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ERROR:root:failed to build spline #72
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Hi The graduate student who has been maintaining this repo has since left and unfortunately we do not yet have a replacement to really dig into this issue, but maybe a similar one can provide some hints: #42 |
Thanks. I took a look at that thread previously and the only solution was to edit the call_peaks script, although the position was slightly ambiguous. Is it possible to take a look at that solution on your end? I've tried placing the while loop in several places to no avail. |
Hi Bridget! In a very weird coincidence, I have been running into the same problem. If I place the while loop from #42 after the following line in call_peak.py, clipper runs, although the warnings mentioned in #42 still apply:
add right after the above line
Sahin |
[similar problem on stackoverflow] (https://stackoverflow.com/questions/32230362/python-interpolate-univariatespline-package-error-mk-failed-for-hidden-m). According to scipy the degree |
Fixed in new CLIPper release |
Hello,
We are having issues running clipper on our system. Specifically, we get the below error for the minimal "clipper --processors=16 -b clip1.k.bam -s hg19 -o clip1.k.peaks.bed." We do not get this error when running clipper with mm10. Is there a fix?
ERROR:root:failed to build spline (m>k) failed for hidden m: fpcurf0:m=2, [0 1], [3. 0.], 11, 3, None
ERROR:root:peak finding failed:, ENSG00000008083.9, (m>k) failed for hidden m: fpcurf0:m=2
Traceback (most recent call last):
File "/home/bebegg/anaconda2/bin/clipper", line 11, in
load_entry_point('clipper==0.2.0', 'console_scripts', 'clipper')()
File "/home/bebegg/anaconda2/lib/python2.7/site-packages/clipper-0.2.0-py2.7-linux-x86_64.egg/clipper/src/peakfinder.py", line 712, in call_main
main(options)
File "/home/bebegg/anaconda2/lib/python2.7/site-packages/clipper-0.2.0-py2.7-linux-x86_64.egg/clipper/src/peakfinder.py", line 568, in main
peaks_dicts.append(job.get(timeout=options.timeout))
File "/home/bebegg/anaconda2/lib/python2.7/multiprocessing/pool.py", line 572, in get
raise self._value
multiprocessing.pool.MaybeEncodingError: Error sending result: 'error('(m>k) failed for hidden m: fpcurf0:m=2',)'. Reason: 'PicklingError("Can't pickle <class 'dfitpack.error'>: import of module dfitpack failed",)'
Thanks!
Bridget
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