tanaylab/misha

object `exp_track_nm` not found in `shaman_score_hic_track()`

Closed this issue · 2 comments

I finished gtrack.2d.import(), gdb.reload() and shaman_shuffle_hic_track() and everything is OK.
However, there is something wrong in shaman_score_hic_track() :

track_name  <- "grnsmile_hic_obs"
score_track_name <- "grnsmile_hic_score_new"
exp_track_name<-'grnsmile_hic_obs_shuffle'
shaman_score_hic_track(
  track_db=groot, 
  work_dir=tempdir(),
  score_track_nm=score_track_name, 
  obs_track_nms=track_name,
  exp_track_nm=exp_track_name,
  max_jobs= 3)

The error is:

1665217234321

This error may indicate that something in the output of shaman_shuffle_hic_track() is missed.

I then checked /db/genome3d/hg38/tracks/, and that directory did have shuffle_hic_track in it, but the shaman_score_hic_track() could not find it.

1665217209936

How could I fix this?

Thank you for your help!

I ran gdb.reload() , and it seemed to be solved.
Let it slide...

I ran gdb.reload() , and it seemed to be solved. Let it slide...

BTW, it seemed to consume too much time (more than 22 hours by shaman.mc_support=20)
1665407647199

Is it typical?
Thank you for your help!