search

segalab / SGVFinder

Other
29 stars 15 forks source link

When run "work_on_collection" got some issues #35

Open nytwhzlg opened 2 weeks ago

nytwhzlg commented 2 weeks ago

Hello, I'm having trouble running "work_on_collection." Below is the error message I'm receiving. Could you please provide me with a solution?

Traceback (most recent call last): File "/home/miniconda3/envs/sgv_finder2_0.0.1/bin/svfinder", line 8, in sys.exit(run()) File "/home/miniconda3/envs/sgv_finder2_0.0.1/lib/python3.10/site-packages/SGVFinder2/cli/svfinder_cli.py", line 95, in run vsgv, dsgv = work_on_collection( File "/home/miniconda3/envs/sgv_finder2_0.0.1/lib/python3.10/site-packages/SGVFinder2/svfinder.py", line 229, in work_on_collection sgvregions, normdf = find_sgvs(bacdf, max_spacing, vsgv_dense_perc, bacname, deldf, File "/home/miniconda3/envs/sgv_finder2_0.0.1/lib/python3.10/site-packages/SGVFinder2/svfinder.py", line 321, in find_sgvs sclusters = cluster_stretches(stretches, nodeldf, _spearman_dissim, dissim_thresh, 'complete') File "/home/miniconda3/envs/sgv_finder2_0.0.1/lib/python3.10/site-packages/SGVFinder2/svfinder.py", line 429, in cluster_stretches Z = linkage(distance, method=linkage_method) File "/home/miniconda3/envs/sgv_finder2_0.0.1/lib/python3.10/site-packages/scipy/cluster/hierarchy.py", line 1064, in linkage raise ValueError("The condensed distance matrix must contain only " ValueError: The condensed distance matrix must contain only finite values.

nytwhzlg commented 2 weeks ago

Above that have some warning messages as these:

/home/miniconda3/envs/sgv_finder2_0.0.1/lib/python3.10/site-packages/scipy/stats/_stats_py.py:5445: ConstantInputWarning: An input array is constant; the correlation coefficient is not defined. warnings.warn(stats.ConstantInputWarning(warn_msg)) /home/miniconda3/envs/sgv_finder2_0.0.1/lib/python3.10/site-packages/scipy/stats/_stats_py.py:5445: ConstantInputWarning: An input array is constant; the correlation coefficient is not defined. warnings.warn(stats.ConstantInputWarning(warn_msg)) /home/miniconda3/envs/sgv_finder2_0.0.1/lib/python3.10/site-packages/scipy/stats/_stats_py.py:5445: ConstantInputWarning: An input array is constant; the correlation coefficient is not defined. warnings.warn(stats.ConstantInputWarning(warn_msg)) /home/miniconda3/envs/sgv_finder2_0.0.1/lib/python3.10/site-packages/scipy/stats/_stats_py.py:5445: ConstantInputWarning: An input array is constant; the correlation coefficient is not defined. warnings.warn(stats.ConstantInputWarning(warn_msg)) /home/miniconda3/envs/sgv_finder2_0.0.1/lib/python3.10/site-packages/scipy/stats/_stats_py.py:5445: ConstantInputWarning: An input array is constant; the correlation coefficient is not defined. warnings.warn(stats.ConstantInputWarning(warn_msg)) /home/miniconda3/envs/sgv_finder2_0.0.1/lib/python3.10/site-packages/scipy/stats/_stats_py.py:5445: ConstantInputWarning: An input array is constant; the correlation coefficient is not defined. warnings.warn(stats.ConstantInputWarning(warn_msg)) /home/miniconda3/envs/sgv_finder2_0.0.1/lib/python3.10/site-packages/scipy/stats/_stats_py.py:5445: ConstantInputWarning: An input array is constant; the correlation coefficient is not defined. warnings.warn(stats.ConstantInputWarning(warn_msg)) /home/miniconda3/envs/sgv_finder2_0.0.1/lib/python3.10/site-packages/scipy/stats/_stats_py.py:5445: ConstantInputWarning: An input array is constant; the correlation coefficient is not defined. warnings.warn(stats.ConstantInputWarning(warn_msg)) /home/miniconda3/envs/sgv_finder2_0.0.1/lib/python3.10/site-packages/scipy/stats/_stats_py.py:5445: ConstantInputWarning: An input array is constant; the correlation coefficient is not defined. warnings.warn(stats.ConstantInputWarning(warn_msg))