Blast Output with only one line

Question

[pablo]

Hello.

I have a reference genome (>3000 sequences/contigs) and a de novo assembly (>600 contigs) obtained with PacBio reads.

I would like to compare these two genomes (~2.7Gb for both) in order to know the concordance between the contigs from both oh them.

For that, I'd like to use blast. I splitted the reference genome in separate files for each contig (so, I got >3000 contigs , ranging from 170Mb to few Kb). Then, I blast each of these files against my de novo assembly (with the variable $SLURM_ARRAY_TASK_ID in order to run the blasts in parallel).

I'd like to get the best hit for each blast, so I use :

blastn -query my_sequences.fasta -db denovo_assembly.fa -out mu_outputs.txt -max_target_seqs 1 -outfmt "6 qseqid qlen sseqid qstart qend evalue score length" -num_threads 32 

The output I get is like that (I show for one blast) :

NC_001913.1     17245   ptg000952l      1       17223   0.0     17081   17265
NC_001913.1     17245   ptg000952l      1       10420   0.0     10397   10428
NC_001913.1     17245   ptg000952l      10383   15925   0.0     5516    5547
NC_001913.1     17245   ptg000952l      10379   12626   0.0     2227    2251
NC_001913.1     17245   ptg000952l      16224   17223   0.0     909     1023
NC_001913.1     17245   ptg000952l      16610   17245   0.0     630     636
NC_001913.1     17245   ptg000952l      16610   17245   0.0     630     636
NC_001913.1     17245   ptg000952l      16610   17070   0.0     458     461
NC_001913.1     17245   ptg000952l      16610   17070   0.0     458     461
NC_001913.1     17245   ptg000952l      16763   17223   0.0     455     461
NC_001913.1     17245   ptg000952l      16763   17223   0.0     455     461
NC_001913.1     17245   ptg000952l      15951   16449   0.0     372     505
NC_001913.1     17245   ptg000952l      16610   16917   1.33e-158       308     308
NC_001913.1     17245   ptg000952l      16610   16917   1.33e-158       308     308
NC_001913.1     17245   ptg000952l      16916   17223   6.19e-157       305     308

Is it possible to get only one line of this output? Because what I want to know is if one contig from the reference matches with one contig from my de novo assembly. So, I don't mind to get all of these output lines, only one would be sufficient.

Best.

[swbarnes2]

Can you pipe the output to head?

[dariober]

I suppose the OP wants one subject hit per query sequence not just the first line of the output?

[pablo]

Thanks for the reply. I'm just looking for the first line of the output . So the -subject_besthit option is ok in my case.

Answer 1

[dariober]

I think you should add to blastn the option -subject_besthit