[maker-devel] MSG: Can't get HSPs: data not collected.

[Carson Holt]

I’m glad it fixed it.

—Carson

> On Sep 6, 2017, at 8:27 PM, zl c <chzelin at gmail.com> wrote:
> 
> Hi Carson,
> 
> I try blast-2.6.0+ and it works. Thank you very much.
> 
> Thanks
> Zelin Chen
> 
> --------------------------------------------
> Zelin Chen [chzelin at gmail.com <mailto:chzelin at gmail.com>]
> 
> NIH/NHGRI
> Building 50, Room 5531
> 50 SOUTH DR, MSC 8004 
> BETHESDA, MD 20892-8004
> 
> On Tue, Sep 5, 2017 at 6:04 PM, Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>> wrote:
> The last time I saw this error, it was with blast-2.5.1+. Not sure if the failure you are seeing is the same one. It was caused by a truncated BLAST report (so some results have no alignments). I have an open ticket with the BLAST development group. I never received confirmation that it is fixed, but you can try updating to 2.6 and see if that fixes it.  If not, switch to legacy BLAST (not blast plus) and see if it goes away.
> 
> —Carson
> 
> 
>> On Sep 5, 2017, at 7:59 AM, zl c <chzelin at gmail.com <mailto:chzelin at gmail.com>> wrote:
>> 
>> Hello,
>> 
>> I run maker for most sequences successfully but fail some long sequences. The error is: 
>> 
>> Widget::tblastx:
>> /usr/local/apps/blast/ncbi-blast-2.5.0+/bin/tblastx -db db.778415-832259.for_tblastx.fasta -query ...778415.832259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -dbsize 1000 -searchsp 500000000 -num_threads 16 -lcase_masking -seg yes -soft_masking true -show_gis -out   OUT.tblastx
>> #-------------------------------#
>> 
>> ------------- EXCEPTION: Bio::Root::Exception -------------
>> MSG: Can't get HSPs: data not collected.
>> STACK: Error::throw
>> STACK: Bio::Root::Root::throw /usr/local/Perl/5.18.2/lib/perl5/site_perl/5.18.2/Bio/Root/Root.pm:486
>> STACK: Bio::Search::Hit::PhatHit::Base::hsps /spin1/home/linux/chenz11/program/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552
>> STACK: Widget::tblastx::keepers /spin1/home/linux/chenz11/program/maker/bin/../lib/Widget/tblastx.pm:192 <http://tblastx.pm:192/>
>> STACK: Widget::tblastx::parse /spin1/home/linux/chenz11/program/maker/bin/../lib/Widget/tblastx.pm:133 <http://tblastx.pm:133/>
>> STACK: GI::tblastx /spin1/home/linux/chenz11/program/maker/bin/../lib/GI.pm:3251
>> STACK: GI::tblastx /spin1/home/linux/chenz11/program/maker/bin/../lib/GI.pm:3260
>> STACK: GI::reblast_merged_hits /spin1/home/linux/chenz11/program/maker/bin/../lib/GI.pm:471
>> STACK: GI::merge_resolve_hits /spin1/home/linux/chenz11/program/maker/bin/../lib/GI.pm:291
>> STACK: Process::MpiChunk::_go /spin1/home/linux/chenz11/program/maker/bin/../lib/Process/MpiChunk.pm:2320
>> STACK: Process::MpiChunk::run /spin1/home/linux/chenz11/program/maker/bin/../lib/Process/MpiChunk.pm:340
>> STACK: Process::MpiChunk::run_all /spin1/home/linux/chenz11/program/maker/bin/../lib/Process/MpiChunk.pm:356
>> STACK: Process::MpiTiers::run_all /spin1/home/linux/chenz11/program/maker/bin/../lib/Process/MpiTiers.pm:287
>> STACK: Process::MpiTiers::run_all /spin1/home/linux/chenz11/program/maker/bin/../lib/Process/MpiTiers.pm:287
>> STACK: /home/chenz11/program/maker/bin/maker:695
>> -----------------------------------------------------------
>> --> rank=NA, hostname=cn3544
>> --> rank=NA, hostname=cn3544
>> --> rank=NA, hostname=cn3544
>> --> rank=NA, hostname=cn3544
>> ERROR: Failed while collecting tblastx reports
>> ERROR: Chunk failed at level:5, tier_type:3
>> FAILED CONTIG:tig00011625_arrow
>> 
>> ERROR: Chunk failed at level:4, tier_type:0
>> FAILED CONTIG:tig00011625_arrow
>> 
>> examining contents of the fasta file and run log
>> 
>> I've read a relative thread on the google group and checked my tblastx output. I found that the number of HSPs should be larger than 1000,000, but only output 1000,000, which make some alignments have no HSPs. Is there any setting that could solve the problem?
>>  
>> Thanks,
>> Zelin
>> 
>> --------------------------------------------
>> Zelin Chen [chzelin at gmail.com <mailto:chzelin at gmail.com>]
>> 
>> 
>> NIH/NHGRI
>> Building 50, Room 5531
>> 50 SOUTH DR, MSC 8004 
>> BETHESDA, MD 20892-8004
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