<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>I'm glad it's working. I think I'll add a check for the '/' characters in the base name as I think having it be a directory will get me in trouble somewhere with hidden bugs.</div><div><br></div><div>Thanks,</div><div>Carson</div><div><br></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, 24 May, 2013 4:00 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">Subject: </span> Re: [maker-devel] Using maker with precomputed transcript / protein alignments<br></div><div><br></div><div dir="ltr"><div><div><div>Oh wow, you are going to LOVE this.<br><br></div>I kept on messing around with things to see if I could tease out any patterns, and eventually it hit me. In my working directory, I have an <b>outputs</b> directory, which is intended to contain output directories from various different maker runs. However, since my submission scripts launch Maker from the working directory, I use <b>-base outputs/blahblahblah</b> as the base parameter. So when it tries to create output files using the base name (the SQLite3 db just happens to be the first), it tries to create <b>outputs/blahblahblah/outputs/blahblahblah.db</b>, and of course that internal <b>outputs</b> directory doesn't exist. Every time I've had problems, I've been using a basename with a <b>/</b> character (relative directory path). Every time I haven't had problems, it was because the / wasn't there.<br><br>Since the <b>base</b> parameter determines the name of the output directory, I assumed I could also use it specify a nested output directory. So it looks like I just need to be more careful that the basenames I use don't contain / characters or any other special UNIX characters. Of course, this could be made explicit in the usage statement, or you could add something like this right after parsing the command line arguments.<br><br><div style="margin-left:40px"><span style="font-family: 'courier new', monospace; ">if($OPT{"out_name"} =~ m/\//)</span><br><span style="font-family: 'courier new', monospace; ">{</span><br><span style="font-family: 'courier new', monospace; "> printf(STDERR "base '%s' invalid: basenames containing relative directory paths cause errors; please provide a simple string instead", $OPT{"out_name"});</span><br><span style="font-family: 'courier new', monospace; "> exit_maker(0);</span><br><span style="font-family: 'courier new', monospace; ">}</span><br></div><br></div>Alternatively, you could handle things like I had originally expected: if I provide <b>path/to/mybase</b> as my base parameter, maker would create the <b>path/to/mybase</b> directory initially, but then in the creation of subsequent files it would simply use <b>mybase</b>. I don't imagine this would be <i>too</i> extensive of a change, but I understand Maker has a huge codebase. Anyway, just some suggestions, take them for what they're worth.<br><br></div>Thanks for your help!<br></div><div class="gmail_extra"><br clear="all"><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></div><br><br><div class="gmail_quote">On Fri, May 24, 2013 at 3:29 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>NFS is weird. It's hard to say why it was freezing the first times, and did not appear to freeze on your very last try. I definitely want to know if it starts to freeze again, or if stack traces show a consistent point where it freezes. If it keeps happening, I can try making the database in the local /tmp and then just copying it to the current working directory once it's populated to get around any weird NFS issues. But before going through all the effort to do that, I'd like to know that it's not some other weird bug related to the perl your using or other modules that are installed. Top candidates on the list would be modules such as forks, forks::shared, DBI, or DBD::SQLite. Try reinstalling those</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, 24 May, 2013 3:19 PM<div><div class="h5"><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">Subject: </span> Re: [maker-devel] Using maker with precomputed transcript / protein alignments<br></div></div></div><div><div class="h5"><div><br></div><div dir="ltr"><div>I admit I killed these last few runs too quickly, I guess I was getting impatient, especially since waiting hours or days hasn't made a difference before. Either way, that was sloppy on my part.<br><br></div>However, I always specify the base parameter, whether or not I'm running mulitple maker jobs from the same directory. And if I ever restarted a job, I have always removed the original output directory entirely before relaunching--precisely to avoid the types of mistakes you mention arising from residual files.<br clear="all"><div class="gmail_extra"><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></div><br><br><div class="gmail_quote">On Fri, May 24, 2013 at 3:10 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>Correct if you use the -base parameter you should get a different output directory. And if you have never used that base before, and it still freezes, then there is a problem. You do need to give it a little more time until killing it, as the stack trace in both cases showed that it was less than 25% finished reading the input GFF3 files and even less than that in the first case (so give it about 5x as long before giving up).</div><div><br></div><div>It might just be that the NFS mount is slow. Or because of how weird the error is, other options include reinstalling perl and all modules. The weirdest bugs are often broken perl or inadvertently using modules from different perl versions via the PERL5LIB environmental variable (this is very common and can cause very wacky behavior). Another option is verifying all software for the lustre NFS mount is up to date. Lastly there was an odd NFS bug that came up on the e-mail list last week that was fixed by a kernel upgrade.</div><div><br></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, 24 May, 2013 3:01 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">Subject: </span> Re: [maker-devel] Using maker with precomputed transcript / protein alignments<br></div></div></div><div><div><div><br></div><div dir="ltr">The file locks are created only in the output directory, no? So there is a problem if I have multiple maker runs launched from the same directory, but writing to different output directories (as specified by different <b>base</b> parameters)?<br></div><div class="gmail_extra"><br clear="all"><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></div><br><br><div class="gmail_quote">On Fri, May 24, 2013 at 2:57 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>To clarify, that means you need to use a different working directory. Can be a subdirectory of your original.</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> Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Friday, 24 May, 2013 2:56 PM<br><span style="font-weight:bold">To: </span> Daniel Standage <<a href="mailto:daniel.standage@gmail.com" target="_blank">daniel.standage@gmail.com</a>><div><div><br><span style="font-weight:bold">Subject: </span> Re: [maker-devel] Using maker with precomputed transcript / protein alignments<br></div></div></div><div><div><div><br></div><div><div style="word-wrap:break-word"><div><font face="Calibri,sans-serif">Both stack traces show different locations in the code and file being read. So it appears it was not frozen, just interrupted by control-C.</font></div><div><font face="Calibri,sans-serif"><br></font></div><div><font face="Calibri,sans-serif">If you restart make sure you do so in a completely new directory from the original run. This is because I wonder if there is a failed job that still has active processes and is holding onto file locks in that directory.</font></div><div><font face="Calibri,sans-serif"><br></font></div><div><font face="Calibri,sans-serif">--Carson</font></div><div><font face="Calibri,sans-serif"><br></font></div><div style="font-size:14px;font-family:Calibri,sans-serif"><br></div><span style="font-size: 14px; font-family: Calibri, sans-serif; "><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, 24 May, 2013 2:50 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">Subject: </span> Re: [maker-devel] Using maker with precomputed transcript / protein alignments<br></div><div><br></div><div dir="ltr">Deleted output directory and re-ran. Stack trace looks pretty similar.<br><br><br><div style="margin-left:40px"><span style="color:rgb(153,0,0)"><span style="font-family: 'courier new', monospace; ">Calling GFFDB::new at /N/u/dstandag/Mason/local/src/maker-dev/bin/maker line 607.</span><br><span style="font-family: 'courier new', monospace; ">SIGINT received</span><br><span style="font-family: 'courier new', monospace; "> at /N/u/dstandag/Mason/local/src/PerlLibs/lib64/perl5/forks/<a href="http://signals.pm" target="_blank">signals.pm</a> line 97, <$IN</span><br><span style="font-family: 'courier new', monospace; ">> line 243676.</span><br><span style="font-family: 'courier new', monospace; "> forks::signals::__ANON__('INT') called at /usr/lib64/perl5/DBI.pm line 1590</span><br><span style="font-family: 'courier new', monospace; "> eval {...} called at /usr/lib64/perl5/DBI.pm line 1590</span><br><span style="font-family: 'courier new', monospace; "> DBD::_::db::do('DBI::db=HASH(0x4987228)', 'INSERT INTO est_gff (seqid, source, parent, start, end, line)...') called at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GFFDB.pm line 493</span><br><span style="font-family: 'courier new', monospace; "> GFFDB::_add_to_db('GFFDB=HASH(0x49727a0)', 'DBI::db=HASH(0x49871e0)', 'est_gff', 'HASH(0x49877e0)') called at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GFFDB.pm line 432</span><br><span style="font-family: 'courier new', monospace; "> GFFDB::_add_type('GFFDB=HASH(0x49727a0)', '/N/dc/scratch/dstandag/PdomGenomic/Annotation/annot-v0.41/inp...', 'est_gff') called at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GFFDB.pm line 324</span><br><span style="font-family: 'courier new', monospace; "> GFFDB::add_est('GFFDB=HASH(0x49727a0)', '/N/dc/scratch/dstandag/PdomGenomic/Annotation/annot-v0.41/inp...') called at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GFFDB.pm line 57</span><br><span style="font-family: 'courier new', monospace; "> GFFDB::new('GFFDB', 'HASH(0x489c488)') called at /N/u/dstandag/Mason/local/src/maker-dev/bin/maker line 608</span></span><br></div></div><div class="gmail_extra"><br clear="all"><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></div><br><br><div class="gmail_quote">
On Fri, May 24, 2013 at 2:45 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>Could you run again, and so I can see if the stack trace is the same each time.</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, 24 May, 2013 2:39 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">Subject: </span> Re: [maker-devel] Using maker with precomputed transcript / protein alignments<br></div></div></div><div><div><div><br></div><div dir="ltr">Restarted in the original NSF-mounted directory, never saw the .db file, and got this as the stack trace upon termination.<br><br><div style="margin-left:40px"><span style="color:rgb(153,0,0)"><span style="font-family: 'courier new', monospace; ">STATUS: Setting up database for any GFF3 input...</span><br><span style="font-family: 'courier new', monospace; ">Calling GFFDB::new at /N/u/dstandag/Mason/local/src/maker-dev/bin/maker line 607.</span><br><span style="font-family: 'courier new', monospace; ">SIGINT received</span><br><span style="font-family: 'courier new', monospace; "> at /N/u/dstandag/Mason/local/src/PerlLibs/lib64/perl5/forks/<a href="http://signals.pm" target="_blank">signals.pm</a> line 97, <$IN> line 170294.</span><br><span style="font-family: 'courier new', monospace; "> forks::signals::__ANON__('INT') called at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GFFDB.pm line 475</span><br><span style="font-family: 'courier new', monospace; "> eval {...} called at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GFFDB.pm line 475</span><br><span style="font-family: 'courier new', monospace; "> GFFDB::_parse_line('GFFDB=HASH(0x4e5c730)', 'SCALAR(0x4e714b8)', 'est_gff') called at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GFFDB.pm line 431</span><br><span style="font-family: 'courier new', monospace; "> GFFDB::_add_type('GFFDB=HASH(0x4e5c730)', '/N/dc/scratch/dstandag/PdomGenomic/Annotation/annot-v0.41/inp...', 'est_gff') called at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GFFDB.pm line 324</span><br><span style="font-family: 'courier new', monospace; "> GFFDB::add_est('GFFDB=HASH(0x4e5c730)', '/N/dc/scratch/dstandag/PdomGenomic/Annotation/annot-v0.41/inp...') called at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GFFDB.pm line 57</span><br><span style="font-family: 'courier new', monospace; "> GFFDB::new('GFFDB', 'HASH(0x4d86488)') called at /N/u/dstandag/Mason/local/src/maker-dev/bin/maker line 608</span></span><br></div></div><div class="gmail_extra"><br clear="all"><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></div><br><br><div class="gmail_quote">
On Fri, May 24, 2013 at 2:25 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>Start a new job in a new directory from the original job (NFS mount). Use the new maker executable I sent. If it still freezes, hit control-C to get a stack trace.</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, 24 May, 2013 2:21 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">Subject: </span> Re: [maker-devel] Using maker with precomputed transcript / protein alignments<br></div></div></div><div><div><div><br></div><div dir="ltr"><div><div>The job from several hours ago is still running with no changes.<br><br></div>I just relaunched the job with a locally mounted working directory: I could see the .db file almost immediately, and it took less than 5 minutes to successfully build the SQLite3 db and proceed to the next steps of the pipeline. Any ideas?<br></div><div class="gmail_extra"><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></div><br><br><div class="gmail_quote">On Fri, May 24, 2013 at 2:01 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;word-wrap:break-word"><div style="font-family:Calibri,sans-serif">The NFS mount appears to be configured correctly.</div><div style="font-family:Calibri,sans-serif"><br></div><div style="font-family:Calibri,sans-serif">
Here is what the maker.output directory should look like while the database is being generated.</div><div style="font-family:Calibri,sans-serif"><br></div><div><div><font face="Courier">drwxr-xr-x 10 cholt staff 340 24 May 13:51 .</font></div><div><font face="Courier">drwxr-xr-x 10 cholt staff 340 24 May 13:50 ..</font></div><div><font face="Courier">-rw------x 1 cholt staff 85 24 May 13:50 .NFSLock.gi_lock.NFSLock</font></div><div><font face="Courier">-rw------- 1 cholt staff 52 24 May 13:50 .NFSLock.pdom-annot-v0.41-1.db.NFSLock</font></div><div><font face="Courier">-rw-r--r-- 1 cholt staff 1413 24 May 13:50 maker_bopts.log</font></div><div><font face="Courier">-rw-r--r-- 1 cholt staff 1666 24 May 13:50 maker_exe.log</font></div><div><font face="Courier">-rw-r--r-- 1 cholt staff 4610 24 May 13:50 maker_opts.log</font></div><div><font face="Courier">drwxr-xr-x 4 cholt staff 136 24 May 13:50 mpi_blastdb</font></div><div><font face="Courier">-rw-r--r-- 1 cholt staff 29326336 24 May 13:51 pdom-annot-v0.41-1.db</font></div><div><font face="Courier">-rw-r--r-- 1 cholt staff 6704 24 May 13:51 pdom-annot-v0.41-1.db-journal</font></div></div><div style="font-family:Calibri,sans-serif"><br></div><div style="font-family:Calibri,sans-serif"><br></div><div style="font-family:Calibri,sans-serif">Could you watch while maker is running to see if this file is created --> <span style="font-family:Courier">.NFSLock.pdom-annot-v0.41-1.db.NFSLock</span></div><div style="font-family:Calibri,sans-serif">You must use ls with the -a flag to see it or it will be hidden.</div><div style="font-family:Calibri,sans-serif"><br></div><div><span style="font-family: Calibri, sans-serif; ">Just k</span>eep letting it run until that file shows up. Shortly after it sows up, this one should appear --> pdom-annot-v0.41-1.db-journal</div><div><br></div><div>Also could you try running MAKER once with the working directory being locally mounted (/tmp for example).</div><div><br></div><div>--Carson</div><div><br></div><div><font face="Courier"><br></font></div><div style="font-family:Calibri,sans-serif"><br></div><span style="font-family: Calibri, sans-serif; "><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, 24 May, 2013 1:36 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">Subject: </span> Re: [maker-devel] Using maker with precomputed transcript / protein alignments<br></div></div></div><div><div><div><br></div><div dir="ltr"><div>Here is the output.<br><br><div style="margin-left:40px"><span style="color:rgb(153,0,0)"><span style="font-family: 'courier new', monospace; ">[dstandag@mason annot-v0.41] ls -al outputs/pdom-annot-v0.41-1.maker.output/</span><br><span style="font-family: 'courier new', monospace; ">total 32</span><br><span style="font-family: 'courier new', monospace; ">drwxr-xr-x 3 dstandag biol 4096 May 24 13:34 .</span><br><span style="font-family: 'courier new', monospace; ">drwxr-xr-x 3 dstandag biol 4096 May 24 12:39 ..</span><br><span style="font-family: 'courier new', monospace; ">-rw-r--r-- 1 dstandag biol 1413 May 24 12:39 maker_bopts.log</span><br><span style="font-family: 'courier new', monospace; ">-rw-r--r-- 1 dstandag biol 1355 May 24 12:39 maker_exe.log</span><br><span style="font-family: 'courier new', monospace; ">-rw-r--r-- 1 dstandag biol 4883 May 24 12:39 maker_opts.log</span><br><span style="font-family: 'courier new', monospace; ">drwxr-xr-x 3 dstandag biol 4096 May 24 12:39 mpi_blastdb</span><br><span style="font-family: 'courier new', monospace; ">-rw------x 1 dstandag biol 70 May 24 13:34 .NFSLock.gi_lock.NFSLock</span><br><span style="font-family: 'courier new', monospace; ">[dstandag@mason annot-v0.41] df outputs/pdom-annot-v0.41-1.maker.output/</span><br><span style="font-family: 'courier new', monospace; ">Filesystem 1K-blocks Used Available Use% Mounted on</span><br><span style="font-family: 'courier new', monospace; ">dc-mds01.uits.indiana.edu:/dc</span><br><span style="font-family: 'courier new', monospace; "> 1144318908992 928977247792 203869022296 83% /N/dc</span><br><span style="font-family: 'courier new', monospace; ">[dstandag@mason annot-v0.41] mount</span><br><span style="font-family: 'courier new', monospace; ">login_x86_64 on / type tmpfs (rw)</span><br><span style="font-family: 'courier new', monospace; ">proc on /proc type proc (rw)</span><br><span style="font-family: 'courier new', monospace; ">sysfs on /sys type sysfs (rw)</span><br><span style="font-family: 'courier new', monospace; ">devpts on /dev/pts type devpts (rw,gid=5,mode=620)</span><br><span style="font-family: 'courier new', monospace; ">tmpfs on /dev/shm type tmpfs (rw)</span><br><span style="font-family: 'courier new', monospace; ">tmpfs on /var/tmp type tmpfs (rw,size=10m)</span><br><span style="font-family: 'courier new', monospace; ">/dev/sdb2 on /tmp type ext4 (rw,relatime,barrier=1,data=ordered)</span><br><span style="font-family: 'courier new', monospace; ">none on /proc/sys/fs/binfmt_misc type binfmt_misc (rw)</span><br><span style="font-family: 'courier new', monospace; ">sunrpc on /var/lib/nfs/rpc_pipefs type rpc_pipefs (rw)</span><br><span style="font-family: 'courier new', monospace; ">AFS on /afs type afs (rw)</span><br><span style="font-family: 'courier new', monospace; ">bl-nas1:/vol/hd00 on /N/hd00 type nfs (rw,nosuid,tcp,rsize=32768,wsize=32768,timeo=600,retrans=2,intr,addr=149.165.226.129)</span><br><span style="font-family: 'courier new', monospace; ">bl-nas1:/vol/hd01 on /N/hd01 type nfs (rw,nosuid,tcp,rsize=32768,wsize=32768,timeo=600,retrans=2,intr,addr=149.165.226.129)</span><br><span style="font-family: 'courier new', monospace; ">bl-nas2:/vol/hd02 on /N/hd02 type nfs (rw,nosuid,tcp,rsize=32768,wsize=32768,timeo=600,retrans=2,intr,addr=149.165.226.130)</span><br><span style="font-family: 'courier new', monospace; ">bl-nas2:/vol/hd03 on /N/hd03 type nfs (rw,nosuid,tcp,rsize=32768,wsize=32768,timeo=600,retrans=2,intr,addr=149.165.226.130)</span><br><span style="font-family: 'courier new', monospace; ">bl-nas1:/vol/hdln on /N/u type nfs (rw,nosuid,tcp,rsize=32768,wsize=32768,timeo=600,retrans=2,intr,addr=149.165.226.129)</span><br><span style="font-family: 'courier new', monospace; ">bl-nas2:/vol/soft on /N/soft type nfs (rw,nosuid,tcp,rsize=32768,wsize=32768,timeo=600,retrans=2,intr,addr=149.165.226.130)</span><br><span style="font-family: 'courier new', monospace; ">bl-nas1:/vol/logs on /N/logs type nfs (rw,nosuid,tcp,rsize=32768,wsize=32768,timeo=600,retrans=2,intr,addr=149.165.226.129)</span><br><span style="font-family: 'courier new', monospace; ">none on /dev/cpuset type cpuset (rw)</span><br><span style="font-family: 'courier new', monospace; ">dc-mds01.uits.indiana.edu:/dc on /N/dc type lustre (rw,localflock)</span><br><span style="font-family: 'courier new', monospace; ">149.165.235.173:/mds-wan/client on /N/dcwan type lustre (rw,localflock)</span><br></span></div></div><br></div><div class="gmail_extra"><br clear="all"><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></div><br><br><div class="gmail_quote">On Fri, May 24, 2013 at 1:29 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>They load fine for me. It is an SQLite database. I know that SQLlite can freeze on NFS if it's not configured properly.</div><div><br></div><div>Could you send me the output from these 3 commands.</div><div><br></div><div>ls -al <maker_output directory></div><div>df <maker_output directory></div><div>mount</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, 24 May, 2013 1:13 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">Subject: </span> Re: [maker-devel] Using maker with precomputed transcript / protein alignments<br></div></div></div><div><div><div><br></div><div dir="ltr"><div><div>I deleted the entire output directory before relaunching. No .db files are even created, only the mpi_blastdb directory with the genomic sequence data and corresponding index, before it hangs.<br><br></div>The GFF3 files are attached.<br><br></div>Thanks.<br></div><div class="gmail_extra"><br clear="all"><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></div><br><br><div class="gmail_quote">On Fri, May 24, 2013 at 12:57 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>Did you delete any *.db files in the maker.output directory first. If not do that, and check on the rerun if that file is growing in size. It is a database to hold the GFF3 file entries. It's final size should be ~ 2x the size of the combined GFF3 files. If it is growing, then it is not really frozen (you just need to give it more time). If it is not growing, send me your GFF3 files and I can try and duplicate the error.</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, 24 May, 2013 12:50 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">Subject: </span> Re: [maker-devel] Using maker with precomputed transcript / protein alignments<br></div></div></div><div><div><div><br></div><div dir="ltr">I installed BioPerl-1.6.901, rebuilt Maker, and re-launched the job. After running for 10-15 minutes, it seems to be hanging in the same place as before.<br></div><div class="gmail_extra"><br clear="all"><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></div><br><br><div class="gmail_quote">On Fri, May 24, 2013 at 11:38 AM, 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>That is the CPAN version and the last stable release on <a href="http://bioperl.org" target="_blank">bioperl.org</a>. Older version as well as the bio-perl live version will cause MAKER to fail. The both have issues with the Fasta indexing module that maker uses.</div><div><br></div><div><a href="http://search.cpan.org/CPAN/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.901.tar.gz" target="_blank">http://search.cpan.org/CPAN/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.901.tar.gz</a></div><div><br></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, 24 May, 2013 11:34 AM<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">Subject: </span> Re: [maker-devel] Using maker with precomputed transcript / protein alignments<br></div><div><div><div><br></div><div dir="ltr"><div>I'm not sure if a rebuild of Maker was necessary, but I tried running it just to be safe. It's complaining about Bio::Root::Version dependency not being met. Looking at the Build.PL file, it requires Bio::Root::Version version 1.006901. Is there really such a version, or should this be changed to 1.006 or 1.006001?<br><br></div>For now I'll change it to 1.006001 (the installed version) and proceed with another test.<br></div><div class="gmail_extra"><br clear="all"><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></div><br><br><div class="gmail_quote">On Fri, May 24, 2013 at 9:45 AM, 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><div style="font-family:Consolas;font-size:medium">
Could you run this command in the maker devel base directory.</div><div style="font-family:Consolas;font-size:medium"><br></div><div style="font-family:Consolas;font-size:medium">svn switch --relocate svn://<a href="http://malachite.genetics.utah.edu/maker/trunk" target="_blank">*</a>************</div><div style="font-family:Consolas;font-size:medium">
svn://<a href="http://topaz.genetics.utah.edu/maker/trunk" target="_blank">*</a>***************</div><div style="font-family:Consolas;font-size:medium"><br></div><div style="font-family:Consolas;font-size:medium">
Then do 'svn update', and then tell me what happens. Make sure to delete the and *.db files in the *.maker.output/ directory before retrying.</div></div><div style="font-family:Consolas;font-size:medium"><br></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, 24 May, 2013 9:10 AM<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> [maker-devel] Using maker with precomputed transcript / protein alignments<br></div><div><div><div><br></div><div dir="ltr"><div><div><div><div>Greetings!<br><br></div>I have some precomputed transcript and protein alignments that I would like to use with Maker. I have converted them into GFF3 format (see attached examples) and provided them to their corresponding entries (est_gff, altest_gff, protein_gff) in the maker_opts.ctl file.<br><br></div>Unfortunately, Maker seems to be getting caught up on processing these GFF3 files. I've tried running Maker 2.10 as well as the development version (checked out a few months ago--svn server isn't responding so I can't give a precise revision number), and in both cases Maker hangs while trying to create the GFF3 database. These are the last lines I see in STDERR when <b>--debug</b> is set.<br><br><div style="margin-left:40px"><span style="font-family: 'courier new', monospace; ">STATUS: Setting up database for any GFF3 input...</span><br><span style="font-family: 'courier new', monospace; ">Calling GFFDB::new at /N/u/dstandag/Mason/local/src/maker-dev/bin/maker line 587.</span><br></div><br></div>I can't find any documentation specifying any explicit requirements for the alignment-containing GFF3 input files. Maker output uses the pretty canonical <b>expressed_sequence_match</b>, <b>protein_match</b>, and <b>match_part</b> features for encoding alignments, and I have used this convention with my input (see attached examples). I have also double-checked that my examples are valid GFF3, so my guess is that Maker has additional constraints/expectations for certain fields in the GFF3 files (score column? required attributes?). Is this correct, and if so would you be able to point me toward any related documentation I may have missed?<br><br></div>Many thanks.<br clear="all"><div><div><div><div><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></div></div></div></div></div></div></div></div></div>
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