chrM error

[tianxiahuihui]

Hello, I have meet an error as the picture shows when used the clipper.

ValueError: invalid contig chrM. Could you tell me how to solve this problem?

Thank you.

[tianxiahuihui]

I have solved this problem because of bedtobam. The hg19.size must have the chrM. But when I run the clipper, I meet a warning as the picture shows.
WARNING:py.warnings:/home/chendenghui/miniconda3/envs/bed/lib/python2.7/site-packages/scipy/interpolate/fitpack2.py:227: UserWarning:
The maximal number of iterations maxit (set to 20 by the program)
allowed for finding a smoothing spline with fp=s has been reached: s
too small.
There is an approximation returned but the corresponding weighted sum
of squared residuals does not satisfy the condition abs(fp-s)/s < tol.
warnings.warn(message)

what is the wrong?

Thank you.

[algaebrown]

It is warning that the spline curve-fitting scipy.interpolate.UnivariateSpline in SmoothingSpline does not fit the data very well. There can be many possible reasons. For example, not enough data points in the defined peak region, need to change smoothing factor ...etc. Right now our SmoothingSpline class will automatically assign s = len(peak).
scipy.interpolate.UnivariateSpline
SmoothingSpline

[jkkbuddika]

I have solved this problem because of bedtobam. The hg19.size must have the chrM. But when I run the clipper, I meet a warning as the picture shows.
WARNING:py.warnings:/home/chendenghui/miniconda3/envs/bed/lib/python2.7/site-packages/scipy/interpolate/fitpack2.py:227: UserWarning:
The maximal number of iterations maxit (set to 20 by the program)
allowed for finding a smoothing spline with fp=s has been reached: s
too small.
There is an approximation returned but the corresponding weighted sum
of squared residuals does not satisfy the condition abs(fp-s)/s < tol.
warnings.warn(message)

what is the wrong?

Thank you.

@tianxiahuihui can you please tell me how exactly you fixed this issue (at least partially)? I am trying to run clipper on a Drosophila dataset and having a hard time getting it to work because of the similar issue (outlined in #79 ). Any advice would help!

Thanks!!!

[maximus-sci]

I have solved this problem because of bedtobam.

I would also love to know how you solved this issue. I cannot run clipper due to the exact same error

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/home/fmax/miniconda3/envs/clipper3/bin/clipper", line 8, in <module>
    sys.exit(call_main())
  File "/home/fmax/miniconda3/envs/clipper3/lib/python3.7/site-packages/clipper/src/main.py", line 266, in call_main
    main(options)
  File "/home/fmax/miniconda3/envs/clipper3/lib/python3.7/site-packages/clipper/src/main.py", line 105, in main
    peaks_dicts.append(job.get(timeout=options.timeout))
  File "/home/fmax/miniconda3/envs/clipper3/lib/python3.7/multiprocessing/pool.py", line 657, in get
    raise self._value
ValueError: invalid contig `chrM`

[tslzs]

I have solved this problem because of bedtobam. The hg19.size must have the chrM. But when I run the clipper, I meet a warning as the picture shows. WARNING:py.warnings:/home/chendenghui/miniconda3/envs/bed/lib/python2.7/site-packages/scipy/interpolate/fitpack2.py:227: UserWarning: The maximal number of iterations maxit (set to 20 by the program) allowed for finding a smoothing spline with fp=s has been reached: s too small. There is an approximation returned but the corresponding weighted sum of squared residuals does not satisfy the condition abs(fp-s)/s < tol. warnings.warn(message)

what is the wrong?

Thank you.

I have met same problem, do you solve it?