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peterk87 / nf-villumina

Generic viral Illumina sequence analysis pipeline
MIT License
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Update BLAST+ to latest version for compatibility with latest releases of NCBI nt #25

Open peterk87 opened 2 years ago

peterk87 commented 2 years ago

Bioconda blast=2.9.0 running through Singularity with 2022-07-31 release of nt downloaded with update_blastdb.pl produces the following error:

Error: NCBI C++ Exception:
    T0 "/opt/conda/conda-bld/blast_1569630873707/work/c++/src/serial/objistrasnb.cpp", line 499: Error: byte 169: overflow error ( at [].[].gi)
    T0 "/opt/conda/conda-bld/blast_1569630873707/work/c++/src/serial/member.cpp", line 770: Error: ncbi::CMemberInfoFunctions::ReadWithSetFlagMember() - error while reading seqid ( at Blast-de
f-line-set.[].[].seqid.[].[].gi)

No such issue with BLAST+ 2.13.0 (build Jul 18 2022 22:49:37) installed from Bioconda into fresh Conda env running locally.

BLAST command:

$ blastn -taxidlist Viruses-10239.taxidlist \
   -num_threads 4 \
   -db blast/nt \
   -query Sample01-assembly.fasta \
   -outfmt "6 qaccver saccver pident length mismatch gapopen qstart qend sstart send evalue bitscore qlen slen stitle staxid ssciname" \
   -evalue 1e-6 \
   -out blastn-Sample01-VS-nt.tsv