I've got a test run (with the dev version) waiting in the queue. But just to be clear, if the temp directory is indeed the problem, I'm assuming that would that be fixed by setting a different temp directory on the same disk as the scratch disk?<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 2:32 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>If running './Build install_deps' to get the prereqs automatically, you can say yes to the local version question if you want those prereqs to be installed just for MAKER rather than globally to whatever perl you are using.</div>
<div><br></div><div>Thanks,</div><div>Carson</div><div><br></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 2:29 PM<div>
<div><br><span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Cc: </span> "<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>" <<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><div><div><br></div>Got this from the compute node. Looks like native disk space to me.<div>
<br></div><div><div><font face="courier new,monospace">[dstandag@mason ~] df /tmp</font></div><div><font face="courier new,monospace">Filesystem 1K-blocks Used Available Use% Mounted on</font></div><div><font face="courier new,monospace">/dev/sda1 478573472 12319684 441943620 3% /tmp</font></div>
<div><br></div><div>Installing a bundle of Perl prereqs for development version, will try that soon.</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><br><br><div class="gmail_quote">On Fri, Oct 26, 2012 at 2:24 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>Ok. Try the developer release and see if it still happens.</div>
<div><br></div><div>Thanks,</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 2:19 PM<div>
<div><br><span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Cc: </span> "<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>" <<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><div><div><br></div>Unfortunately, the job is no longer running and as a result I cannot connect to the compute nodes as I could while it was running. On the interactive node, it looks like it's real disk, although it looks like there are some tmpfs mounts.<div>
<br></div><div><div><font face="courier new,monospace">[dstandag@mason src] df /tmp</font></div><div><font face="courier new,monospace">Filesystem 1K-blocks Used Available Use% Mounted on</font></div><div>
<font face="courier new,monospace">/dev/sdb2 462824304 180235660 259078476 42% /tmp</font></div>
<div><font face="courier new,monospace">[dstandag@mason src] df</font></div><div><font face="courier new,monospace">Filesystem 1K-blocks Used Available Use% Mounted on</font></div><div><font face="courier new,monospace">login_x86_64 16497564 3077352 13420212 19% /</font></div>
<div><font face="courier new,monospace">tmpfs 16497564 0 16497564 0% /dev/shm</font></div><div><font face="courier new,monospace">tmpfs 10240 0 10240 0% /var/tmp</font></div>
<div><font face="courier new,monospace">/dev/sdb2 462824304 180235660 259078476 42% /tmp</font></div><div><font face="courier new,monospace">AFS 9000000 0 9000000 0% /afs</font></div>
<div><font face="courier new,monospace">bl-nas1:/vol/hd00 3435973856 1775658144 1660315712 52% /N/hd00</font></div><div><font face="courier new,monospace">bl-nas1:/vol/hd01 3435973856 1684116928 1751856928 50% /N/hd01</font></div>
<div><font face="courier new,monospace">bl-nas2:/vol/hd02 3435973856 1856598656 1579375200 55% /N/hd02</font></div><div><font face="courier new,monospace">bl-nas2:/vol/hd03 3435973856 2747626240 688347616 80% /N/hd03</font></div>
<div><font face="courier new,monospace">bl-nas1:/vol/hdln 81920 3424 78496 5% /N/u</font></div><div><font face="courier new,monospace">bl-nas2:/vol/soft 1258291200 837003424 421287776 67% /N/soft</font></div>
<div><font face="courier new,monospace">bl-nas1:/vol/logs 419430400 67163328 352267072 17% /N/logs</font></div><div><font face="courier new,monospace">...</font></div><div><font face="courier new,monospace">...</font></div>
<div><br></div><div>I'll see if I can launch another short job and verify this on the compute nodes.</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><br><br><div class="gmail_quote">On Fri, Oct 26, 2012 at 2:14 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>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><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 2:12 PM<br>
<span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Cc: </span> "<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>><div>
<div><br><span style="font-weight:bold">Subject: </span> Re: [maker-devel] Strange error at blastn step<br></div></div></div><div><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><br><span style="font-weight:bold">Subject: </span> Re: [maker-devel] Strange error at blastn step<br>
</div></div><div><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>
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>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><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><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><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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