[maker-devel] maker problem

Mon Jul 18 11:58:46 MDT 2016

Nothing specific I’m aware. Their error is occurring immediately following the blast report parse. The hit is defined, but the hash key of the object holding the HSPs is not defined.

Half the time I see an error that come up through the BioPerl Bio::Root::Root::throw mechanism it goes away when the user installs the current CPAN version of BioPerl (they either have really old BioPerl or are using the live version). So I always have the user check that first. The other half of the time it ends up being an IO error (truncated file because they used NFS for temporary file space). Truncated can cause failures in multiple ways.

Then less often it is a blast issue (there are a handful of subversions of blast+ that give frequent failures).

—Carson

> On Jul 18, 2016, at 11:46 AM, Fields, Christopher J <cjfields at illinois.edu> wrote:
> 
> 
>> On Jul 18, 2016, at 10:03 AM, Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>> wrote:
>> 
>> 1. Make sure you are using the current CPAN version of BioPerl, and not BioPerl live.
> 
> Just curious, is there anything broken w/ bioperl-live we need to know about?  We’re about to release BioPerl v1.7.0 (I’m already on RC5), it would be nice to know if we’re missing anything that would potentially break downstream applications.
> 
> chris
> 
>> 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 <mailto: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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