I had created databases of different sets of metagenome datasets - one with 6 runs, other with 48 runs, another with 100 runs, etc using the accession list for each of these datasets and makeblastdb command. Since I wanted to check the abundance of one specific 16S rRNA gene sequence, I ran a blastn command using this 16S sequence (F7) as the query against each of the created databases with a txt file (F7_droughtS.txt, F7_Dy.txt, so on) as the output. Ideally I should have got differently sized files with different number of OTU matches. I did get different files since the SRR ids were different for each database, but the results did not go beyond 500 lines for any database search. Can anyone explain why this is so?
Following is the command I used for blastn of:
sequence.fasta against database
blastn -query sequence.fasta -db firstdb -outfmt 6 -out output1.txt
Also ran the following to know the default number of lines :
blastn -help -max_target_seqs
Number of database sequences to show one-line descriptions for
Not applicable for outfmt > 4 Default = 500' * Incompatible with: max_target_seqs -num_alignments <Integer, >=0> Number of database sequences to show alignments for Default = 250' * Incompatible with: max_target_seqs