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

[zl c]

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

STACK: Widget::tblastx::parse
/spin1/home/linux/chenz11/program/maker/bin/../lib/Widget/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]


NIH/NHGRI
Building 50, Room 5531
50 SOUTH DR, MSC 8004
BETHESDA, MD 20892-8004
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