[maker-devel] maker problem

[Carson Holt]

Also with when trying 1, 2, or 3, run just the failed contig as a separate job or the old archived files will be reused rather than regenerating following the change (because MAKER archives partial results in theVoid directory).

—Carson


> On Jul 18, 2016, at 9:03 AM, Carson Holt <carsonhh at gmail.com> wrote:
> 
> 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 <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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