Multiple empty hits?

[mw55309]

Hello

I'm using minimap2 to map against NCBI nt. The SAM output contains multiple entries for the same query that are basically "no hit" i.e. column 3 is a *.

The last read I checked had 27 such entries (the run hadn't finished) which were identical.

Is this a feature? What am I missing? Why would minimap2 output multiple "no hit" lines for the same read?

I have checked and the input only has one copy of this read.

It's not unique to this read, it happens to all of them

Cheers
Mick

[lh3]

When you have a huge database like "nt", minimap2 will split it into multiple parts and align all queries against each part independently. For most parts, minimap2 will print unmapped records. This is a limitation of minimap2.

I think @hasindu2008 has a preliminary solution to this issue. See #141.

[mw55309]

Thanks Heng, I specifically gave the job 4x as much RAM as the size of nt (uncompressed) so technically no reason for it to split the index.

is the creation of a multi-part index (in memory) turned on by default?

[lh3]

Yes, multi-part is turned on by default. You can increase option -I to 500G (a number larger than the total size of nt) to force minimap2 to generate one index. Depending on -k and -w in use, 4x as much might not be enough.

[hasindu2008]

@mw55309

You can try the merging solution I implemented from the following method. It is still preliminary and only works for single ended reads at the moment. It basically merges the results from a multi-part index to achieve a considerably similar output from a single-part index. I have done testing only on some simulated pacbio reads.
git clone https://github.com/hasindu2008/minimap2 && cd minimap2 && git checkout multipart-merge-tmp && make

Make sure that you use the option --multi-prefix to enable mergine
eg :
./minimap2 -x <profile> -I<partsize> --multi-prefix tmp ref.fa read.fastq

[lh3]

The latest minimap2 has an --split-prefix option:

minimap2 -a --split-prefix tmp ref.fa query.fa

With this option, minimap2 won't write a unmapped record multiple times.