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?
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?