[maker-devel] maker problem

[Carson Holt]

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.

Thanks,
Carson  


> On Jul 13, 2016, at 4:10 AM, Chuanlin Yin <yincl2013 at 126.com> wrote:
> 
> 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  
>  
>  
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