unable to untangle injected graph

[michael-olufemi]

Hello,

when I try to untangle a graph with injected gene annotations, I get this error
[odgi::algorithms::stepindex] unable to index empty path CNV1
commands used is
odgi untangle -i inject.cnv.og -r NAM#1#chrI:32999-44495 -j 0.5 -t 4 -g | less

I get this error when I use this command
odgi untangle -i inject.cnv.og -r CNV1 -j 0.5 -t 4 -g | less

[odgi::untangle] error: no path CNV1 found in graph.

when I do this
odgi paths -i inject.cnv.og -L | less
The path is represent and I can see it when I visualize it

Thanks for the help

[michael-olufemi]

I see the problem now,
when I do this
odgi paths -i inject.cnv.og -f > inject.fa | grep 'CNV1'
It produces no sequence
When I ran odgi inject, it prodeuces no error.
Why is the path empty?

Thanks

[ekg]

That is strange. What's it look like in the GFA?

[michael-olufemi]

Hello @ekg,
I realized that the coordinates I provided during odgi inject is wrong. I corrected it and this command below works now
odgi untangle -i inject.cnv.og -r NAM#1#chrI:32999-44495 -j 0.5 -t 4 -g | less
However, this is still not working
odgi untangle -i inject.cnv.og -r CNV1 -j 0.5 -t 4 -g | less

[odgi::untangle] error: no path CNV1 found in graph.