utah.edu>, Maker Mailing List <maker-devel@yandell-lab.org><br>
<b>Subject: </b>Re: [maker-devel] MAKER Commercial User -- Install and run issues<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">Hello again, Carson,<br>
<br>
I was able to get most of these contigs to run... turns out the fasta headers were too long. Two of them still failed in augustus, though. I was able to run them with no ab-initio gene prediction, but not sure how to proceed at this point as the results for
those two contigs are not treated as "genes" when generating the transcript files, etc. What do you recommend?<br>
<br>
Thanks,<br>
<br>
Hayley<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">On Tue, Sep 26, 2023 at 2:07 PM Carson Hinton Holt <<a href="mailto:carson.holt@genetics.utah.edu">carson.holt@genetics.utah.edu</a>> wrote:<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">What does the error say? One thing you can do is run on a single thread (i.e. no mpiexec, just call maker directly - increase try count before doing this). That will run up to where the error happens, and
the last thing it prints out before the error is the Repeatmasker command line used. You can then cut and paste that command to test it outside of MAKER.
<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">—Carson<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"><br>
<br>
<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">On Sep 26, 2023, at 8:22 AM, Hayley Mangelson <<a href="mailto:hayley@phasegenomics.com" target="_blank">hayley@phasegenomics.com</a>> wrote:<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">Hi Carson,<br>
<br>
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?<br>
<br>
Thanks,<br>
<br>
Hayley<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">On Wed, Sep 13, 2023 at 11:20 AM Carson Hinton Holt <<a href="mailto:carson.holt@genetics.utah.edu" target="_blank">carson.holt@genetics.utah.edu</a>> wrote:<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">The seg fault is being thrown by MPI itself. That is why MAKER can run on its own.
<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">There are several things you can check (or just do them all as a sort of nuclear option):<o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:11.0pt">*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.<o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:11.0pt">*Next you may need to install OpenMPI or MPICH yourself (i.e. don’t use apt-get or other package install managers). <a href="https://www.mpich.org/downloads/" target="_blank">https://www.mpich.org/downloads/</a>.<o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:11.0pt">*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.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">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).<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">Here is a step by step (comments marked with ‘#'):<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New"">#create a directory to prep install</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New"">mkdir $HOME/install_prep</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New"">#install MPICH</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New"">cd $HOME/install_prep</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New"">wget
<a href="https://www.mpich.org/static/downloads/4.1.2/mpich-4.1.2.tar.gz" target="_blank">
https://www.mpich.org/static/downloads/4.1.2/mpich-4.1.2.tar.gz</a></span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New"">tar -zxvf mpich-4.1.2.tar.gz</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New"">cd mpich-4.1.2/</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New"">./configure --prefix=$HOME/opt/mpich</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New"">make</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New"">make install</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New"">echo 'export PATH=$HOME/opt/mpich/bin:$PATH' >> ~/.bash_profile</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New"">source ~/.bash_profile</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New"">#install a new Perl</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New"">cd $HOME/install_prep</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New"">wget
<a href="https://www.cpan.org/src/5.0/perl-5.38.0.tar.gz" target="_blank">https://www.cpan.org/src/5.0/perl-5.38.0.tar.gz</a> --no-check-certificate</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New"">tar -zxvf perl-5.38.0.tar.gz</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New"">cd perl-5.38.0</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New"">./Configure -d -Dprefix=$HOME/opt/perl5</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New"">make</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New"">make install</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New"">echo 'export PATH=$HOME/opt/perl5/bin:$PATH' >> ~/.bash_profile</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New"">source ~/.bash_profile</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New"">#install MAKER with MPI support</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New"">cd $HOME/opt</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New"">wget
<a href="http://weatherby.genetics.utah.edu/maker_downloads/AD6E/A1B0/C2B7/558563CFD35E343BA1B888148294/maker-3.01.04.tgz" target="_blank">
http://weatherby.genetics.utah.edu/maker_downloads/AD6E/A1B0/C2B7/558563CFD35E343BA1B888148294/maker-3.01.04.tgz</a></span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New"">tar -zxvf maker-3.01.04.tgz</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New"">rm -rf maker-3.01.04.tgz</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New"">cd maker/src</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New"">perl Build.PL ##say yes to MPI question</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New"">./Build installdeps ##just hit 'enter' to accept any defaults</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New"">### if you get errors mentioning '--no-check-certificate', run the command 'cpan' in your terminal.</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New"">### If it asks to set up everything automatically, say 'yes'.</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New"">### Next, whil einside cpan, run the command 'o conf init pushy_https'.</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New"">### Say 'no' to the question it asks, and then run 'o conf commit' to save changes and 'q' to exit.</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New"">### Then retry the './Build installdeps' command</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New"">./Build installexes</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New"">./Build install</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New"">echo 'export PATH=$HOME/opt/maker/bin:$PATH' >> ~/.bash_profile</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New"">source ~/.bash_profile</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New"">#test MAKER</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New"">cd $HOME/install_prep</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New"">mpiexec -n 10 maker --help ##should print a single help message</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New"">cp -R $HOME/opt/maker/data ./test</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New"">cd test</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New"">maker -CTL</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New"">mpiexec -n 10 maker --protein dpp_protein.fasta --genome dpp_contig.fasta --est dpp_est.fasta ##should run MAKER under MPI</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">—Carson<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><br>
<br>
<o:p></o:p></span></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">On Sep 12, 2023, at 2:22 PM, Hayley Mangelson <<a href="mailto:hayley@phasegenomics.com" target="_blank">hayley@phasegenomics.com</a>> wrote:<o:p></o:p></span></p>
</div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-size:11.0pt">Hi Carson,<br>
<br>
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.<o:p></o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo">===================================================================================<o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo">= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo">= PID 35952 RUNNING AT ip-172-31-12-194<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo">= EXIT CODE: 9<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo">= CLEANING UP REMAINING PROCESSES<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo">= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo">===================================================================================<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo">YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo">This typically refers to a problem with your application.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo">Please see the FAQ page for debugging suggestions<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">On Thu, Aug 24, 2023 at 6:26 PM Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>> wrote:<o:p></o:p></span></p>
</div>
<blockquote style="border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in">
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">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. <o:p></o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">Here is an example —> <a href="https://efish.integrativebiology.msu.edu/2015/02/10/annotate.html" target="_blank">https://efish.integrativebiology.msu.edu/2015/02/10/annotate.html</a><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">That example uses StarCluster which is now deprecated, but the MPI install and MAKER run still apply.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">Here is another example of using MPi —> <a href="https://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_WGS_Assembly_and_Annotation_Winter_School_2018#MPI_Support" target="_blank">https://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_WGS_Assembly_and_Annotation_Winter_School_2018#MPI_Support</a><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">Note that for OpenMPI you have to set the LD_PRELOAD environmental variable before launch.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Courier New";color:#222222;background:white">export LD_PRELOAD=/usr/lib64/openmpi-1.10/lib/libmpi.so</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">—Carson<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><br>
<br>
<o:p></o:p></span></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">On Aug 18, 2023, at 2:53 PM, Hayley Mangelson <<a href="mailto:hayley@phasegenomics.com" target="_blank">hayley@phasegenomics.com</a>> wrote:<o:p></o:p></span></p>
</div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">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.<o:p></o:p></span></p>
</div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">On Tue, Aug 15, 2023 at 5:08 PM Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>> wrote:<o:p></o:p></span></p>
</div>
<blockquote style="border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in">
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">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)?<o:p></o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">—Carson<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><br>
<br>
<o:p></o:p></span></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">On Aug 15, 2023, at 9:34 AM, Hayley Mangelson <<a href="mailto:hayley@phasegenomics.com" target="_blank">hayley@phasegenomics.com</a>> wrote:<o:p></o:p></span></p>
</div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">Hi Carson,<br>
<br>
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?<br>
<br>
Thanks,<br>
<br>
Hayley<o:p></o:p></span></p>
</div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">On Fri, Aug 11, 2023 at 4:04 PM Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>> wrote:<o:p></o:p></span></p>
</div>
<blockquote style="border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in">
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">The error is coming from Augustus. There is a problem with the species file you selected. Or you put it in the wrong place.
<o:p></o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">This is the error —> <o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New"">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</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">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/<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">You can also place the species files somewhere else but you need to set the AUGUSTUS_CONFIG_PATH so Augustus knows where to look.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">Example (in your ~/.bash_profile):<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New"">export AUGUSTUS_CONFIG_PATH=$HOME/muy_augustus_species</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">Thanks,<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">Carson<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><br>
<br>
<o:p></o:p></span></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">On Aug 11, 2023, at 7:20 AM, Hayley Mangelson <<a href="mailto:hayley@phasegenomics.com" target="_blank">hayley@phasegenomics.com</a>> wrote:<o:p></o:p></span></p>
</div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">Hi Carson, <o:p></o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">Sure thing! Sorry for the delay, I was on vacation. I reran with just a single scaffold. Here is the STDERR.<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">On Mon, Jul 31, 2023 at 12:06 PM Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>> wrote:<o:p></o:p></span></p>
</div>
<blockquote style="border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in">
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">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
<o:p></o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">--Carson <o:p></o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">Sent from my iPhone<o:p></o:p></span></p>
</div>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><br>
<br>
<o:p></o:p></span></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-size:11.0pt">On Jul 31, 2023, at 10:04 AM, Hayley Mangelson <<a href="mailto:hayley@phasegenomics.com" target="_blank">hayley@phasegenomics.com</a>> wrote:<o:p></o:p></span></p>
</blockquote>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> <o:p></o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">Hi!<br>
<br>
I am trying to get a fresh install of MAKER to work for me and am having a few issues. <br>
<br>
1. I got MAKER installed (I thought) and now the log is saying all contigs failed. See attached log.<br>
2. Having tried several versions and methods of installation, I cannot get multithreading to work.<br>
<br>
Could you help me work through these issues?<br clear="all">
<o:p></o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt">Thanks,<br>
<br>
Hayley<o:p></o:p></span></p>
</div>
<p class="MsoNormal"><span class="gmailsignatureprefix"><span style="font-size:11.0pt">--
</span></span><span style="font-size:11.0pt"><o:p></o:p></span></p>
<div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#666666">Hayley Mangelson</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#666666">Senior Bioinformatics Lead</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#666666">Phase Genomics, Inc</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><a href="http://www.phasegenomics.com/" target="_blank"><span style="color:#1155CC">www.phasegenomics.com</span></a><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><PGA_assembly_hap1_master_datastore_index.log><o:p></o:p></span></p>
</div>
<p class="MsoNormal"><span style="font-size:11.0pt">_______________________________________________<br>
maker-devel mailing list<br>
<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a><br>
<a href="http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org" target="_blank">http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org</a><o:p></o:p></span></p>
</div>
</blockquote>
</div>
</div>
</blockquote>
</div>
<p class="MsoNormal"><span style="font-size:11.0pt"><br clear="all">
<o:p></o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
</div>
<p class="MsoNormal"><span class="gmailsignatureprefix"><span style="font-size:11.0pt">--
</span></span><span style="font-size:11.0pt"><o:p></o:p></span></p>
<div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#666666">Hayley Mangelson</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#666666">Senior Bioinformatics Lead</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#666666">Phase Genomics, Inc</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><a href="http://www.phasegenomics.com/" target="_blank"><span style="color:#1155CC">www.phasegenomics.com</span></a><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
</div>
</div>
</div>
</div>
</div>
</div>
<p class="MsoNormal"><span style="font-size:11.0pt"><all_output.txt><o:p></o:p></span></p>
</div>
</blockquote>
</div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
</div>
</div>
</blockquote>
</div>
<p class="MsoNormal"><span style="font-size:11.0pt"><br clear="all">
<o:p></o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
</div>
<p class="MsoNormal"><span class="gmailsignatureprefix"><span style="font-size:11.0pt">--
</span></span><span style="font-size:11.0pt"><o:p></o:p></span></p>
<div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#666666">Hayley Mangelson</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#666666">Senior Bioinformatics Lead</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#666666">Phase Genomics, Inc</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><a href="http://www.phasegenomics.com/" target="_blank"><span style="color:#1155CC">www.phasegenomics.com</span></a><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</blockquote>
</div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
</div>
</blockquote>
</div>
<p class="MsoNormal"><span style="font-size:11.0pt"><br clear="all">
<o:p></o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
</div>
<p class="MsoNormal"><span class="gmailsignatureprefix"><span style="font-size:11.0pt">--
</span></span><span style="font-size:11.0pt"><o:p></o:p></span></p>
<div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#666666">Hayley Mangelson</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#666666">Senior Bioinformatics Lead</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#666666">Phase Genomics, Inc</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><a href="http://www.phasegenomics.com/" target="_blank"><span style="color:#1155CC">www.phasegenomics.com</span></a><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</blockquote>
</div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
</div>
</div>
</blockquote>
</div>
<p class="MsoNormal"><span style="font-size:11.0pt"><br clear="all">
<o:p></o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
</div>
<p class="MsoNormal"><span class="gmailsignatureprefix"><span style="font-size:11.0pt">--
</span></span><span style="font-size:11.0pt"><o:p></o:p></span></p>
<div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#666666">Hayley Mangelson</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#666666">Senior Bioinformatics Lead</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#666666">Phase Genomics, Inc</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><a href="http://www.phasegenomics.com/" target="_blank"><span style="color:#1155CC">www.phasegenomics.com</span></a><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
</div>
</div>
</div>
</div>
</div>
</div>
<p class="MsoNormal"><span style="font-size:11.0pt"><all_output.txt><o:p></o:p></span></p>
</div>
</blockquote>
</div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
</div>
</div>
</div>
</div>
</blockquote>
</div>
<p class="MsoNormal"><span style="font-size:11.0pt"><br clear="all">
<o:p></o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
</div>
<p class="MsoNormal"><span class="gmailsignatureprefix"><span style="font-size:11.0pt">--
</span></span><span style="font-size:11.0pt"><o:p></o:p></span></p>
<div>
<div>
<div>
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<p class="MsoNormal"><span style="font-size:11.0pt;color:#666666">Hayley Mangelson</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;color:#666666">Senior Bioinformatics Lead</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;color:#666666">Phase Genomics, Inc</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"><a href="http://www.phasegenomics.com/" target="_blank"><span style="color:#1155CC">www.phasegenomics.com</span></a><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;color:#666666">Hayley Mangelson</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;color:#666666">Senior Bioinformatics Lead</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;color:#666666">Phase Genomics, Inc</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"><a href="http://www.phasegenomics.com/" target="_blank"><span style="color:#1155CC">www.phasegenomics.com</span></a><br>
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