You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
hello!
I use this command to generate the hic matrix :hicBuildMatrix --samFiles mate_R1_sorted.bam mate_R2_sorted.bam
--binSize 10000
--restrictionSequence GATC
--threads 8
--inputBufferSize 1000000000
--outBam hic.bam
-o hic_matrix.h5
--QCfolder ./hicQC
Then use this command to draw:hicCorrectMatrix diagnostic_plot -m hic_matrix.h5 -o hic_corrected.png
But when this command runs, an error is reported. As shown below:
INFO:numexpr.utils:Note: NumExpr detected 48 cores but "NUMEXPR_MAX_THREADS" not set, so enforcing safe limit of 8.
INFO:numexpr.utils:NumExpr defaulting to 8 threads.
INFO:hicexplorer.hicCorrectMatrix:Removing 5172 zero value bins
INFO:hicmatrix.HiCMatrix:Number of poor regions to remove: 5172 {'smo01': 675, 'smo02': 721, 'smo03': 623, 'smo04': 455, 'smo05': 472, 'smo06': 363, 'smo07': 524, 'smo08': 414, 'smo09': 441, 'smo10': 484}
Traceback (most recent call last):
File "/home/lanmeifang/anaconda3/bin/hicCorrectMatrix", line 7, in
main()
File "/home/lanmeifang/anaconda3/lib/python3.9/site-packages/hicexplorer/hicCorrectMatrix.py", line 568, in main
plot_total_contact_dist(ma, args)
File "/home/lanmeifang/anaconda3/lib/python3.9/site-packages/hicexplorer/hicCorrectMatrix.py", line 494, in plot_total_contact_dist
plot_histogram(row_sum, mad, ax)
File "/home/lanmeifang/anaconda3/lib/python3.9/site-packages/hicexplorer/hicCorrectMatrix.py", line 428, in plot_histogram
ax2.set_xlim(mad_values.value_to_mad(np.array(ax1.get_xlim())))
File "/home/lanmeifang/anaconda3/lib/python3.9/site-packages/matplotlib/axes/_base.py", line 3688, in set_xlim
left = self._validate_converted_limits(left, self.convert_xunits)
File "/home/lanmeifang/anaconda3/lib/python3.9/site-packages/matplotlib/axes/_base.py", line 3605, in _validate_converted_limits
raise ValueError("Axis limits cannot be NaN or Inf")
ValueError: Axis limits cannot be NaN or Inf
What problem may I be encountering here? How can I solve this problem?
The text was updated successfully, but these errors were encountered:
hello!
I use this command to generate the hic matrix :hicBuildMatrix --samFiles mate_R1_sorted.bam mate_R2_sorted.bam
--binSize 10000
--restrictionSequence GATC
--threads 8
--inputBufferSize 1000000000
--outBam hic.bam
-o hic_matrix.h5
--QCfolder ./hicQC
Then use this command to draw:hicCorrectMatrix diagnostic_plot -m hic_matrix.h5 -o hic_corrected.png
But when this command runs, an error is reported. As shown below:
INFO:numexpr.utils:Note: NumExpr detected 48 cores but "NUMEXPR_MAX_THREADS" not set, so enforcing safe limit of 8.
INFO:numexpr.utils:NumExpr defaulting to 8 threads.
INFO:hicexplorer.hicCorrectMatrix:Removing 5172 zero value bins
INFO:hicmatrix.HiCMatrix:Number of poor regions to remove: 5172 {'smo01': 675, 'smo02': 721, 'smo03': 623, 'smo04': 455, 'smo05': 472, 'smo06': 363, 'smo07': 524, 'smo08': 414, 'smo09': 441, 'smo10': 484}
Traceback (most recent call last):
File "/home/lanmeifang/anaconda3/bin/hicCorrectMatrix", line 7, in
main()
File "/home/lanmeifang/anaconda3/lib/python3.9/site-packages/hicexplorer/hicCorrectMatrix.py", line 568, in main
plot_total_contact_dist(ma, args)
File "/home/lanmeifang/anaconda3/lib/python3.9/site-packages/hicexplorer/hicCorrectMatrix.py", line 494, in plot_total_contact_dist
plot_histogram(row_sum, mad, ax)
File "/home/lanmeifang/anaconda3/lib/python3.9/site-packages/hicexplorer/hicCorrectMatrix.py", line 428, in plot_histogram
ax2.set_xlim(mad_values.value_to_mad(np.array(ax1.get_xlim())))
File "/home/lanmeifang/anaconda3/lib/python3.9/site-packages/matplotlib/axes/_base.py", line 3688, in set_xlim
left = self._validate_converted_limits(left, self.convert_xunits)
File "/home/lanmeifang/anaconda3/lib/python3.9/site-packages/matplotlib/axes/_base.py", line 3605, in _validate_converted_limits
raise ValueError("Axis limits cannot be NaN or Inf")
ValueError: Axis limits cannot be NaN or Inf
What problem may I be encountering here? How can I solve this problem?
The text was updated successfully, but these errors were encountered: