I have since installed Maker on a different machine and tried it out. The test run completed successfully, but as I commenced with the full genome annotation, I have noticed the following error popping up frequently.<div><br>
</div><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><span style="font-family:'courier new',monospace">formating database...</span></div><div><div><font face="courier new, monospace">#--------- command -------------#</font></div>
</div><div><div><font face="courier new, monospace">Widget::formater:</font></div></div><div><div><font face="courier new, monospace">/N/u/dstandag/Mason/local/bin/makeblastdb -dbtype prot -in /tmp/maker_1YQF9o/Amel3%2E2_Dmel5%2E47%2Efaa.mpi.10.8</font></div>
</div><div><div><font face="courier new, monospace">#-------------------------------#</font></div></div><div><div><font face="courier new, monospace">running blast search.</font></div></div><div><div><font face="courier new, monospace">#--------- command -------------#</font></div>
</div><div><div><font face="courier new, monospace">Widget::blastx:</font></div></div><div><div><font face="courier new, monospace">/N/u/dstandag/Mason/local/bin/blastx -db /tmp/maker_1YQF9o/Amel3%2E2_Dmel5%2E47%2Efaa.mpi.10.8 -query /tmp/maker_1YQF9o/rank0/scaffold_0.0 -num_alignments 100000 -num_descriptions 100000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 16 -seg yes -soft_masking true -lcase_masking -show_gis -out /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.1.mason.maker.output/maker.pdom.1.mason_datastore/scaffold_0/theVoid.scaffold_0/scaffold_0.0.Amel3%2E2_Dmel5%2E47%2Efaa.blastx.temp_dir/Amel3%2E2_Dmel5%2E47%2Efaa.mpi.10.8.blastx</font></div>
</div><div><div><font face="courier new, monospace">#-------------------------------#</font></div></div><div><div><font face="courier new, monospace">deleted:-10 hits</font></div></div><div><div><font face="courier new, monospace">formating database...</font></div>
</div><div><div><font face="courier new, monospace">#--------- command -------------#</font></div></div><div><div><font face="courier new, monospace">Widget::formater:</font></div></div><div><div><font face="courier new, monospace">/N/u/dstandag/Mason/local/bin/makeblastdb -dbtype prot -in /tmp/maker_1YQF9o/Amel3%2E2_Dmel5%2E47%2Efaa.mpi.10.9</font></div>
</div><div><div><font face="courier new, monospace">#-------------------------------#</font></div></div><div><div><font face="courier new, monospace">running blast search.</font></div></div><div><div><font face="courier new, monospace">#--------- command -------------#</font></div>
</div><div><div><font face="courier new, monospace">Widget::blastx:</font></div></div><div><div><font face="courier new, monospace">/N/u/dstandag/Mason/local/bin/blastx -db /tmp/maker_1YQF9o/Amel3%2E2_Dmel5%2E47%2Efaa.mpi.10.9 -query /tmp/maker_1YQF9o/rank0/scaffold_0.0 -num_alignments 100000 -num_descriptions 100000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 16 -seg yes -soft_masking true -lcase_masking -show_gis -out /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.1.mason.maker.output/maker.pdom.1.mason_datastore/scaffold_0/theVoid.scaffold_0/scaffold_0.0.Amel3%2E2_Dmel5%2E47%2Efaa.blastx.temp_dir/Amel3%2E2_Dmel5%2E47%2Efaa.mpi.10.9.blastx</font></div>
</div><div><div><font face="courier new, monospace">#-------------------------------#</font></div></div><div><div><font face="courier new, monospace">deleted:-6 hits</font></div></div><div><div><font face="courier new, monospace">WARNING: Cannot find> comp59088_c1_seq7, trying to re-index the fasta.</font></div>
</div><div><div><font face="courier new, monospace">stop here:comp59088_c1_seq7</font></div></div><div><div><font face="courier new, monospace">ERROR: Fasta index error</font></div></div><div><div><font face="courier new, monospace"><br>
</font></div></div><div><div><font face="courier new, monospace">FATAL ERROR</font></div></div><div><div><font face="courier new, monospace">ERROR: Failed while polishig ESTs!!</font></div></div><div><div><font face="courier new, monospace"><br>
</font></div></div><div><div><font face="courier new, monospace">ERROR: Chunk failed at level 14</font></div></div><div><div><font face="courier new, monospace">!!</font></div></div><div><div><font face="courier new, monospace">FAILED CONTIG:scaffold_0</font></div>
</div><div><div><font face="courier new, monospace"><br></font></div></div><div><div><font face="courier new, monospace"><br></font></div></div><div><div><font face="courier new, monospace"><br></font></div></div><div><div>
<font face="courier new, monospace"><br></font></div></div><div><div><font face="courier new, monospace">--Next Contig--</font></div></div><div><div><font face="courier new, monospace"><br></font></div></div><div><div><font face="courier new, monospace">#---------------------------------------------------------------------</font></div>
</div><div><div><font face="courier new, monospace">Now starting the contig!!</font></div></div><div><div><font face="courier new, monospace">SeqID: scaffold_1</font></div></div><div><div><font face="courier new, monospace">Length: 5805686</font></div>
</div><div><div><font face="courier new, monospace">#---------------------------------------------------------------------</font></div></div></blockquote><div><br></div><div>My first thought based on the message is that <b>blastdbcmd</b> could not find the sequence in the database. I verified this was the case--I could not extract sequence <b>comp59088_c1_seq7</b> from the database Maker had created under /tmp. However, after removing the index files and re-running <b>makeblastdb</b> with the <b>-parse_seqids</b> option set, <b>blastdbcmd</b> successfully extracted the sequence.</div>
<div><br></div><div>I was initially happy with this finding, but upon closer inspection it looks like Maker does not use <b>blastdbcmd</b> to extract sequences, but rather its own internal code. Therefore I'm still not sure where the problem is and how I might fix it. Any insights?</div>
<div><br></div><div>Thanks!<br clear="all"><br>--<br>Daniel S. Standage<br>Ph.D. Candidate<br>Bioinformatics and Computational Biology Program<br>Department of Genetics, Development, and Cell Biology<br>Iowa State University<br>
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<br><br><div class="gmail_quote">On Thu, Oct 25, 2012 at 3:30 PM, Daniel Standage <span dir="ltr"><<a href="mailto:daniel.standage@gmail.com" target="_blank">daniel.standage@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Greetings!<div><br></div><div>I am doing a test run of my Maker setup on a new machine, annotating a pretty short contig (about 3kb). However, there seems to be a hiccup during the blastn stage. This is the terminal message.</div>
<div><br></div><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><div><font face="courier new, monospace">#--------- command -------------#</font></div></div><div><div><font face="courier new, monospace">Widget::blastn:</font></div>
</div><div><div><font face="courier new, monospace">/share/home/01854/standage/local/bin/blastn -db /tmp/2881473.1.development/maker_i6ZSJi/Pdom%2ETrinity%2ETrimmomatic%2Efasta.mpi.10.7 -query /</font><span style="font-family:'courier new',monospace">tmp/2881473.1.development/maker_i6ZSJi/rank0/scaffold_866.0 -num_alignments 100000 -num_descriptions 100000 -evalue 1e-10 -gapextend 3 -wo</span><span style="font-family:'courier new',monospace">rd_size 15 -reward 1 -penalty -3 -gapopen 3 -dbsize 1000 -searchsp 500000000 -num_threads 16 -lcase_masking -dust yes -soft_masking true -sh</span><span style="font-family:'courier new',monospace">ow_gis -out /scratch/01854/standage/PdomGenomic/Annotation/scripts/maker.bogus.maker.output/maker.bogus_datastore/scaffold_866/theVoid.scaff</span><span style="font-family:'courier new',monospace">old_866/scaffold_866.0.Pdom%2ETrinity%2ETrimmomatic%2Efasta.blastn.temp_dir/Pdom%2ETrinity%2ETrimmomatic%2Efasta.mpi.10.7.blastn</span></div>
</div><div><div><font face="courier new, monospace">#-------------------------------#</font></div></div><div><div><font face="courier new, monospace">deleted:0 hits</font></div></div><div><div><font face="courier new, monospace">ERROR: Could not obtain lock to format database</font></div>
</div><div><div><font face="courier new, monospace"><br></font></div></div><div><div><font face="courier new, monospace"><br></font></div></div><div><div><font face="courier new, monospace">FATAL ERROR</font></div></div>
<div>
<div><font face="courier new, monospace">ERROR: Failed while doing blastn of ESTs!!</font></div></div><div><div><font face="courier new, monospace"><br></font></div></div><div><div><font face="courier new, monospace">ERROR: Chunk failed at level 8</font></div>
</div><div><div><font face="courier new, monospace">!!</font></div></div><div><div><font face="courier new, monospace">FAILED CONTIG:scaffold_866</font></div></div></blockquote><div><br></div><div>Several blastn steps appeared to have completed successfully to this one failing. Any ideas what could be causing this?</div>
<div><br></div><div>Thanks!</div><div><br>--<br>Daniel S. Standage<br>Ph.D. Candidate<br>Bioinformatics and Computational Biology Program<br>Department of Genetics, Development, and Cell Biology<br>Iowa State University<br>
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</div>
</blockquote></div><br></div>