vaquerizaslab/chess

Error when run chess_extract

Opened this issue · 3 comments

yanchunzhang commented

Hi, I always got this error recently when run the chess_extarct command:
do you have any idea about this error?

Traceback (most recent call last):
File "/home/ch220811/.local/bin/chess", line 585, in
Chess()
File "/home/ch220811/.local/bin/chess", line 75, in init
getattr(self, args.command)([sys.argv[0]] + sys.argv[option_ix:])
File "/home/ch220811/.local/bin/chess", line 567, in extract
args.closing_square)
File "/home/ch220811/.local/lib/python3.6/site-packages/chess/get_structures.py", line 148, in extract_structures
filter1 = filters.threshold_otsu(filter_positive, nbins=size)
File "/home/ch220811/.local/lib/python3.6/site-packages/skimage/filters/thresholding.py", line 285, in threshold_otsu
hist, bin_centers = histogram(image.ravel(), nbins, source_range='image')
File "/home/ch220811/.local/lib/python3.6/site-packages/skimage/exposure/exposure.py", line 139, in histogram
hist, bin_edges = np.histogram(image, bins=nbins, range=hist_range)
File "<array_function internals>", line 6, in histogram
File "/home/ch220811/software/lib/python3.6/site-packages/numpy/lib/histograms.py", line 856, in histogram
decrement = tmp_a < bin_edges[indices]
IndexError: index -9223372036854775808 is out of bounds for axis 0 with size 102

Somtimes I also got this error:
/slurm/reports/var/spool/slurm/d/job466467/slurm_script: line 15: 45401 Killed /home/ch220811/.local/bin/chess extract ${TSV} ${MATRIX1} ${MATRIX2} ${OUT}
Is this because my task got killed by my IT manager or the system due to memory size limit?

Thank you!

sgalan commented
yanchunzhang commented

Thank you for your reply, @sgalan !
I see the numpy_histogram bug you mentioned but I'm still not sure how to avoid this happening.
Why do you think there could be a number larger than 2**53 generated in the process of chess_extract? What the numbers used for histogam reresent? And do i need to modify the code of chess_extract or numpy_histogram by myself?

sgalan commented