Question: Blast+ window_masker_taxid parameter
0
gravatar for mbekaert
2.9 years ago by
mbekaert0
mbekaert0 wrote:

Blast has two incompatible parameters to limit the taxonomical searches:

  • -entrez_query in association with -remote
  • -window_masker_taxid (local database only)

if -entrez_query="txid8030[Organism:exp]” works perfectly well remotely, I need to run locally most of my blast searches, so -window_masker_taxid looks promissing. But I cannot figure our how to use it! Each attempt end-up with “BLAST EXCEPTION” errors!

Only documentation

I downloaded the last version of "taxdb" and “refseq_rna” pre-compiled and tried:

$ blastdbcmd -db refseq_rna -entry 929050848 > test.fasta

$ blastdbcmd -db refseq_rna -entry 929050848 -outfmt "%T”

8030

$ blastn -query test.fasta -db refseq_rna -task blastn -window_masker_taxid 8030

BLASTN 2.2.31+

Reference: Stephen F. Altschul, Thomas L. Madden, Alejandro A.

Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J.

Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of

protein database search programs", Nucleic Acids Res. 25:3389-3402.

Database: NCBI Transcript Reference Sequences

16,094,088 sequences; 37,021,796,207 total letters

BLAST engine error: Warning: NCBI C++ Exception:

T0 "/build/ncbi-blast+-bzPf_D/ncbi-blast+-2.2.31/c++/src/algo/winmask/seq_masker_istat_factory.cpp", line 72: Error: ncbi::CSeqMaskerIstatFactory::create() - could not open

T0 "/build/ncbi-blast+-bzPf_D/ncbi-blast+-2.2.31/c++/src/algo/winmask/seq_masker_istat_factory.cpp", line 103: Error: ncbi::CSeqMaskerIstatFactory::create() - could not create a unit counts container

Then, I created a masking database as documented:

cd /data/blast_databases

windowmasker -in refseq_rna -infmt blastdb -mk_counts -parse_seqids -out refseq_rna_mask.counts -sformat obinary

windowmasker -in refseq_rna -infmt blastdb -ustat refseq_rna_mask.counts -outfmt maskinfo_asn1_bin -parse_seqids -out refseq_rna_mask.asnb

makeblastdb -in refseq_rna -input_type blastdb -dbtype nucl -parse_seqids -mask_data refseq_rna_mask.asnb -out refseq_rna_mask -title "NCBI Transcript Reference Sequences"

blastdbcmd -db refseq_rna_mask -entry 929050848 -outfmt "%T”

8030

blastn -query test.fasta -db refseq_rna_mask -task blastn -window_masker_taxid 8030

BLASTN 2.2.31+

Reference: Stephen F. Altschul, Thomas L. Madden, Alejandro A.

Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J.

Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of

protein database search programs", Nucleic Acids Res. 25:3389-3402.

Database: NCBI Transcript Reference Sequences

BLAST engine error: Warning: NCBI C++ Exception: T0 "/build/ncbi-blast+-bzPf_D/ncbi-blast+-2.2.31/c++/src/algo/winmask/seq_masker_istat_factory.cpp", line 72: Error: ncbi::CSeqMaskerIstatFactory::create() - could not open T0 "/build/ncbi-blast+-bzPf_D/ncbi-blast+-2.2.31/c++/src/algo/winmask/seq_masker_istat_factory.cpp", line 103: Error: ncbi::CSeqMaskerIstatFactory::create() - could not create a unit counts container

I cannot find any reference to the problem anywhere (I tried to google it)! Am I the only stupid one here or nobodyelse tried to use the option?

blast software error • 1.2k views
ADD COMMENTlink written 2.9 years ago by mbekaert0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 472 users visited in the last hour