Detail about SURVIVOR simSV

harazono commented 6 years ago

Hi fritz.

I tried to make simulated reads using SURVIVOR simSV I created SV parameter file as bellow:

$ cat parameter_file 
PARAMETER FILE: DO JUST MODIFY THE VALUES AND KEEP THE SPACES!
DUPLICATION_minimum_length: 100
DUPLICATION_maximum_length: 10000
DUPLICATION_number: 3
INDEL_minimum_length: 20
INDEL_maximum_length: 500
INDEL_number: 1
TRANSLOCATION_minimum_length: 1000
TRANSLOCATION_maximum_length: 3000
TRANSLOCATION_number: 2
INVERSION_minimum_length: 600
INVERSION_maximum_length: 800
INVERSION_number: 4
INV_del_minimum_length: 600
INV_del_maximum_length: 800
INV_del_number: 2
INV_dup_minimum_length: 600
INV_dup_maximum_length: 800
INV_dup_number: 2

and, I run this command:

SURVIVOR simSV ~/human_reference_genome/GRCh38_p12_chr22.fa parameter_file 0.1 0 simulated

This script takes more than 2 days for generating SVs.

Can you explain how SURVIVOR simSV works and why it takes so long time? I imaged that just modifying reference sequence doesn't take so long time.

Sorry for bothering you. Thanks.

harazono

fritzsedlazeck commented 6 years ago

The main reason is that it tries to place SVs in an non overlapping way, which might get tricky for such a short chromosome. Second reason is that you requested 2 translation which cannot be simulated with only one Chr.

I thought I put in some warnings, but it seems that they did not catch this. I will try to improve this. Thanks for letting me know Fritz

fritzsedlazeck commented 6 years ago

I have just checked the code and changed it so it gives a warning much sooner. I hope that helps. Fritz

harazono commented 6 years ago

I reduced number of SVs and set 0 for TRA. It looks works well. Thanks a lot !

harazono

fritzsedlazeck commented 6 years ago

Thanks for reporting it. Yes it should run in a few minutes. I will close this now, but feel free to open it again if something comes up. Thanks Fritz

fritzsedlazeck / SURVIVOR

Detail about SURVIVOR simSV #40