COBS for 600K genomes

[davidmaimoun]

Hi,
I am in charge to find presence of specific genes in 600.000 Salmonella's genomes.
I used COBS on few genomes for training
But I don't really understand the output...
I copied a subsequence (55 bp) from one of my genomes, and run COBS to see if it get it.
In the output I got 24 (see bellow).
And when I choose bigger sub sequence, sometimes it doesn't find it at all.

Another issue: how I can see if my query fully matchs or partially?

--- end of document list (5 entries) ---
documents: 5
minimum 31-mers: 2811023
maximum 31-mers: 2874904
average 31-mers: 2834688
total 31-mers: 14173442
DIE: Output file exists, will not overwrite without --clobber @ /opt/conda/conda-bld/cobs_1646087618998/work/cobs/construction/compact_index.cpp:213
terminate called without an active exception

SRR18349609 24
SRR18349610 24
SRR18349611 24

TIMER info=search hashes=9.929e-06 io=0.000567883 total=0.000577812

Query length 55

I'd really appreciate your help

Thank you!

[iqbal-lab]

Hi there. Sorry to be a pain but could you raise this issue here https://github.com/iqbal-lab-org/cobs, and we can answer there tomorrow .
Can you also give the command you ran? Thanks

[davidmaimoun]

It is very kind from you to help me
I'll do that!

Thank you for all

[davidmaimoun]

Hi Mr Iqbal,
Sorry to disturb you again, but I submitted my question 9 days ago and I didn't get an answer. I also try the web site, but no answer yet.
Do you know if there is another way to reach somebody for help

Thank you