Question: blastn_vdb "- Error opening the following db(s): "
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gravatar for musta1234
2.2 years ago by
musta123410
musta123410 wrote:

Background:

I used blastn_vdb, part of the sra toolkit, to blast a set of genomes on the ncbi wgs database following the instructions provided at: ftp://ftp.ncbi.nlm.nih.gov/blast/WGS_TOOLS/README_BLASTWGS.txt I attempted running blastn_vdb using a nucleotide fasta query (4 sequences, ~1kb each) on all gammaproteobacteria WGS sequences (24,507 wgs genomes). blastn_vdb downloaded 24040 genomes (XXX00N.cache) and 439 other XXX00N files without .cache extension before exiting with the following error messages. I have more than enough available disk space for wgs and blast output folders.

Commands:

taxid2wgs.pl -title "Gammaprot" -alias_file Gammaprot 1236
blastn_vdb -query ../queries/queries.fna -db Gammaprot -outfmt '6 std qlen slen' -out Gammaprot_v_queries.txt

Error message:

NCBI C++ Exception:
T0 "/export/home/tomcat/TeamCity/Agent3/work/9b0ff710cbae2b8c/blastn/c++/src/internal/blast/vdb/vdb2blast_util.cpp", line 266: Error: ncbi::CVDBBlastUtil::x_MakeSRASeqSrc() - Error opening the following db(s): MPCP01

This error is reported for 100s of wgs IDs and I checked a few of these wgs IDs and found intact sequences on ncbi web interface.

Any help or hint is appreciated.

ADD COMMENTlink modified 2.2 years ago by RamRS21k • written 2.2 years ago by musta123410
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