ValueError: could not broadcast input array from shape (0,) into shape (0,2)

[Edison2021]

Hi Firas

Got an error below

Traceback (most recent call last):
File "/home/manager/src/amiga-master/amiga.py", line 392, in
AMiGA()
File "/home/manager/src/amiga-master/amiga.py", line 90, in init
getattr(self, args.command)()
File "/home/manager/src/amiga-master/amiga.py", line 210, in fit
Command(args).fit()
File "/home/manager/src/amiga-master/libs/commands.py", line 114, in fit
runGrowthFitting(data,mappings,self.directory,args,verbose=args.verbose)
File "/home/manager/src/amiga-master/libs/analyze.py", line 168, in runGrowthFitting
sub_plate.model(nthin=args.time_step_size,store=store,verbose=verbose)
File "/home/manager/src/amiga-master/libs/growth.py", line 705, in model
curve = gm.run(name=sample_id)
File "/home/manager/src/amiga-master/libs/model.py", line 249, in run
curve = GrowthCurve(x=time,y=actual_input,y0=self.y0,y1=self.y1,y2=self.y2,
File "/home/manager/src/amiga-master/libs/curve.py", line 132, in init
self.describe()
File "/home/manager/src/amiga-master/libs/curve.py", line 192, in describe
dx = detectDiauxie(self.x,self.y0,self.y1,self.y2,self.cov0,self.cov1,
File "/home/manager/src/amiga-master/libs/diauxie.py", line 88, in detectDiauxie
ret[:,4:6] = [[y1[l-1],y1[r-1]] for l,r in bounds] # growth rate at both bounds
ValueError: could not broadcast input array from shape (0,) into shape (0,2)

What kind of problems caused the error?

Thanks
Edison

[Firas Midani]

Hmm, error suggests that there is a problem with the function that detects diauxic shifts. My best guess is that your data set has a particular growth curve with a weird behavior that the function has not seen before and does not know how to handle. But it's hard to tell without replicating the error myself.

Can you try to re-run your command with the --verbose argument? This will help you determine which well in which file or plate causes the problem. If you share that particular growth curve with me here, I can try to replicate the error. You can also share the whole file with me too instead.

[Firas Midani]

Thanks for sharing your data. I was able to replicate the error and it was a fairly simple fix. Please re-install AMiGA and run again. If you cloned the repository, you can simply git pull, otherwise, just simply replace the old amiga folder with the new one. Let me know if that fixes the problem.

[Edison2021]

Thanks for your prompt response. It is working now,