Importing blastn output to Megan

User Questions
1

I cannot get Megan to open my blast output. It seems it is not in the correct format. Here is my code:
blastn -db blastNT -query SRR10512818_R1.fasta -evalue 0.001 -outfmt ‘6 queryId subjectId pident length mismatch gapopen qstart qend sstart send evalue bitscore’ -num_alignments 5 -out SRR10512818_R1_blastn.out

2

That line of code looks weird, is it really your code or did you accidentally make an insertion when you posted this? i.e. delete the highlight (below) and it should work fine. Your output format (-outfmt) is set to ‘6’ which is recognized by MEGAN.

blastn -db blastNT -query SRR10512818_R1.fasta -evalue 0.001 -outfmt ‘6 queryId subjectId pident length mismatch gapopen qstart qend sstart send evalue bitscore’ -num_alignments 5 -out SRR10512818_R1_blastn.out

3

I ended up completely removing the -outfmt bit and then it worked. Thank you!