<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">I’m glad it fixed it.<div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Sep 6, 2017, at 8:27 PM, zl c <<a href="mailto:chzelin@gmail.com" class="">chzelin@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class="">Hi Carson,</div><div class=""><br class=""></div>I try blast-2.6.0+ and it works. Thank you very much.<div class=""><br class=""></div><div class="">Thanks</div><div class="">Zelin Chen</div><div class="gmail_extra"><br clear="all" class=""><div class=""><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div class="">--------------------------------------------</div>Zelin Chen [<a href="mailto:chzelin@gmail.com" target="_blank" class="">chzelin@gmail.com</a>]<br class=""></div><div class=""><br class=""></div><div class=""><div class="">NIH/NHGRI</div><div class=""><span style="font-family: Verdana, Geneva, sans-serif; font-size: 12px;" class="">Building 50, Room 5531</span><br style="font-family: Verdana, Geneva, sans-serif; font-size: 12px;" class=""><span style="font-family: Verdana, Geneva, sans-serif; font-size: 12px;" class="">50 SOUTH DR, MSC 8004 </span><br style="font-family: Verdana, Geneva, sans-serif; font-size: 12px;" class=""><span style="font-family: Verdana, Geneva, sans-serif; font-size: 12px;" class="">BETHESDA, MD 20892-8004</span></div></div></div></div></div></div></div>
<br class=""><div class="gmail_quote">On Tue, Sep 5, 2017 at 6:04 PM, Carson Holt <span dir="ltr" class=""><<a href="mailto:carsonhh@gmail.com" target="_blank" class="">carsonhh@gmail.com</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word" class=""><div class="">The last time I saw this error, it was with blast-2.5.1+. Not sure if the failure you are seeing is the same one. It was caused by a truncated BLAST report (so some results have no alignments). I have an open ticket with the BLAST development group. I never received confirmation that it is fixed, but you can try updating to 2.6 and see if that fixes it. If not, switch to legacy BLAST (not blast plus) and see if it goes away.</div><div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""></div><div class=""><br class=""><div class=""><blockquote type="cite" class=""><div class="">On Sep 5, 2017, at 7:59 AM, zl c <<a href="mailto:chzelin@gmail.com" target="_blank" class="">chzelin@gmail.com</a>> wrote:</div><br class="m_8995632240918925060Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hello,<div class=""><br class=""></div><div class="">I run maker for most sequences successfully but fail some long sequences. The error is: </div><div class=""><br class=""></div><div class=""><div style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">Widget::tblastx:</span></div><div style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">/usr/local/apps/blast/ncbi-<wbr class="">blast-2.5.0+/bin/tblastx -db db.778415-832259.for_tblastx.<wbr class="">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></div><div style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">#-----------------------------<wbr class="">--#</span></div><div style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150);min-height:14px" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class=""></div><div style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">------------- EXCEPTION: Bio::Root::Exception -------------</span></div><div style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">MSG: Can't get HSPs: data not collected.</span></div><div style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">STACK: Error::throw</span></div><div style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">STACK: Bio::Root::Root::throw /usr/local/Perl/5.18.2/lib/<wbr class="">perl5/site_perl/5.18.2/Bio/<wbr class="">Root/Root.pm:486</span></div><div style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">STACK: Bio::Search::Hit::PhatHit::<wbr class="">Base::hsps /spin1/home/linux/chenz11/<wbr class="">program/maker/bin/../lib/Bio/<wbr class="">Search/Hit/PhatHit/Base.pm:552</span></div><div style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">STACK: Widget::tblastx::keepers /spin1/home/linux/chenz11/<wbr class="">program/maker/bin/../lib/<wbr class="">Widget/<a href="http://tblastx.pm:192/" target="_blank" class="">tblastx.pm:192</a></span></div><div style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">STACK: Widget::tblastx::parse /spin1/home/linux/chenz11/<wbr class="">program/maker/bin/../lib/<wbr class="">Widget/<a href="http://tblastx.pm:133/" target="_blank" class="">tblastx.pm:133</a></span></div><div style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">STACK: GI::tblastx /spin1/home/linux/chenz11/<wbr class="">program/maker/bin/../lib/GI.<wbr class="">pm:3251</span></div><div style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">STACK: GI::tblastx /spin1/home/linux/chenz11/<wbr class="">program/maker/bin/../lib/GI.<wbr class="">pm:3260</span></div><div style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">STACK: GI::reblast_merged_hits /spin1/home/linux/chenz11/<wbr class="">program/maker/bin/../lib/GI.<wbr class="">pm:471</span></div><div style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">STACK: GI::merge_resolve_hits /spin1/home/linux/chenz11/<wbr class="">program/maker/bin/../lib/GI.<wbr class="">pm:291</span></div><div style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">STACK: Process::MpiChunk::_go /spin1/home/linux/chenz11/<wbr class="">program/maker/bin/../lib/<wbr class="">Process/MpiChunk.pm:2320</span></div><div style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">STACK: Process::MpiChunk::run /spin1/home/linux/chenz11/<wbr class="">program/maker/bin/../lib/<wbr class="">Process/MpiChunk.pm:340</span></div><div style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">STACK: Process::MpiChunk::run_all /spin1/home/linux/chenz11/<wbr class="">program/maker/bin/../lib/<wbr class="">Process/MpiChunk.pm:356</span></div><div style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">STACK: Process::MpiTiers::run_all /spin1/home/linux/chenz11/<wbr class="">program/maker/bin/../lib/<wbr class="">Process/MpiTiers.pm:287</span></div><div style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">STACK: Process::MpiTiers::run_all /spin1/home/linux/chenz11/<wbr class="">program/maker/bin/../lib/<wbr class="">Process/MpiTiers.pm:287</span></div><div style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">STACK: /home/chenz11/program/maker/<wbr class="">bin/maker:695</span></div><div style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">------------------------------<wbr class="">-----------------------------</span></div><div style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">--> rank=NA, hostname=cn3544</span></div><div style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">--> rank=NA, hostname=cn3544</span></div><div style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">--> rank=NA, hostname=cn3544</span></div><div style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">--> rank=NA, hostname=cn3544</span></div><div style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">ERROR: Failed while collecting tblastx reports</span></div><div style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">ERROR: Chunk failed at level:5, tier_type:3</span></div><div style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">FAILED CONTIG:tig00011625_arrow</span></div><div style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150);min-height:14px" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class=""></div><div style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">ERROR: Chunk failed at level:4, tier_type:0</span></div><div style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">FAILED CONTIG:tig00011625_arrow</span></div><div style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150);min-height:14px" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class=""></div><div style="margin:0px;font-size:12px;line-height:normal;font-family:Menlo;background-color:rgb(255,222,150)" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">examining contents of the fasta file and run log</span></div></div><div class=""><br class=""></div><div class="">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 class=""> </div><div class="">Thanks,</div><div class="">Zelin</div><div class=""><br clear="all" class=""><div class=""><div class="m_8995632240918925060gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div class="">------------------------------<wbr class="">--------------</div>Zelin Chen [<a href="mailto:chzelin@gmail.com" target="_blank" class="">chzelin@gmail.com</a>]<br class=""><br class=""></div><div class=""><br class=""></div><div class=""><div class="">NIH/NHGRI</div><div class=""><span style="font-family:Verdana,Geneva,sans-serif;font-size:12px" class="">Building 50, Room 5531</span><br style="font-family:Verdana,Geneva,sans-serif;font-size:12px" class=""><span style="font-family:Verdana,Geneva,sans-serif;font-size:12px" class="">50 SOUTH DR, MSC 8004 </span><br style="font-family:Verdana,Geneva,sans-serif;font-size:12px" class=""><span style="font-family:Verdana,Geneva,sans-serif;font-size:12px" class="">BETHESDA, MD 20892-8004</span></div></div></div></div></div></div></div>
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