Running 2.10.<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><br>
<br><br><div class="gmail_quote">On Fri, Oct 26, 2012 at 2:19 PM, Barry Moore <span dir="ltr"><<a href="mailto:barry.moore@genetics.utah.edu" target="_blank">barry.moore@genetics.utah.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">Hi Daniel,<div><br></div><div>What version or revision of MAKER are you running. This sounds like something we were seeing here last night. We traced it as far as what appeared to be soft links in /tmp being set incorrectly. The FastaDB objects had pointers to fasta files in the void for the correct fasta file, but their dir attribute pointed to a /tmp directory in where there were soft links to another (incorrect) fasta file with it's index. It would look appeared that it was looking in the /tmp index (which pointed to an incorrect fasta file) and when it failed to find what it was looking for it would re-index the fasta file in the void (the correct one) and then look again in the index in tmp. Don't know if that helps, but the errors look similar and that's as far as I got with our error here… This was on one of Mike's annotation projects, so I don't know for sure what revision he was running, but I think it was the latest.</div>
<div><br></div><div>B</div><div><br><div><div><div class="h5"><div>On Oct 26, 2012, at 11:52 AM, Daniel Standage wrote:</div><br></div></div><blockquote type="cite"><div><div class="h5">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>
<br>
<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>
<br>
</div>
</blockquote></div><br></div></div></div><div class="im">
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<span style="font-family:Arial;font-size:12px"><div>Barry Moore</div><div>Research Scientist</div><div>Dept. of Human Genetics</div><div>University of Utah</div><div>Salt Lake City, UT 84112</div><div>--------------------------------------------</div>
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