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incorrect SAM format when using blastn_vdb and blast_formatter_vdb #949

Closed djleite closed 3 months ago

djleite commented 3 months ago

Hi,

I have an issue with SAM file header formatting. The input FASTA contains two queries, and the blastn_vdb search is against one SRA accession.

After running (example)...

blastn_vdb -db SRR23038822 -query input.fasta -out ASN.asn -outfmt 11

and...

blast_formatter_vdb -archive ASN.asn -outfmt "17 SQ" -out bad_formatted.sam

The SAM has the header split, with query 1 and 2 headers and alignments appearing concatenated, rather than correctly combined headers.

I cannot identify why this example causes this issue, and I would appreciate some guidance on how to resolve it or if there are some issues with the tools/commands.

Many thanks

ASN.asn.gz bad_formatted.sam.gz input.fasta.gz

klymenko commented 3 months ago

blastn_vdb and tblastn_vdb binaries are now distributed and supported by Blast team.

E-mail blast-help@ncbi.nlm.nih.gov with questions or comments.