[maker-devel] maker problem

[Chuanlin Yin]

Hello,  

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.  

Here is a part of main error log:   
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Can't get HSPs: data not collected.
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:449
STACK: Bio::Search::Hit::PhatHit::Base::hsps /disk/home/yincl/software/maker/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552
STACK: Widget::blastx::keepers /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:190
STACK: Widget::blastx::parse /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:132
STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2622
STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2631
STACK: GI::reblast_merged_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:445
STACK: GI::merge_resolve_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:289
STACK: Process::MpiChunk::_go /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:2821
STACK: Process::MpiChunk::run /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:341
STACK: Process::MpiChunk::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:357
STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287
STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287
STACK: /disk/home/yincl/software/maker/maker/bin/maker:686
-----------------------------------------------------------
--> rank=NA, hostname=localhost.localdomain
--> rank=NA, hostname=localhost.localdomain
--> rank=NA, hostname=localhost.localdomain
ERROR: Failed while collecting blastx reports
ERROR: Chunk failed at level:9, tier_type:3
FAILED CONTIG:QPacbio.Hiseq_683

ERROR: Chunk failed at level:4, tier_type:0
FAILED CONTIG:QPacbio.Hiseq_683

examining contents of the fasta file and run log
Thanks!  

Best regards,  
Ian  
Department of Entomology, College of Plant Protection, Nanjing Agricultural University   
No. 1, Weigang Road, Xuanwu District, Nanjing, Jiangsu 210095, China  
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20160713/688e9f05/attachment-0002.html>