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Another possibility could be that MPICH2 wasn’t build properly, no? I remember something with enabling shared libraries during the compilation of mpich, without which the error below would appear.
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<div>/Marc<br>
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<div>Marc P. Hoeppner, PhD</div>
<div>Team Leader</div>
<div>BILS Genome Annotation Platform</div>
<div>Department for Medical Biochemistry and Microbiology</div>
<div>Uppsala University, Sweden</div>
<div><a href="mailto:marc.hoeppner@imbim.uu.se">marc.hoeppner@imbim.uu.se</a></div>
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<div>On 30 Sep 2014, at 21:33, Carson Holt <<a href="mailto:carson.holt@genetics.utah.edu">carson.holt@genetics.utah.edu</a>> wrote:</div>
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<div>The message is warning that there are multiple instances of MAKER running, but no MPI communication. When you build MAKER (perl Build.PL step when installing MAKER), you need to specify the location of 'mpicc' and 'mpi.h' to build with MPI support. Otherwise
you won't be able to link against MPICH2 shared libraries. You probably need to rerun that step.</div>
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<div>--Carson</div>
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<span style="font-weight:bold">From: </span>Goutham atla <<a href="mailto:goutham.atla@gmail.com">goutham.atla@gmail.com</a>><br>
<span style="font-weight:bold">Date: </span>Tuesday, September 30, 2014 at 10:49 AM<br>
<span style="font-weight:bold">To: </span>Carson Holt <<a href="mailto:carson.holt@genetics.utah.edu">carson.holt@genetics.utah.edu</a>><br>
<span style="font-weight:bold">Cc: </span>"<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br>
<span style="font-weight:bold">Subject: </span>URGENT: Re: maker failure with example data<br>
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<div>Hi Carson,<br>
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I figured out the problem is with RepeatMasker installation and I fixed it.<br>
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I am running maker with MPICH2 and I get the following warning when I start it:<br>
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<b>STATUS: Processing and indexing input FASTA files...<br>
WARNING: Multiple MAKER processes have been started in the<br>
same directory.</b><br>
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I would like to if this is common.<br>
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Regards,<br>
Goutham<br>
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<div class="gmail_quote">On Tue, Sep 30, 2014 at 12:02 PM, Goutham atla <span dir="ltr">
<<a href="mailto:goutham.atla@gmail.com" target="_blank">goutham.atla@gmail.com</a>></span> wrote:<br>
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<div dir="ltr">Dear Carson,
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<div>Thank you for the reply. I reinstalled the BioPerl and now I am getting the following error on test data.</div>
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ERROR: RepeatMasker failed</div>
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--> rank=NA, hostname=motif</div>
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ERROR: Failed while doing repeat masking</div>
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ERROR: Chunk failed at level:0, tier_type:1</div>
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FAILED CONTIG:contig-dpp-500-500</div>
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<div class="gmail_quote">On Mon, Sep 29, 2014 at 8:17 PM, Carson Holt <span dir="ltr">
<<a href="mailto:carson.holt@genetics.utah.edu" target="_blank">carson.holt@genetics.utah.edu</a>></span> wrote:<br>
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<div style="font-family: Consolas; font-size: 12px;">The error is caused by the BioPerl indexer returning an empty length for the indexed fasta sequence (possibly because of a corrupt index file or other reasons). You may need to reinstall BioPerl (use the
CPAN version not the BioPerl-live version), or reinstall Berkley DB (used by the BioPerl indexer), or reinstall the Perl module DB_File via CPAN (Perl's interface to Berkley DB). After reinstalling BioPerl, delete the mpi_blastdb directory for the MAKER run
before retrying.</div>
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<div>Also verify that the /tmp directory on your system or the directory pointed to by TMP= in the maker_opts,ctl file is not full and that TMP= is not set to an NFS mounted location.</div>
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<div>Thanks,</div>
<div>Carson</div>
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<span style="font-weight:bold">From: </span>Goutham atla <<a href="mailto:goutham.atla@gmail.com" target="_blank">goutham.atla@gmail.com</a>><br>
<span style="font-weight:bold">Date: </span>Monday, September 29, 2014 at 6:33 AM<br>
<span style="font-weight:bold">To: </span><<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>><br>
<span style="font-weight:bold">Subject: </span>maker failure with example data<br>
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<div style="margin: 0px; font-size: 16px; font-family: Monaco;"><font style="background-color:rgb(255,255,255)">Dear All, </font></div>
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<div style="margin: 0px; font-size: 16px; font-family: Monaco;"><font style="background-color:rgb(255,255,255)">I am running maker with the demo file, i.e dip_contig.fasta by keeping all other parameters in .ctl files as default. But it do not progress and
shows the following message that the length of the sequence is 0. Can anybody help me ?</font></div>
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--Next Contig--</div>
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MAKER WARNING: All old files will be erased before continuing</div>
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#---------------------------------------------------------------------</div>
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Skipping the contig because it is too short!!</div>
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SeqID: contig-dpp-500-500</div>
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Length: 0</div>
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#---------------------------------------------------------------------</div>
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<div>Regards,</div>
<div>Goutham</div>
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<div>Goutham Atla<br>
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<div>Goutham Atla<br>
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