blast: error while reading seqid using ncbi database
Entering edit mode
11 months ago

I'm getting "error while reading seqid" using blast databases from NCBI. The following is just to reproduce the error, don't worry about whether it makes sense or not. Does anybody know what is happening?

Get a blast database from NCBI - I tried 28S_fungal_sequences and 16S_ribosomal_RNA: --decompress 28S_fungal_sequences
# So far so good:
# Connected to NCBI
# Decompressing 28S_fungal_sequences.tar.gz ... [OK]

Extracting sequences from the database gives the first error:

blastdbcmd -entry all -db 28S_fungal_sequences > reads.fa
Error: [blastdbcmd] error while reading seqid

reads.fa is truncated but corretly formatted, let's try to blast it anyway:

blastn -query reads.fa -db 28S_fungal_sequences

BLASTN 2.11.0+

Reference: Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb
Miller (2000), "A greedy algorithm for aligning DNA sequences", J
Comput Biol 2000; 7(1-2):203-14.

Database: 28S ribosomal RNA sequences (LSU) from Fungi type and reference
           8,722 sequences; 8,465,898 total letters

Error: NCBI C++ Exception:
    T0 "/opt/conda/conda-bld/blast_1615544030046/work/blast/c++/src/serial/objistrasnb.cpp", line 499: Error: (CSerialException::eOverflow) byte 112: overflow error ( at [].[].gi)
    T0 "/opt/conda/conda-bld/blast_1615544030046/work/blast/c++/src/serial/member.cpp", line 768: Error: (CSerialException::eOverflow) ncbi::CMemberInfoFunctions::ReadWithSetFlagMember() - error while reading seqid ( at Blast-def-line-set.[].[].seqid.[].[].gi)
ncbi blast • 843 views
Entering edit mode
11 months ago

Re-installing / upgrading blast seems to fix it...:

mamba install 'blast>=2.12'

blastn -query reads.fa -db 28S_fungal_sequences > test.out # OK

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