Incorrect output + Slow VCF writing

[GuillaumeHolley]

Hi,

I am trying to use NanoSV to call SVs on a 7 Mbp region of chromosome 15. I am only interested in SVs longer than 250 kb. I have been using a BED file which looks like this: chr15 20000000 27000000

And I used the default config.ini with the following modified parameters:

min_mapq = 10
min_indel_size = 250000
qual_flag = 10

First, I don't know if it is normal behavior but the tool has spent the last 45min on step Busy with printing to vcf... and it hasn't finished (seems related to #62). Memory is not an issue (I have 128 GB of RAM) and I am the only one using the machine.

Second, in the output currently being written, there are SVs in chr14 and chr16 but not in chr15. Also, most of these SVs have a length much smaller than 250kb.

Do you know what is happening and how to fix it?

Thank you for your time and help. Guillaume