<div dir="ltr">Hello,<div><br></div><div>I run maker for most sequences successfully but fail some long sequences. The error is: </div><div><br></div><div><p style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)"><span style="font-variant-ligatures:no-common-ligatures">Widget::tblastx:</span></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)"><span style="font-variant-ligatures:no-common-ligatures">/usr/local/apps/blast/ncbi-blast-2.5.0+/bin/tblastx -db db.778415-832259.for_tblastx.fasta -query ...778415.832259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -dbsize 1000 -searchsp 500000000 -num_threads 16 -lcase_masking -seg yes -soft_masking true -show_gis -out   OUT.tblastx</span></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)"><span style="font-variant-ligatures:no-common-ligatures">#-------------------------------#</span></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150);min-height:14px"><span style="font-variant-ligatures:no-common-ligatures"></span><br></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)"><span style="font-variant-ligatures:no-common-ligatures">------------- EXCEPTION: Bio::Root::Exception -------------</span></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)"><span style="font-variant-ligatures:no-common-ligatures">MSG: Can't get HSPs: data not collected.</span></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)"><span style="font-variant-ligatures:no-common-ligatures">STACK: Error::throw</span></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)"><span style="font-variant-ligatures:no-common-ligatures">STACK: Bio::Root::Root::throw /usr/local/Perl/5.18.2/lib/perl5/site_perl/5.18.2/Bio/Root/Root.pm:486</span></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)"><span style="font-variant-ligatures:no-common-ligatures">STACK: Bio::Search::Hit::PhatHit::Base::hsps /spin1/home/linux/chenz11/program/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552</span></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)"><span style="font-variant-ligatures:no-common-ligatures">STACK: Widget::tblastx::keepers /spin1/home/linux/chenz11/program/maker/bin/../lib/Widget/<a href="http://tblastx.pm:192">tblastx.pm:192</a></span></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)"><span style="font-variant-ligatures:no-common-ligatures">STACK: Widget::tblastx::parse /spin1/home/linux/chenz11/program/maker/bin/../lib/Widget/<a href="http://tblastx.pm:133">tblastx.pm:133</a></span></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)"><span style="font-variant-ligatures:no-common-ligatures">STACK: GI::tblastx /spin1/home/linux/chenz11/program/maker/bin/../lib/GI.pm:3251</span></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)"><span style="font-variant-ligatures:no-common-ligatures">STACK: GI::tblastx /spin1/home/linux/chenz11/program/maker/bin/../lib/GI.pm:3260</span></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)"><span style="font-variant-ligatures:no-common-ligatures">STACK: GI::reblast_merged_hits /spin1/home/linux/chenz11/program/maker/bin/../lib/GI.pm:471</span></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)"><span style="font-variant-ligatures:no-common-ligatures">STACK: GI::merge_resolve_hits /spin1/home/linux/chenz11/program/maker/bin/../lib/GI.pm:291</span></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)"><span style="font-variant-ligatures:no-common-ligatures">STACK: Process::MpiChunk::_go /spin1/home/linux/chenz11/program/maker/bin/../lib/Process/MpiChunk.pm:2320</span></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)"><span style="font-variant-ligatures:no-common-ligatures">STACK: Process::MpiChunk::run /spin1/home/linux/chenz11/program/maker/bin/../lib/Process/MpiChunk.pm:340</span></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)"><span style="font-variant-ligatures:no-common-ligatures">STACK: Process::MpiChunk::run_all /spin1/home/linux/chenz11/program/maker/bin/../lib/Process/MpiChunk.pm:356</span></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)"><span style="font-variant-ligatures:no-common-ligatures">STACK: Process::MpiTiers::run_all /spin1/home/linux/chenz11/program/maker/bin/../lib/Process/MpiTiers.pm:287</span></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)"><span style="font-variant-ligatures:no-common-ligatures">STACK: Process::MpiTiers::run_all /spin1/home/linux/chenz11/program/maker/bin/../lib/Process/MpiTiers.pm:287</span></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)"><span style="font-variant-ligatures:no-common-ligatures">STACK: /home/chenz11/program/maker/bin/maker:695</span></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)"><span style="font-variant-ligatures:no-common-ligatures">-----------------------------------------------------------</span></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)"><span style="font-variant-ligatures:no-common-ligatures">--> rank=NA, hostname=cn3544</span></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)"><span style="font-variant-ligatures:no-common-ligatures">--> rank=NA, hostname=cn3544</span></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)"><span style="font-variant-ligatures:no-common-ligatures">--> rank=NA, hostname=cn3544</span></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)"><span style="font-variant-ligatures:no-common-ligatures">--> rank=NA, hostname=cn3544</span></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)"><span style="font-variant-ligatures:no-common-ligatures">ERROR: Failed while collecting tblastx reports</span></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)"><span style="font-variant-ligatures:no-common-ligatures">ERROR: Chunk failed at level:5, tier_type:3</span></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)"><span style="font-variant-ligatures:no-common-ligatures">FAILED CONTIG:tig00011625_arrow</span></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150);min-height:14px"><span style="font-variant-ligatures:no-common-ligatures"></span><br></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)"><span style="font-variant-ligatures:no-common-ligatures">ERROR: Chunk failed at level:4, tier_type:0</span></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)"><span style="font-variant-ligatures:no-common-ligatures">FAILED CONTIG:tig00011625_arrow</span></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150);min-height:14px"><span style="font-variant-ligatures:no-common-ligatures"></span><br></p>
<p style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)"><span style="font-variant-ligatures:no-common-ligatures">examining contents of the fasta file and run log</span></p></div><div><br></div><div>I've read a relative thread on the google group and checked my tblastx output. I found that the number of HSPs should be larger than 1000,000, but only output 1000,000, which make some alignments have no HSPs. Is there any setting that could solve the problem?</div><div> </div><div>Thanks,</div><div>Zelin</div><div><br clear="all"><div><div class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div>--------------------------------------------</div>Zelin Chen [<a href="mailto:chzelin@gmail.com" target="_blank">chzelin@gmail.com</a>]<br><br></div><div><br></div><div><div>NIH/NHGRI</div><div><span style="color:rgb(0,0,0);font-family:Verdana,Geneva,sans-serif;font-size:12px">Building 50, Room 5531</span><br style="color:rgb(0,0,0);font-family:Verdana,Geneva,sans-serif;font-size:12px"><span style="color:rgb(0,0,0);font-family:Verdana,Geneva,sans-serif;font-size:12px">50 SOUTH DR, MSC 8004 </span><br style="color:rgb(0,0,0);font-family:Verdana,Geneva,sans-serif;font-size:12px"><span style="color:rgb(0,0,0);font-family:Verdana,Geneva,sans-serif;font-size:12px">BETHESDA, MD 20892-8004</span></div></div></div></div></div></div></div>
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