[maker-devel] maker problem

[Carson Holt]

1. Make sure you are using the current CPAN version of BioPerl, and not BioPerl live.
2. Try installing a different version of BLAST incase the BLAST report is somehow not created correctly.
3. Make sure  TMP= in the maker_opts.ctl file is not set to a network mounted disk

—Carson


> On Jul 18, 2016, at 9:00 AM, Chuanlin Yin <yincl2013 at 126.com> wrote:
> 
> Thank you very much!
>  
> 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.
>  
> Thanks!
>  
> Best wishes!
> Ian
>  
> 2016-07-18 
> Chuanlin Yin
> 发件人：Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>>
> 发送时间：2016-07-18 22:53
> 主题：Re: [maker-devel] maker problem
> 收件人："Chuanlin Yin"<yincl2013 at 126.com <mailto:yincl2013 at 126.com>>
> 抄送："maker-devel"<maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
>  
> 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 <mailto: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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