Odd results with BLAST remote

Question

[Begonia_pavonina]

I am running a blast remote with the following code:

  blastn \ 
      -db nt \ 
      -query queries.fasta \ 
      -out results.csv \ 
      -outfmt 6  \ 
      -evalue 1e-20 \ 
      -remote \ 
      -max_target_seqs 5

And most of the result file is correct, however an odd thing happen close to the end. Instead of having five outputs for each queries, I got several hundreds of them for one query (query 98 in the example below). Would anyone know why? Or have you seen this before?

97,gi|1769129387|gb|MN604303.1|,91.515,330,MN604303,3039,5.05e-122,451,244,2661874
97,gi|1769129386|gb|MN604302.1|,91.515,330,MN604302,3064,5.05e-122,451,244,2661874
97,gi|1933758030|gb|MW267283.1|,91.411,326,MW267283,691,8.46e-120,444,240,2079346
97,gi|2610379270|gb|OR693297.1|,90.606,330,OR693297,3054,1.42e-117,436,236,3081772
97,gi|344227739|gb|JN558110.1|,90.549,328,JN558110,1206,1.83e-116,433,234,89957
98,gi|1855019016|gb|MT610943.1|,100.000,329,MT610943,5802,2.84e-169,608,329,3879
98,gi|1043523995|gb|KU321683.1|,100.000,329,KU321683,128574,2.84e-169,608,329,3879
98,gi|2532442601|emb|OY283139.1|,100.000,329,OY283139,91320517,2.84e-169,608,329,47085
98,gi|2532442601|emb|OY283139.1|,100.000,329,OY283139,91320517,2.84e-169,608,329,47085
98,gi|2532442601|emb|OY283139.1|,100.000,329,OY283139,91320517,2.84e-169,608,329,47085
98,gi|2532442601|emb|OY283139.1|,99.088,329,OY283139,91320517,2.86e-164,592,320,47085
98,gi|2532442601|emb|OY283139.1|,99.088,329,OY283139,91320517,2.86e-164,592,320,47085
98,gi|2532442601|emb|OY283139.1|,99.088,329,OY283139,91320517,2.86e-164,592,320,47085
98,gi|2532442601|emb|OY283139.1|,99.088,329,OY283139,91320517,2.86e-164,592,320,47085
98,gi|2532442601|emb|OY283139.1|,99.088,329,OY283139,91320517,2.86e-164,592,320,47085
98,gi|2532442601|emb|OY283139.1|,99.088,329,OY283139,91320517,2.86e-164,592,320,47085
98,gi|2532442601|emb|OY283139.1|,99.088,329,OY283139,91320517,2.86e-164,592,320,47085
98,gi|2532442601|emb|OY283139.1|,99.088,329,OY283139,91320517,2.86e-164,592,320,47085
98,gi|2532442601|emb|OY283139.1|,99.088,329,OY283139,91320517,2.86e-164,592,320,47085
98,gi|2532442601|emb|OY283139.1|,99.088,329,OY283139,91320517,2.86e-164,592,320,47085
98,gi|2532442601|emb|OY283139.1|,99.088,329,OY283139,91320517,2.86e-164,592,320,47085
98,gi|2532442601|emb|OY283139.1|,99.088,329,OY283139,91320517,2.86e-164,592,320,47085
98,gi|2532442601|emb|OY283139.1|,99.088,329,OY283139,91320517,2.86e-164,592,320,47085
98,gi|2532442601|emb|OY283139.1|,99.088,329,OY283139,91320517,2.86e-164,592,320,47085
98,gi|2532442601|emb|OY283139.1|,99.088,329,OY283139,91320517,2.86e-164,592,320,47085
98,gi|2532442601|emb|OY283139.1|,99.088,329,OY283139,91320517,2.86e-164,592,320,47085
98,gi|2532442601|emb|OY283139.1|,99.088,329,OY283139,91320517,2.86e-164,592,320,47085
98,gi|2532442601|emb|OY283139.1|,99.088,329,OY283139,91320517,2.86e-164,592,320,47085
98,gi|2532442601|emb|OY283139.1|,99.088,329,OY283139,91320517,2.86e-164,592,320,47085
98,gi|2532442601|emb|OY283139.1|,99.088,329,OY283139,91320517,2.86e-164,592,320,47085
98,gi|2532442601|emb|OY283139.1|,99.088,329,OY283139,91320517,2.86e-164,592,320,47085

[GenoMax]

Can you manually try query 98 via web blast to see what you get with the same command options?

outfmt 6 should have 12 fields. Looks like you have only 10 in your output. Is that correct?

[Begonia_pavonina]

Thanks for the answer GenoMax, I have made a blast online and it indeed gave me the answer.

When I blast it online I have only one line of result:

98,gi|2532442601|emb|OY283139.1|,100.000,329,OY283139,91320517,2.84e-169,608,329,47085

But in my result file, there is more than 600 of this same line. I am not sure why, but it is the case.

Regarding the outfmt 6 format, I had specified the 10 output columns, but did not put this in my question here.

Answer 1

[b.contreras.moreira]

It would seem that gi|2532442601|emb|OY283139.1| contains several domains/repeats that match query 98...

[Begonia_pavonina]

Thanks @b.contreras.moreira, It is indeed the case. The odd thing is that online blastn query does not return several results for this query, only one.

[Begonia_pavonina]

The slength column seems indeed related to the number of matches in the results. If anyone know how to lower the rows of output to 5 max, it would be a welcome information!

[b.contreras.moreira]

See What is the difference between using -max_target_seqs 1 -max_hsps 1 versus just the defaults and then filtering for top hit? and parameter -max_hsps 1