Does some one has experience with using the -seqidlist parameter in blast? If I make a selection of sequences from the nt database and build a database with those extracted sequences it takes about 5 seconds to blast 50 reads. If I extract the accessions of that sub selection and write them to a file and use -seqidlist to blast against the nt database it takes much longer (I stopped it after half an hour or so)
The file contains 2346860 accessions.
The command I used
sudo ncbi-blast-2.7.1+/bin/blastn -query 50_otus.fasta -db nt -outfmt 6 -out test -num_threads 10 -seqidlist accession_list
The accession_list file contain one accession on each line.