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The final transcript and proteins fasta files will only exists if there were gene models with evidence support. If you did not provide an HMM for one of the ab initio gene predictors (SNAP, Augustus, etc.) then there will be no gene models, and if you do
not provide protein or est evidence fastas, then there will be no evidence support. Also if your contigs are too short to contain gene models then there will be no models.
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<div class="">Thanks,</div>
<div class="">Carson</div>
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<blockquote type="cite" class="">
<div class="">On Nov 5, 2014, at 11:49 PM, Goutham atla <<a href="mailto:goutham.atla@gmail.com" class="">goutham.atla@gmail.com</a>> wrote:</div>
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<div dir="ltr" class="">Dear All,
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<div class="">I have finished running maker. But I realised that there are no *transcripts.fasta and *protein.fasta files in any of the directories that make has created. It has only gtf files.</div>
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<div class="">Example output of a test run: I have similar results on original file also:</div>
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[User@motif jcf7180001838744]$ pwd</div>
<div style="margin: 0px; font-size: 16px; font-family: Monaco; color: rgb(0, 212, 6); background-color: rgb(0, 0, 0);" class="">
/home/User/Maker_Annotation/Maker_test.maker.output/Maker_test_datastore/35/C1/jcf7180001838744</div>
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[User@motif jcf7180001838744]$ ls</div>
<div style="margin: 0px; font-size: 16px; font-family: Monaco; color: rgb(0, 212, 6); background-color: rgb(0, 0, 0);" class="">
jcf7180001838744.gff run.log <span style="color:rgb(76,122,255)" class="">theVoid.jcf7180001838744</span></div>
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</font></span></div>
<div style="margin: 0px;" class=""><font face="Monaco" size="3" style="background-color:rgb(255,255,255)" class="">Any help from you in figuring out why there are no protein.fasta and transcripts.fast would be very helpful.</font></div>
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<div style="margin: 0px;" class=""><font face="Monaco" size="3" style="background-color:rgb(255,255,255)" class="">Regards,</font></div>
<div style="margin: 0px;" class=""><font face="Monaco" size="3" style="background-color:rgb(255,255,255)" class="">Goutham</font></div>
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<div class="gmail_quote">On Wed, Oct 1, 2014 at 11:28 AM, Goutham atla <span dir="ltr" class="">
<<a href="mailto:goutham.atla@gmail.com" target="_blank" class="">goutham.atla@gmail.com</a>></span> wrote:<br class="">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr" class="">Dear All,
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<div class="">Thank you. I figured out th problem is with mpich2. I was behind mpich2 but was unsuccessful. I installed mpich v3 and its working fine now. Thank you all. The old GMDO tutorials are bit misleading as the new versions have come up.</div>
</div>
<div class="gmail_extra"><br class="">
<div class="gmail_quote">On Wed, Oct 1, 2014 at 11:09 AM, Marc Höppner <span dir="ltr" class="">
<<a href="mailto:marc.hoeppner@imbim.uu.se" target="_blank" class="">marc.hoeppner@imbim.uu.se</a>></span> wrote:<br class="">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word" class="">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 class="">/Marc<br class="">
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<div class="">Marc P. Hoeppner, PhD</div>
<div class="">Team Leader</div>
<div class="">BILS Genome Annotation Platform</div>
<div class="">Department for Medical Biochemistry and Microbiology</div>
<div class="">Uppsala University, Sweden</div>
<div class=""><a href="mailto:marc.hoeppner@imbim.uu.se" target="_blank" class="">marc.hoeppner@imbim.uu.se</a></div>
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<div class="">
<div class="">On 30 Sep 2014, at 21:33, Carson Holt <<a href="mailto:carson.holt@genetics.utah.edu" target="_blank" class="">carson.holt@genetics.utah.edu</a>> wrote:</div>
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<div class="">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 class="">--Carson</div>
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<span style="font-weight:bold" class="">From: </span>Goutham atla <<a href="mailto:goutham.atla@gmail.com" target="_blank" class="">goutham.atla@gmail.com</a>><br class="">
<span style="font-weight:bold" class="">Date: </span>Tuesday, September 30, 2014 at 10:49 AM<br class="">
<span style="font-weight:bold" class="">To: </span>Carson Holt <<a href="mailto:carson.holt@genetics.utah.edu" target="_blank" class="">carson.holt@genetics.utah.edu</a>><br class="">
<span style="font-weight:bold" class="">Cc: </span>"<a href="mailto:maker-devel@yandell-lab.org" target="_blank" class="">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org" target="_blank" class="">maker-devel@yandell-lab.org</a>><br class="">
<span style="font-weight:bold" class="">Subject: </span>URGENT: Re: maker failure with example data<br class="">
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<div class="">Hi Carson,<br class="">
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I figured out the problem is with RepeatMasker installation and I fixed it.<br class="">
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I am running maker with MPICH2 and I get the following warning when I start it:<br class="">
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<b class="">STATUS: Processing and indexing input FASTA files...<br class="">
WARNING: Multiple MAKER processes have been started in the<br class="">
same directory.</b><br class="">
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I would like to if this is common.<br class="">
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Regards,<br class="">
Goutham<br class="">
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<div class="gmail_quote">On Tue, Sep 30, 2014 at 12:02 PM, Goutham atla <span dir="ltr" class="">
<<a href="mailto:goutham.atla@gmail.com" target="_blank" class="">goutham.atla@gmail.com</a>></span> wrote:<br class="">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex" type="cite">
<div dir="ltr" class="">Dear Carson,
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<div class="">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" class="">
<<a href="mailto:carson.holt@genetics.utah.edu" target="_blank" class="">carson.holt@genetics.utah.edu</a>></span> wrote:<br class="">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex" type="cite">
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<div style="font-family:Consolas;font-size:12px" class="">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 style="font-family:Consolas;font-size:12px" class="">
<div class="">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 class="">Thanks,</div>
<div class="">Carson</div>
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<span style="font-weight:bold" class="">From: </span>Goutham atla <<a href="mailto:goutham.atla@gmail.com" target="_blank" class="">goutham.atla@gmail.com</a>><br class="">
<span style="font-weight:bold" class="">Date: </span>Monday, September 29, 2014 at 6:33 AM<br class="">
<span style="font-weight:bold" class="">To: </span><<a href="mailto:maker-devel@yandell-lab.org" target="_blank" class="">maker-devel@yandell-lab.org</a>><br class="">
<span style="font-weight:bold" class="">Subject: </span>maker failure with example data<br class="">
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<div style="margin:0px;font-size:16px;font-family:Monaco" class=""><font style="background-color:rgb(255,255,255)" class="">Dear All, </font></div>
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</font></div>
<div style="margin:0px;font-size:16px;font-family:Monaco" class=""><font style="background-color:rgb(255,255,255)" class="">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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<div style="margin:0px;font-size:16px;font-family:Monaco;color:rgb(0,212,6);background-color:rgb(0,0,0)" class="">
--Next Contig--</div>
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<div style="margin:0px;font-size:16px;font-family:Monaco;color:rgb(0,212,6);background-color:rgb(0,0,0)" class="">
MAKER WARNING: All old files will be erased before continuing</div>
<div style="margin:0px;font-size:16px;font-family:Monaco;color:rgb(0,212,6);background-color:rgb(0,0,0)" class="">
#---------------------------------------------------------------------</div>
<div style="margin:0px;font-size:16px;font-family:Monaco;color:rgb(0,212,6);background-color:rgb(0,0,0)" class="">
Skipping the contig because it is too short!!</div>
<div style="margin:0px;font-size:16px;font-family:Monaco;color:rgb(0,212,6);background-color:rgb(0,0,0)" class="">
SeqID: contig-dpp-500-500</div>
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Length: 0</div>
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#---------------------------------------------------------------------</div>
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<div class="">Regards,</div>
<div class="">Goutham</div>
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<div class="">Goutham Atla<br class="">
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<div class="">Goutham Atla<br class="">
</div>
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</font></span></font></span></div>
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<span class="HOEnZb"><font color="#888888" class="">_______________________________________________<br class="">
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<div class="">Goutham Atla<br class="">
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<div class="">Goutham Atla<br class="">
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