[ensembl-dev] Ensembl Genomes BLAST: Parsing failed ERROR

Rafael Hernández rafahd87 at gmail.com
Mon Mar 4 12:48:55 GMT 2013


Hi Ensembl devs!

I've got some troubles with Ensembl Genomes BLAST (for fungi, protists, ...)

When I run the BLAST tool it crashes after the alignment step, when tries
to parse the *blastall* results.
I've repeated manually the *blastall* command (below these lines) and it
works correctly, returning the alignments, so the error should be after
this step...

export
PATH=/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/Applications/Server.app/Contents/ServerRoot/usr/bin:/Applications/Server.app/Contents/ServerRoot/usr/sbin:/opt/local/bin/:/opt/local/sbin/:/usr/local/ncbi/blast/bin/:/usr/local/biotools/blast/blast/bin/:/local/bin:/local/bin/wu_blast:/local/bin:/local/bin/wu_blast;
export BLASTMAT=/local/bin/wu_blast/matrix; export
BLASTFILTER=/local/bin/wu_blast/filter; export
BLASTDB=/usr/local/blastdb/ensembl_protists;  cat
/usr/local/ensembl_protists/blastqueue/BLA_Lj/KT7L2A1/sZC1hF1Y.fasta |
blastall -d Plasmodium_falciparum.ASM276v1.17.dna.toplevel.fa -p blastn  -b
250 -e 10


Could be a configuration error?
My MULTI.ini file only contains the following settings, maybe something is
misconfigured (maybe Ensembl tryes to parse the output of another BLAST
method instead ncbi blastn output...).

 [BLAST_DATASOURCES]
; Registers blast datasources. Key values are used as labels
; Keys should be registered against methods in species.ini files
DEFAULT         = LATESTGP
CDNA_ALL        = cDNAs
CDNA_ABINITIO   = Ab-initio cDNAs (Genscan/SNAP)
PEP_ALL         = Peptides
PEP_ABINITIO    = Ab-initio Peptides (Genscan/SNAP)
RNA_NC          = Ensembl Non-coding RNA genes
LATESTGP        = Genomic sequence
LATESTGP_MASKED = Genomic sequence (masked)


[ENSEMBL_BLAST_METHODS]
BLASTN   = [blast dna dna ncbiblastn]  ; alternatives: ncbiblastn,
 ensembl_wublastn, sge_wublastn
BLASTX   = [blast dna peptide ncbiblastx]  ; alternatives: ncbiblastx,
 ensembl_wublastx, sge_wublastx
BLASTP   = [blast peptide peptide ncbiblastp]  ; alternatives: ncbiblastp,
 ensembl_wublastp, sge_wublastp
TBLASTN  = [blast peptide dna ncbitblastn] ; alternatives: ncbitblastn,
ensembl_wutblastn, sge_wutblastn
TBLASTX  = [blast dna dna ncbitblastx] ; alternatives: ncbitblastx,
ensembl_wutblastx, sge_wutblastx
BLAT     = [blat dna dna blat_gfclient]

[databases]
DATABASE_BLAST = ensembl_blast
[DATABASE_BLAST]
HOST = localhost
PORT = 3306
USER = ***********
PASS = ***********


BTW, in spite of this configuration, in the BLAST page the combobox for the
*dna database* (LATEST GP, ...) or *protein database *selection are empty
(I'll open another thread for this issue).

Below the error log:


db: Plasmodium_falciparum_LATESTGP
 dbprefix: LATESTGP
 db_key:
 sp: Plasmodium_falciparum


BLA_LjKT7L2A1 at /usr/local/ensembl_protists/perl/Multi/blastview line 272.
STORING BLAST: BLA_LjKT7L2A1 [PID=3860 TIME=301800054] at
/usr/local/ensembl_protists/perl/Multi/blastview line 274.
/usr/local/ensembl_protists/blastqueue/BLA_Lj/KT7L2A1/sZC1hF1Y at
/usr/local/ensembl_protists/perl/Multi/blastview line 279.

RUNNING  Bio::Tools::Run::Search::ncbiblastn=HASH(0x7fb9346188e8) at
/usr/local/ensembl_protists/perl/Multi/blastview line 280.
==> export
PATH=/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/Applications/Server.app/Contents/ServerRoot/usr/bin:/Applications/Server.app/Contents/ServerRoot/usr/sbin:/opt/local/bin/:/opt/local/sbin/:/usr/local/ncbi/blast/bin/:/usr/local/biotools/blast/blast/bin/:/local/bin:/local/bin/wu_blast:/local/bin:/local/bin/wu_blast;
export BLASTMAT=/local/bin/wu_blast/matrix; export
BLASTFILTER=/local/bin/wu_blast/filter; export
BLASTDB=/usr/local/blastdb/ensembl_protists;  cat
/usr/local/ensembl_protists/blastqueue/BLA_Lj/KT7L2A1/sZC1hF1Y.fasta |
blastall -d Plasmodium_falciparum.ASM276v1.17.dna.toplevel.fa -p blastn  -b
250 -e 10  >
 /usr/local/ensembl_protists/blastqueue/BLA_Lj/KT7L2A1/sZC1hF1Y.out >
/usr/local/ensembl_protists/blastqueue/BLA_Lj/KT7L2A1/sZC1hF1Y.out_ 2>&1 ;
mv /usr/local/ensembl_protists/blastqueue/BLA_Lj/KT7L2A1/sZC1hF1Y.out_
/usr/local/ensembl_protists/blastqueue/BLA_Lj/KT7L2A1/sZC1hF1Y.out at
/usr/local/ensembl_protists/modules/Bio/Tools/Run/Search/NCBIBlast.pm line
223.

--------------------- WARNING ---------------------
MSG: Command export
PATH=/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/Applications/Server.app/Contents/ServerRoot/usr/bin:/Applications/Server.app/Contents/ServerRoot/usr/sbin:/opt/local/bin/:/opt/local/sbin/:/usr/local/ncbi/blast/bin/:/usr/local/biotools/blast/blast/bin/:/local/bin:/local/bin/wu_blast:/local/bin:/local/bin/wu_blast;
export BLASTMAT=/local/bin/wu_blast/matrix; export
BLASTFILTER=/local/bin/wu_blast/filter; export
BLASTDB=/usr/local/blastdb/ensembl_protists;  cat
/usr/local/ensembl_protists/blastqueue/BLA_Lj/KT7L2A1/sZC1hF1Y.fasta |
blastall -d Plasmodium_falciparum.ASM276v1.17.dna.toplevel.fa -p blastn  -b
250 -e 10  >
 /usr/local/ensembl_protists/blastqueue/BLA_Lj/KT7L2A1/sZC1hF1Y.out >
/usr/local/ensembl_protists/blastqueue/BLA_Lj/KT7L2A1/sZC1hF1Y.out_ 2>&1 ;
mv /usr/local/ensembl_protists/blastqueue/BLA_Lj/KT7L2A1/sZC1hF1Y.out_
/usr/local/ensembl_protists/blastqueue/BLA_Lj/KT7L2A1/sZC1hF1Y.out failed

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Parsing failed

-------------------- EXCEPTION --------------------
MSG: seq_region_name argument is required
STACK Bio::EnsEMBL::DBSQL::SliceAdaptor::fetch_by_region
/usr/local/ensembl_protists/ensembl/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm:201
STACK Bio::Search::HSP::EnsemblHSP::_map
/usr/local/ensembl_protists/eg-plugins/common/modules/Bio/Search/HSP/EnsemblHSP.pm:435
STACK Bio::Search::Result::EnsemblResult::map_to_genome
/usr/local/ensembl_protists/modules/Bio/Search/Result/EnsemblResult.pm:271
STACK Bio::Tools::Run::Search::parse
/usr/local/ensembl_protists/modules/Bio/Tools/Run/Search.pm:1082
STACK (eval)
/usr/local/ensembl_protists/modules/Bio/Tools/Run/Search.pm:1005
STACK Bio::Tools::Run::Search::dispatch
/usr/local/ensembl_protists/modules/Bio/Tools/Run/Search.pm:1005
STACK (eval) /usr/local/ensembl_protists/modules/Bio/Tools/Run/Search.pm:935
STACK Bio::Tools::Run::Search::run
/usr/local/ensembl_protists/modules/Bio/Tools/Run/Search.pm:935
STACK (eval) /usr/local/ensembl_protists/perl/Multi/blastview:281
STACK (eval) /usr/local/ensembl_protists/perl/Multi/blastview:281
STACK (eval) (eval 725):1
STACK EnsEMBL::Web::Apache::SpeciesHandler::handler_species
/usr/local/ensembl_protists/modules/EnsEMBL/Web/Apache/SpeciesHandler.pm:123
STACK EnsEMBL::Web::Apache::Handlers::handler
/usr/local/ensembl_protists/modules/EnsEMBL/Web/Apache/Handlers.pm:369
STACK (eval) /usr/local/ensembl_protists/perl/Multi/blastview:0
STACK toplevel /usr/local/ensembl_protists/perl/Multi/blastview:0
Date (localtime)    = Mon Mar  4 13:27:35 2013
Ensembl API version = 70
---------------------------------------------------

STACK: Error::throw
STACK: Bio::Root::Root::throw /Library/Perl/5.12/Bio/Root/Root.pm:472
STACK: Bio::Tools::Run::Search::dispatch
/usr/local/ensembl_protists/modules/Bio/Tools/Run/Search.pm:1019
STACK: Bio::Tools::Run::Search::run
/usr/local/ensembl_protists/modules/Bio/Tools/Run/Search.pm:935
STACK: EnsEMBL::Web::Apache::SpeciesHandler::handler_species
/usr/local/ensembl_protists/perl/Multi/blastview:281
STACK: EnsEMBL::Web::Apache::Handlers::handler
/usr/local/ensembl_protists/modules/EnsEMBL/Web/Apache/Handlers.pm:369
STACK: /usr/local/ensembl_protists/perl/Multi/blastview:0
-----------------------------------------------------------

---------------------------------------------------

RUN      Bio::Tools::Run::Search::ncbiblastn=HASH(0x7fb9346188e8)  at
/usr/local/ensembl_protists/perl/Multi/blastview line 282.
HERE.... FAILED at /usr/local/ensembl_protists/perl/Multi/blastview line
287.
Bio::Tools::Run::Search::ncbiblastn at
/usr/local/ensembl_protists/perl/Multi/blastview line 288.
STORED.... at /usr/local/ensembl_protists/perl/Multi/blastview line 290.
*** BLAST ERROR:
/usr/local/ensembl_protists/blastqueue/BLA_Lj/KT7L2A1/sZC1hF1Y ***
Blast job resulted in
/usr/local/ensembl_protists/blastqueue/BLA_Lj/KT7L2A1/sZC1hF1Y.fail file:
Command export
PATH=/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/Applications/Server.app/Contents/ServerRoot/usr/bin:/Applications/Server.app/Contents/ServerRoot/usr/sbin:/opt/local/bin/:/opt/local/sbin/:/usr/local/ncbi/blast/bin/:/usr/local/biotools/blast/blast/bin/:/local/bin:/local/bin/wu_blast:/local/bin:/local/bin/wu_blast;
export BLASTMAT=/local/bin/wu_blast/matrix; export
BLASTFILTER=/local/bin/wu_blast/filter; export
BLASTDB=/usr/local/blastdb/ensembl_protists;  cat
/usr/local/ensembl_protists/blastqueue/BLA_Lj/KT7L2A1/sZC1hF1Y.fasta |
blastall -d Plasmodium_falciparum.ASM276v1.17.dna.toplevel.fa -p blastn  -b
250 -e 10  >
 /usr/local/ensembl_protists/blastqueue/BLA_Lj/KT7L2A1/sZC1hF1Y.out >
/usr/local/ensembl_protists/blastqueue/BLA_Lj/KT7L2A1/sZC1hF1Y.out_ 2>&1 ;
mv /usr/local/ensembl_protists/blastqueue/BLA_Lj/KT7L2A1/sZC1hF1Y.out_
/usr/local/ensembl_protists/blastqueue/BLA_Lj/KT7L2A1/sZC1hF1Y.out failed

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Parsing failed

-------------------- EXCEPTION --------------------
MSG: seq_region_name argument is required
STACK Bio::EnsEMBL::DBSQL::SliceAdaptor::fetch_by_region
/usr/local/ensembl_protists/ensembl/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm:201
STACK Bio::Search::HSP::EnsemblHSP::_map
/usr/local/ensembl_protists/eg-plugins/common/modules/Bio/Search/HSP/EnsemblHSP.pm:435
STACK Bio::Search::Result::EnsemblResult::map_to_genome
/usr/local/ensembl_protists/modules/Bio/Search/Result/EnsemblResult.pm:271
STACK Bio::Tools::Run::Search::parse
/usr/local/ensembl_protists/modules/Bio/Tools/Run/Search.pm:1082
STACK (eval)
/usr/local/ensembl_protists/modules/Bio/Tools/Run/Search.pm:1005
STACK Bio::Tools::Run::Search::dispatch
/usr/local/ensembl_protists/modules/Bio/Tools/Run/Search.pm:1005
STACK (eval) /usr/local/ensembl_protists/modules/Bio/Tools/Run/Search.pm:935
STACK Bio::Tools::Run::Search::run
/usr/local/ensembl_protists/modules/Bio/Tools/Run/Search.pm:935
STACK (eval) /usr/local/ensembl_protists/perl/Multi/blastview:281
STACK (eval) /usr/local/ensembl_protists/perl/Multi/blastview:281
STACK (eval) (eval 725):1
STACK EnsEMBL::Web::Apache::SpeciesHandler::handler_species
/usr/local/ensembl_protists/modules/EnsEMBL/Web/Apache/SpeciesHandler.pm:123
STACK EnsEMBL::Web::Apache::Handlers::handler
/usr/local/ensembl_protists/modules/EnsEMBL/Web/Apache/Handlers.pm:369
STACK (eval) /usr/local/ensembl_protists/perl/Multi/blastview:0
STACK toplevel /usr/local/ensembl_protists/perl/Multi/blastview:0
Date (localtime)    = Mon Mar  4 13:27:35 2013
Ensembl API version = 70
---------------------------------------------------

STACK: Error::throw
STACK: Bio::Root::Root::throw /Library/Perl/5.12/Bio/Root/Root.pm:472
STACK: Bio::Tools::Run::Search::dispatch
/usr/local/ensembl_protists/modules/Bio/Tools/Run/Search.pm:1019
STACK: Bio::Tools::Run::Search::run
/usr/local/ensembl_protists/modules/Bio/Tools/Run/Search.pm:935
STACK: EnsEMBL::Web::Apache::SpeciesHandler::handler_species
/usr/local/ensembl_protists/perl/Multi/blastview:281
STACK: EnsEMBL::Web::Apache::Handlers::handler
/usr/local/ensembl_protists/modules/EnsEMBL/Web/Apache/Handlers.pm:369
STACK: /usr/local/ensembl_protists/perl/Multi/blastview:0
-----------------------------------------------------------
*** BLAST ERROR:
/usr/local/ensembl_protists/blastqueue/BLA_Lj/KT7L2A1/sZC1hF1Y ***
Blast job resulted in
/usr/local/ensembl_protists/blastqueue/BLA_Lj/KT7L2A1/sZC1hF1Y.fail file:
Command export
PATH=/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/Applications/Server.app/Contents/ServerRoot/usr/bin:/Applications/Server.app/Contents/ServerRoot/usr/sbin:/opt/local/bin/:/opt/local/sbin/:/usr/local/ncbi/blast/bin/:/usr/local/biotools/blast/blast/bin/:/local/bin:/local/bin/wu_blast:/local/bin:/local/bin/wu_blast;
export BLASTMAT=/local/bin/wu_blast/matrix; export
BLASTFILTER=/local/bin/wu_blast/filter; export
BLASTDB=/usr/local/blastdb/ensembl_protists;  cat
/usr/local/ensembl_protists/blastqueue/BLA_Lj/KT7L2A1/sZC1hF1Y.fasta |
blastall -d Plasmodium_falciparum.ASM276v1.17.dna.toplevel.fa -p blastn  -b
250 -e 10  >
 /usr/local/ensembl_protists/blastqueue/BLA_Lj/KT7L2A1/sZC1hF1Y.out >
/usr/local/ensembl_protists/blastqueue/BLA_Lj/KT7L2A1/sZC1hF1Y.out_ 2>&1 ;
mv /usr/local/ensembl_protists/blastqueue/BLA_Lj/KT7L2A1/sZC1hF1Y.out_
/usr/local/ensembl_protists/blastqueue/BLA_Lj/KT7L2A1/sZC1hF1Y.out failed

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Parsing failed

-------------------- EXCEPTION --------------------
MSG: seq_region_name argument is required
STACK Bio::EnsEMBL::DBSQL::SliceAdaptor::fetch_by_region
/usr/local/ensembl_protists/ensembl/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm:201
STACK Bio::Search::HSP::EnsemblHSP::_map
/usr/local/ensembl_protists/eg-plugins/common/modules/Bio/Search/HSP/EnsemblHSP.pm:435
STACK Bio::Search::Result::EnsemblResult::map_to_genome
/usr/local/ensembl_protists/modules/Bio/Search/Result/EnsemblResult.pm:271
STACK Bio::Tools::Run::Search::parse
/usr/local/ensembl_protists/modules/Bio/Tools/Run/Search.pm:1082
STACK (eval)
/usr/local/ensembl_protists/modules/Bio/Tools/Run/Search.pm:1005
STACK Bio::Tools::Run::Search::dispatch
/usr/local/ensembl_protists/modules/Bio/Tools/Run/Search.pm:1005
STACK (eval) /usr/local/ensembl_protists/modules/Bio/Tools/Run/Search.pm:935
STACK Bio::Tools::Run::Search::run
/usr/local/ensembl_protists/modules/Bio/Tools/Run/Search.pm:935
STACK (eval) /usr/local/ensembl_protists/perl/Multi/blastview:281
STACK (eval) /usr/local/ensembl_protists/perl/Multi/blastview:281
STACK (eval) (eval 725):1
STACK EnsEMBL::Web::Apache::SpeciesHandler::handler_species
/usr/local/ensembl_protists/modules/EnsEMBL/Web/Apache/SpeciesHandler.pm:123
STACK EnsEMBL::Web::Apache::Handlers::handler
/usr/local/ensembl_protists/modules/EnsEMBL/Web/Apache/Handlers.pm:369
STACK (eval) /usr/local/ensembl_protists/perl/Multi/blastview:0
STACK toplevel /usr/local/ensembl_protists/perl/Multi/blastview:0
Date (localtime)    = Mon Mar  4 13:27:35 2013
Ensembl API version = 70
---------------------------------------------------

STACK: Error::throw
STACK: Bio::Root::Root::throw /Library/Perl/5.12/Bio/Root/Root.pm:472
STACK: Bio::Tools::Run::Search::dispatch
/usr/local/ensembl_protists/modules/Bio/Tools/Run/Search.pm:1019
STACK: Bio::Tools::Run::Search::run
/usr/local/ensembl_protists/modules/Bio/Tools/Run/Search.pm:935
STACK: EnsEMBL::Web::Apache::SpeciesHandler::handler_species
/usr/local/ensembl_protists/perl/Multi/blastview:281
STACK: EnsEMBL::Web::Apache::Handlers::handler
/usr/local/ensembl_protists/modules/EnsEMBL/Web/Apache/Handlers.pm:369
STACK: /usr/local/ensembl_protists/perl/Multi/blastview:0
-----------------------------------------------------------

Thank you again,

Best regards

Rafa Hernández de Diego

SLU-Global Bioinformatics Center
Swedish University for Agricultural Sciences (SLU)
Gerda Nilssons väg 2,
 Box 7023, 750 07 Uppsala, Sweden.
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