<div dir="ltr">Hii Daniel<div><br></div><div style>It was failing for 1 contig only. The contig length is approx 1.5 Mb. Excluding that contig the run was successful. I am using RepeatMasker libraries only for masking the sequences. I used Fusarium graminearum species as Augustus model species.</div>
<div style><br></div><div style>I have one more query about Maker annotation results. Only augustus as gene predictor can be a good predictor for annotations or I have to retrain it using the previous results from first runs of MAKER in order to get validated gene models.</div>
<div style><br></div><div style>Thanks.</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Fri, Dec 21, 2012 at 9:23 AM, Daniel Ence <span dir="ltr"><<a href="mailto:dence@genetics.utah.edu" target="_blank">dence@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>
<div style="direction:ltr;font-size:10pt;font-family:Tahoma">Hi Indu,
<div><br>
</div>
<div>I'm going to echo Barry's request for more details about this problem too. Does augustus fail on more than one contig or does it fail repeatedly on the same contig? If its only contig, how big is that contig and is it possibly all masked out by repeatmasker?
If you exclude that one contig, do the rest run successfully? What are you using to mask the repeats in the genome? Which augustus model are you using, and how did you choose that model?</div>
<div><br>
</div>
<div>Thanks,</div>
<div>Daniel</div>
<div>
<div><br>
<div><font>
<div>Daniel Ence<br>
Graduate Student<br>
Eccles Institute of Human Genetics<br>
University of Utah<div class="im"><br>
15 North 2030 East, Room 2100<br>
Salt Lake City, UT 84112-5330</div></div>
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<div style="direction:ltr"><font face="Tahoma" color="#000000"><b>From:</b> indu khatri [<a href="mailto:indu2287@gmail.com" target="_blank">indu2287@gmail.com</a>]<br>
<b>Sent:</b> Thursday, December 20, 2012 12:41 PM<br>
<b>To:</b> <a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a><br>
<b>Cc:</b> Barry Moore; Daniel Ence<br>
<b>Subject:</b> Fwd: [maker-devel] query<br>
</font><br>
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<div></div>
<div>
<div dir="ltr"><br>
<span style="font-family:arial,sans-serif;font-size:12.800000190734863px">Thanks Daniel and Barry for your reply.</span><br>
<div class="gmail_quote">
<div dir="ltr">
<div><br style="font-family:arial,sans-serif;font-size:12.800000190734863px">
<span style="font-family:arial,sans-serif;font-size:12.800000190734863px">I have sorted out that problem. It was due to very distant homolog species I chose for training.</span><br style="font-family:arial,sans-serif;font-size:12.800000190734863px">
<br style="font-family:arial,sans-serif;font-size:12.800000190734863px">
<span style="font-family:arial,sans-serif;font-size:12.800000190734863px">But, I am still getting some errors while running MAKER.</span><br style="font-family:arial,sans-serif;font-size:12.800000190734863px">
<span style="font-family:arial,sans-serif;font-size:12.800000190734863px">ERROR: Augustus failed</span><br style="font-family:arial,sans-serif;font-size:12.800000190734863px">
<span style="font-family:arial,sans-serif;font-size:12.800000190734863px">ERROR: Failed while preparing ab-inits</span><br style="font-family:arial,sans-serif;font-size:12.800000190734863px">
<span style="font-family:arial,sans-serif;font-size:12.800000190734863px">ERROR: Chunk failed at level:4, tier_type:0</span><br style="font-family:arial,sans-serif;font-size:12.800000190734863px">
<span style="font-family:arial,sans-serif;font-size:12.800000190734863px">FAILED CONTIG</span><br style="font-family:arial,sans-serif;font-size:12.800000190734863px">
<br style="font-family:arial,sans-serif;font-size:12.800000190734863px">
<span style="font-family:arial,sans-serif;font-size:12.800000190734863px">Can you please tell me what is the possible reason for this error?</span><br style="font-family:arial,sans-serif;font-size:12.800000190734863px">
<br style="font-family:arial,sans-serif;font-size:12.800000190734863px">
<span style="font-family:arial,sans-serif;font-size:12.800000190734863px">Thanks in advance.</span><br style="font-family:arial,sans-serif;font-size:12.800000190734863px">
<br style="font-family:arial,sans-serif;font-size:12.800000190734863px">
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<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On Thu, Dec 20, 2012 at 10:50 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 Indu,
<div><br>
</div>
<div>The error output as Daniel suggested would be great and also a bit more detail on the problem. Is it stalled on a long contig - how long? How long has it been stalled for? How many cpus are you running? Are you running under MPI? How big is the protein
evidence file? If you're using the altest function for your ESTs then it's running tblastx which is up to 10X slower than blastn with regular ESTs, is it possible that you're stuck on tblastx?</div>
<div><br>
</div>
<div>Finally, it can help if you isolate the problem a bit. Can you run successfully on any of your contigs by running single contigs in your fasta file? If it's stalled on a large contig, iteratively cut it in half and see if the problem isolates to one
part of the contig.</div>
<div><br>
</div>
<div>B<br>
<div>
<div>
<div>
<div><br>
</div>
<div>On Dec 19, 2012, at 10:33 PM, indu khatri wrote:</div>
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<div dir="ltr"><span style="font-family:arial,sans-serif;font-size:12.800000190734863px"> Hello Maker-devel</span><br style="font-family:arial,sans-serif;font-size:12.800000190734863px">
<span style="font-family:arial,sans-serif;font-size:12.800000190734863px"> Thanks for adding me to the list. I am new to this field.</span><span style="font-family:arial,sans-serif;font-size:12.800000190734863px"> I have a query regarding maker annotation.</span>
<div><span style="font-family:arial,sans-serif;font-size:12.800000190734863px"> I have assembled a fungal Genome with 1590 contigs and was trying to</span><br style="font-family:arial,sans-serif;font-size:12.800000190734863px">
<span style="font-family:arial,sans-serif;font-size:12.800000190734863px"> annotate it using MAKER pipeline. I only have paired end WGS sequence from</span><br style="font-family:arial,sans-serif;font-size:12.800000190734863px">
<span style="font-family:arial,sans-serif;font-size:12.800000190734863px"> Illumina HiSeq sequencing which were assembled using CLCbio. I dont have</span><br style="font-family:arial,sans-serif;font-size:12.800000190734863px">
<span style="font-family:arial,sans-serif;font-size:12.800000190734863px"> any transcriptome data. I am using ESTs of a closer species for validation</span><br style="font-family:arial,sans-serif;font-size:12.800000190734863px">
<span style="font-family:arial,sans-serif;font-size:12.800000190734863px"> and similarly the protein sequences. I have started annotation but the</span><br style="font-family:arial,sans-serif;font-size:12.800000190734863px">
<span style="font-family:arial,sans-serif;font-size:12.800000190734863px"> problem is the pipeline gets stuck to the first contig on blastx step and</span><br style="font-family:arial,sans-serif;font-size:12.800000190734863px">
<span style="font-family:arial,sans-serif;font-size:12.800000190734863px"> doesn't move further. I could not make out the problem. Can you please help</span><br style="font-family:arial,sans-serif;font-size:12.800000190734863px">
<span style="font-family:arial,sans-serif;font-size:12.800000190734863px"> me out of this.</span>
<div><span style="font-family:arial,sans-serif;font-size:12.800000190734863px"><br>
</span></div>
<div><span style="font-family:arial,sans-serif;font-size:12.800000190734863px">Thanks and regards</span><br clear="all">
<div><br>
</div>
-- <br>
<a href="https://mail.google.com/mail/?ui=2&ik=8ec2492227&view=att&th=130da06dcd7f8e6a&attid=0.0.1&disp=emb&realattid=b8967bbd6e93d49d_0.25&zw" target="_blank"></a>Indu Khatri<br>
PhD Research Fellow,
<div>C/o Dr. Srikrishna Subramanian<br>
Institute of Microbial Technology,<br>
Chandigarh-160036,<br>
India<br>
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<div>--------------------------------------------</div>
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-- <br>
<a href="https://mail.google.com/mail/?ui=2&ik=8ec2492227&view=att&th=130da06dcd7f8e6a&attid=0.0.1&disp=emb&realattid=b8967bbd6e93d49d_0.25&zw" target="_blank"></a>Indu Khatri<br>
<div>Institute of Microbial Technology,<br>
Chandigarh-160036,<br>
India<br>
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Institute of Microbial Technology,<br>
<div>Chandigarh-160036,<br>
India<br>
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<br></blockquote></div><br><br clear="all"><div><br></div>-- <br><a href="https://mail.google.com/mail/?ui=2&ik=8ec2492227&view=att&th=130da06dcd7f8e6a&attid=0.0.1&disp=emb&realattid=b8967bbd6e93d49d_0.25&zw" target="_blank"></a>Indu Khatri<br>
PhD Research Fellow,<div>C/o Dr. Srikrishna Subramanian<br>Institute of Microbial Technology,<br>Chandigarh-160036,<br>India<br><br></div>
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