WARNING Cannot find normalisation 'XXX' #169
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Sorry for my format： 2023-09-27 18:30:25,870 INFO Using non-interactive backend |
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For https://fan-c.readthedocs.io/en/latest/fanc-executable/compatibility.html#juicer-hic-files In your post you mention using But the normalisation might be called differently internally. If it does not work, see this post for a way to get the available normalisations in your object. |
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Thank you for your help. I tested the initial Hi-C files generated using different workflows, and found that the options "none", "VC", "VC_SQRT", and "NONE" worked fine, but I encountered the same problem with "KR" and "ICE". Additionally, when using data processed by Juicer, only the "NONE" option worked for visualization, while other options did not. I'm wondering if this is because my workflow is not compatible with FAN-C (where one dataset is generated using the complete HiCPro workflow and the other dataset is generated using Juicer's pair conversion). |
Dear FAN-C providers：
I wanted to use fancplot to plot a Hic map, but I encountered an error.
2023-09-27 17:33:32,993 INFO Using non-interactive backend /public/home/qqfu/miniconda3/envs/fan-c/lib/python3.7/site-packages/fanc/compatibility/juicer.py:353: UserWarning: Support for Juicer .hic v9 is still in beta. Please report any issues to https://github.com/vaquerizaslab/fanc/issues/92 warnings.warn(f"Support for Juicer .hic v{self.version} is still in beta. " /public/home/qqfu/miniconda3/envs/fan-c/lib/python3.7/site-packages/fanc/compatibility/juicer.py:353: UserWarning: Support for Juicer .hic v9 is still in beta. Please report any issues to https://github.com/vaquerizaslab/fanc/issues/92 warnings.warn(f"Support for Juicer .hic v{self.version} is still in beta. " 2023-09-27 17:33:33,732 INFO Found 1 regions /public/home/qqfu/miniconda3/envs/fan-c/lib/python3.7/site-packages/fanc/compatibility/juicer.py:797: UserWarning: Cannot find normalisation vector for chromosome: HPV16, normalisation: SCALE, resolution: 500000, unit: BP. This could indicate that SCALE normalisation did not work for this chromosome. Will return NaN instead. res=resolution, unit=unit /public/home/qqfu/miniconda3/envs/fan-c/lib/python3.7/site-packages/fanc/compatibility/juicer.py:797: UserWarning: Cannot find normalisation vector for chromosome: HPV18, normalisation: SCALE, resolution: 500000, unit: BP. This could indicate that SCALE normalisation did not work for this chromosome. Will return NaN instead. res=resolution, unit=unit /public/home/qqfu/miniconda3/envs/fan-c/bin/fancplot:189: UserWarning: There was an error with plot 0, region chr2:0-240000000 (Traceback (most recent call last): File "/public/home/qqfu/miniconda3/envs/fan-c/bin/fancplot", line 169, in __init__ fig, axes = gf.plot(plot_region) File "/public/home/qqfu/miniconda3/envs/fan-c/lib/python3.7/site-packages/fanc/plotting/plotter.py", line 211, in plot p.plot(r) File "/public/home/qqfu/miniconda3/envs/fan-c/lib/python3.7/site-packages/fanc/plotting/base_plotter.py", line 785, in plot plot_output = self._plot((x_region, y_region)) File "/public/home/qqfu/miniconda3/envs/fan-c/lib/python3.7/site-packages/fanc/plotting/hic_plotter.py", line 299, in _plot self._refresh(region) File "/public/home/qqfu/miniconda3/envs/fan-c/lib/python3.7/site-packages/fanc/plotting/hic_plotter.py", line 342, in _refresh self.current_matrix = self.hic_buffer.get_matrix(*region) File "/public/home/qqfu/miniconda3/envs/fan-c/lib/python3.7/site-packages/fanc/plotting/hic_plotter.py", line 143, in get_matrix self._BUFFERING_STRATEGIES[self.buffering_strategy](self, *regions) File "/public/home/qqfu/miniconda3/envs/fan-c/lib/python3.7/site-packages/fanc/plotting/hic_plotter.py", line 186, in _buffer_relative norm=self.norm, oe=self.oe, log=self.log) File "/public/home/qqfu/miniconda3/envs/fan-c/lib/python3.7/site-packages/fanc/architecture/comparisons.py", line 587, in matrix m_bottom = self.matrix_bottom.matrix(*args, **kwargs) * self.scaling_factor File "/public/home/qqfu/miniconda3/envs/fan-c/lib/python3.7/site-packages/fanc/matrix.py", line 1025, in matrix **kwargs) File "/public/home/qqfu/miniconda3/envs/fan-c/lib/python3.7/site-packages/fanc/matrix.py", line 963, in regions_and_matrix_entries row_regions, col_regions, edges_iter = self.regions_and_edges(key, *args, **kwargs) File "/public/home/qqfu/miniconda3/envs/fan-c/lib/python3.7/site-packages/fanc/matrix.py", line 869, in regions_and_edges row_regions = list(row_regions) File "/public/home/qqfu/miniconda3/envs/fan-c/lib/python3.7/site-packages/fanc/compatibility/juicer.py", line 900, in _region_subset norm = self.normalisation_vector(region.chromosome) File "/public/home/qqfu/miniconda3/envs/fan-c/lib/python3.7/site-packages/fanc/compatibility/juicer.py", line 789, in normalisation_vector raise ValueError("Cannot find normalisation '{}'".format(normalisation)) ValueError: Cannot find normalisation 'SCALE' ) tb)) 2023-09-27 17:33:34,785 WARNING Cannot find normalisation 'SCALE'Here is my code：
fancplot chr2:0-240mb -o ./SiHa.500kb.ic.png -p split -l /public/home/qqfu/HPV-PoreC/HiPore-C/Use.hg38_hpv16_18.Res-02/Result/normal.PoreC.hic/SiHa.norm.hic@500kb /public/home/qqfu/HPV-PoreC/HiPore-C/Use.hg38_hpv16_18.Res-02/Result/hic.hicpro/SiHa_HiC.allValidPairs.hic@500kbMy Hi-C data was processed using the "addNorm" method in Juicer.
code：
java -Xmx20g -jar /public/home/qqfu/software/juicer/juicer_tools.2.20.00.jar addNorm $HIC_FILE -j 20 -k IC -w 1000Many thanks for your help!
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