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<DIV>Thank you very much!</DIV>
<DIV> </DIV>
<DIV>I know the error is saying that there is a hit with no HSPs, but why other
scaffolds are all OK except that one. I have checked that scaffold for many
times and the format is correct.</DIV>
<DIV> </DIV>
<DIV>Thanks!</DIV>
<DIV> </DIV>
<DIV>Best wishes!</DIV>
<DIV>Ian</DIV>
<DIV> </DIV>
<DIV style="FONT-SIZE: 10pt; FONT-FAMILY: Verdana; COLOR: #c0c0c0"
align=left>2016-07-18
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<SPAN id=_FlashSignName>Chuanlin Yin</SPAN> </DIV>
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<DIV><STRONG>发件人：</STRONG>Carson Holt <carsonhh@gmail.com></DIV>
<DIV><STRONG>发送时间：</STRONG>2016-07-18 22:53</DIV>
<DIV><STRONG>主题：</STRONG>Re: [maker-devel] maker problem</DIV>
<DIV><STRONG>收件人：</STRONG>"Chuanlin Yin"<yincl2013@126.com></DIV>
<DIV><STRONG>抄送：</STRONG>"maker-devel"<maker-devel@yandell-lab.org></DIV>
<DIV> </DIV>
<DIV>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><BR></DIV>
<DIV>Thanks,</DIV>
<DIV>Carson
<DIV><BR></DIV>
<DIV><BR>
<DIV>
<BLOCKQUOTE type="cite">
<DIV>On Jul 13, 2016, at 4:10 AM, Chuanlin Yin <<A
href="mailto:yincl2013@126.com">yincl2013@126.com</A>> wrote:</DIV><BR
class=Apple-interchange-newline>
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<DIV>
<DIV><FONT face="Times New Roman">Hello, </FONT></DIV>
<DIV><FONT face="Times New Roman"></FONT> </DIV>
<DIV><FONT
face="Times New Roman">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><FONT face="Times New Roman"></FONT> </DIV>
<DIV><FONT
face="Times New Roman">Here is a part of main error log: </FONT></DIV>
<BLOCKQUOTE style="MARGIN-RIGHT: 0px" dir=ltr>
<DIV><FONT face="Times New Roman">------------- EXCEPTION:
Bio::Root::Exception -------------<BR>MSG: Can't get HSPs: data not
collected.<BR>STACK: Error::throw<BR>STACK: Bio::Root::Root::throw
/usr/local/share/perl5/Bio/Root/Root.pm:449<BR>STACK:
Bio::Search::Hit::PhatHit::Base::hsps
/disk/home/yincl/software/maker/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552<BR>STACK:
Widget::blastx::keepers
/disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:190<BR>STACK:
Widget::blastx::parse
/disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:132<BR>STACK:
GI::blastx
/disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2622<BR>STACK:
GI::blastx
/disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2631<BR>STACK:
GI::reblast_merged_hits
/disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:445<BR>STACK:
GI::merge_resolve_hits
/disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:289<BR>STACK:
Process::MpiChunk::_go
/disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:2821<BR>STACK:
Process::MpiChunk::run
/disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:341<BR>STACK:
Process::MpiChunk::run_all
/disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:357<BR>STACK:
Process::MpiTiers::run_all
/disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287<BR>STACK:
Process::MpiTiers::run_all
/disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287<BR>STACK:
/disk/home/yincl/software/maker/maker/bin/maker:686<BR>-----------------------------------------------------------<BR>-->
rank=NA, hostname=localhost.localdomain<BR>--> rank=NA,
hostname=localhost.localdomain<BR>--> rank=NA,
hostname=localhost.localdomain<BR>ERROR: Failed while collecting blastx
reports<BR>ERROR: Chunk failed at level:9, tier_type:3<BR>FAILED
CONTIG:QPacbio.Hiseq_683</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face="Times New Roman">ERROR: Chunk failed at level:4,
tier_type:0<BR>FAILED CONTIG:QPacbio.Hiseq_683</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face="Times New Roman">examining contents of the fasta file and
run log</FONT></DIV></BLOCKQUOTE>
<DIV><FONT face="Times New Roman">Thanks! </FONT></DIV>
<DIV><FONT face="Times New Roman"></FONT> </DIV>
<DIV><FONT
face="Times New Roman">Best regards, </FONT></DIV>
<DIV><FONT face="Times New Roman">Ian </FONT></DIV>
<DIV><FONT
face="Times New Roman">Department of Entomology, College of Plant Protection, Nanjing Agricultural University </FONT></DIV>
<DIV><FONT
face="Times New Roman">No. 1, Weigang Road, Xuanwu District, Nanjing, Jiangsu 210095, China </FONT></DIV>
<DIV><FONT face="Times New Roman"></FONT> </DIV>
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