<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">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><br></div><div>On Dec 19, 2012, at 10:33 PM, indu khatri wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"><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><br></div>
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