<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="">The error is saying that there is a hit with no HSPs. Make sure you are using the current CPAN version of BioPerl, and not BioPerl live. Also you can try a different version of BLAST if the BLAST report is somehow not created correctly. Finally do not set your TMP= location to a network mounted disk (on many clusters your home directory is network mounted). This will cause IO errors and partial result files. I can’t tell what your temporary directory is set to because your STDERR is truncated.<div class=""><br class=""></div><div class="">Thanks,</div><div class="">Carson <div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Jul 13, 2016, at 4:10 AM, Chuanlin Yin <<a href="mailto:yincl2013@126.com" class="">yincl2013@126.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><stationery style="font-family: 微软雅黑; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><div class=""><div class=""><font face="Times New Roman" class="">Hello, </font></div><div class=""><font face="Times New Roman" class=""></font> </div><div class=""><font face="Times New Roman" class="">When I use the maker for geomic annotation pipeline, I met a very big problem. My genome has 7282 scaffolds, all is success but for one scaffold is failed. I don‘t konw why and I have check the log, but I still can't fix the problem. So I need you help, and I will appreciate it very much. </font></div><div class=""><font face="Times New Roman" class=""></font> </div><div class=""><font face="Times New Roman" class="">Here is a part of main error log: </font></div><blockquote dir="ltr" style="margin-right: 0px;" class=""><div class=""><font face="Times New Roman" class="">------------- EXCEPTION: Bio::Root::Exception -------------<br class="">MSG: Can't get HSPs: data not collected.<br class="">STACK: Error::throw<br class="">STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:449<br class="">STACK: Bio::Search::Hit::PhatHit::Base::hsps /disk/home/yincl/software/maker/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552<br class="">STACK: Widget::blastx::keepers /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:190<br class="">STACK: Widget::blastx::parse /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:132<br class="">STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2622<br class="">STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2631<br class="">STACK: GI::reblast_merged_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:445<br class="">STACK: GI::merge_resolve_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:289<br class="">STACK: Process::MpiChunk::_go /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:2821<br class="">STACK: Process::MpiChunk::run /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:341<br class="">STACK: Process::MpiChunk::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:357<br class="">STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287<br class="">STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287<br class="">STACK: /disk/home/yincl/software/maker/maker/bin/maker:686<br class="">-----------------------------------------------------------<br class="">--> rank=NA, hostname=localhost.localdomain<br class="">--> rank=NA, hostname=localhost.localdomain<br class="">--> rank=NA, hostname=localhost.localdomain<br class="">ERROR: Failed while collecting blastx reports<br class="">ERROR: Chunk failed at level:9, tier_type:3<br class="">FAILED CONTIG:QPacbio.Hiseq_683</font></div><div class=""> </div><div class=""><font face="Times New Roman" class="">ERROR: Chunk failed at level:4, tier_type:0<br class="">FAILED CONTIG:QPacbio.Hiseq_683</font></div><div class=""> </div><div class=""><font face="Times New Roman" class="">examining contents of the fasta file and run log</font></div></blockquote><div class=""><font face="Times New Roman" class="">Thanks! </font></div><div class=""><font face="Times New Roman" class=""></font> </div><div class=""><font face="Times New Roman" class="">Best regards, </font></div><div class=""><font face="Times New Roman" class="">Ian </font></div><div class=""><font face="Times New Roman" class="">Department of Entomology, College of Plant Protection, Nanjing Agricultural University </font></div><div class=""><font face="Times New Roman" class="">No. 1, Weigang Road, Xuanwu District, Nanjing, Jiangsu 210095, China </font></div><div class=""><font face="Times New Roman" class=""></font> </div><div class=""><font face="Times New Roman" class=""></font> </div></div></stationery><span style="font-family: 微软雅黑; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">_______________________________________________</span><br style="font-family: 微软雅黑; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="font-family: 微软雅黑; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">maker-devel mailing list</span><br style="font-family: 微软雅黑; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><a href="mailto:maker-devel@box290.bluehost.com" style="font-family: 微软雅黑; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">maker-devel@box290.bluehost.com</a><br style="font-family: 微软雅黑; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org" style="font-family: 微软雅黑; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a></div></blockquote></div><br class=""></div></div></body></html>