MSG: Can't get HSPs: data not collected.

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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 [[hidden email]]


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

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Re: MSG: Can't get HSPs: data not collected.

Carson Holt-2
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 <[hidden email]> 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
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 [[hidden email]]


NIH/NHGRI
Building 50, Room 5531
50 SOUTH DR, MSC 8004 
BETHESDA, MD 20892-8004
_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
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Re: MSG: Can't get HSPs: data not collected.

Carson Holt-2
I’m glad it fixed it.

—Carson

On Sep 6, 2017, at 8:27 PM, zl c <[hidden email]> wrote:

Hi Carson,

I try blast-2.6.0+ and it works. Thank you very much.

Thanks
Zelin Chen

--------------------------------------------
Zelin Chen [[hidden email]]

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 <[hidden email]> 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 <[hidden email]> 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
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 [[hidden email]]


NIH/NHGRI
Building 50, Room 5531
50 SOUTH DR, MSC 8004 
BETHESDA, MD 20892-8004
_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org