<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif; "><div>The command 'df /tmp' will tell you whether /tmp is a tmpfs mount</div><div><br></div><div>Thanks,</div><div>Carson</div><div><br></div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> Daniel Standage <<a href="mailto:daniel.standage@gmail.com">daniel.standage@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Friday, 26 October, 2012 2:12 PM<br><span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</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> Re: [maker-devel] Strange error at blastn step<br></div><div><br></div>It looks like /tmp is indeed being used: the files I played with were under <b>/tmp/maker_1YQF9o</b>.<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 2:09 PM, Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word"><div>Check to see where /tmp is located? Some clusters have it set up as a tmpfs directory and I have had problems with fasta indexes running from tmpfs mounts in the past.</div><div><br></div><div>--Carson</div><div><br></div><div><br></div><span><div style="border-right:medium none;padding-right:0in;padding-left:0in;padding-top:3pt;text-align:left;font-size:11pt;border-bottom:medium none;font-family:Calibri;border-top:#b5c4df 1pt solid;padding-bottom:0in;border-left:medium none"><span style="font-weight:bold">From: </span> Daniel Standage <<a href="mailto:daniel.standage@gmail.com" target="_blank">daniel.standage@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Friday, 26 October, 2012 2:05 PM<br><span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>><div class="im"><br><span style="font-weight:bold">Subject: </span> Re: [maker-devel] Strange error at blastn step<br></div></div><div class="im"><div><br></div>The maker working directory is in a cluster environment with shared scratch space (I'm guessing NFS-mounted). I didn't change the temp directory setting, so it should be the local default (/tmp).<div><br></div></div><div><div class="im">
I'll give the dev version a shot. 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><div class="gmail_quote"><div class="im">On Fri, Oct 26, 2012 at 1:57 PM, Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word"><div><div class="im"><div style="font-family:Consolas;font-size:medium">
Could you try this development version and tell me if the error still happens?</div><div style="font-family:Consolas;font-size:medium"><br></div><div style="font-family:Consolas;font-size:medium">Use this command to download --></div></div><div style="font-family:Consolas;font-size:medium"><<blanked out from the mailing list>></div><div style="font-family:Consolas;font-size:medium"><br></div><div style="font-family:Consolas;font-size:medium">
Username: <<blanked out from the mailing list>></div><div style="font-family:Consolas;font-size:medium">Password: <<blanked out from the mailing list>></div><div><div class="h5"><div style="font-family:Consolas;font-size:medium"><br></div><div style="font-family:Consolas;font-size:medium">Are you running in an NFS mounted directory or are you resetting TMP to a different location?</div></div></div></div><div><div class="h5"><div style="font-family:Consolas;font-size:medium"><br></div><div style="font-family:Consolas;font-size:medium">Thanks,</div><div style="font-family:Consolas;font-size:medium">Carson</div><div style="font-family:Consolas;font-size:medium"><br></div><div><br></div><span><div style="border-right:medium none;padding-right:0in;padding-left:0in;padding-top:3pt;text-align:left;font-size:11pt;border-bottom:medium none;font-family:Calibri;border-top:#b5c4df 1pt solid;padding-bottom:0in;border-left:medium none"><span style="font-weight:bold">From: </span> Daniel Standage <<a href="mailto:daniel.standage@gmail.com" target="_blank">daniel.standage@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Friday, 26 October, 2012 1:52 PM<br><span style="font-weight:bold">To: </span> Maker Mailing List <<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> Re: [maker-devel] Strange error at blastn step<br></div><div><div><div><br></div>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>
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