I have been trying to run LRBinner on a metagenomics dataset from ONT reads. I first run it just for the reads and it worked perfectly. However, when I try to bin the contigs created by metaFlye, I get the following error when the HDBSCAN is running:
2023-07-26 09:59:54,654 - INFO - Clustering using HDBSCAN running
Traceback (most recent call last):
File "/home/metac/bin/lrbinner", line 203, in
main()
File "/home/metac/bin/lrbinner", line 185, in main
pipelines.run_contig_binning(args)
File "/home/metac/Programs/LRBinner/mbcclr_utils/pipelines.py", line 239, in run_contig_binning
cluster_utils.perform_contig_binning_HDBSCAN(
File "/home/metac/Programs/LRBinner/mbcclr_utils/cluster_utils.py", line 494, in perform_contig_binning_HDBSCAN
labels = HDBSCAN(min_cluster_size=250).fitpredict(latent)
File "/home/metac/anaconda3/envs/snakemake/envs/lrbinner/lib/python3.10/site-packages/hdbscan/hdbscan.py", line 1243, in fitpredict
self.fit(X)
File "/home/metac/anaconda3/envs/snakemake/envs/lrbinner/lib/python3.10/site-packages/hdbscan/hdbscan.py", line 1205, in fit
) = hdbscan(cleandata, **kwargs)
File "/home/metac/anaconda3/envs/snakemake/envs/lrbinner/lib/python3.10/site-packages/hdbscan/hdbscan.py", line 884, in hdbscan
_tree_tolabels(
File "/home/metac/anaconda3/envs/snakemake/envs/lrbinner/lib/python3.10/site-packages/hdbscan/hdbscan.py", line 80, in _tree_to_labels
labels, probabilities, stabilities = get_clusters(
File "hdbscan/_hdbscan_tree.pyx", line 659, in hdbscan._hdbscan_tree.get_clusters
File "hdbscan/_hdbscan_tree.pyx", line 733, in hdbscan._hdbscan_tree.get_clusters
TypeError: 'numpy.float64' object cannot be interpreted as an integer
Could you give me some insight on what may be happening?
Hi,
I have been trying to run LRBinner on a metagenomics dataset from ONT reads. I first run it just for the reads and it worked perfectly. However, when I try to bin the contigs created by metaFlye, I get the following error when the HDBSCAN is running:
2023-07-26 09:59:54,654 - INFO - Clustering using HDBSCAN running Traceback (most recent call last): File "/home/metac/bin/lrbinner", line 203, in
main()
File "/home/metac/bin/lrbinner", line 185, in main
pipelines.run_contig_binning(args)
File "/home/metac/Programs/LRBinner/mbcclr_utils/pipelines.py", line 239, in run_contig_binning
cluster_utils.perform_contig_binning_HDBSCAN(
File "/home/metac/Programs/LRBinner/mbcclr_utils/cluster_utils.py", line 494, in perform_contig_binning_HDBSCAN
labels = HDBSCAN(min_cluster_size=250).fitpredict(latent)
File "/home/metac/anaconda3/envs/snakemake/envs/lrbinner/lib/python3.10/site-packages/hdbscan/hdbscan.py", line 1243, in fitpredict
self.fit(X)
File "/home/metac/anaconda3/envs/snakemake/envs/lrbinner/lib/python3.10/site-packages/hdbscan/hdbscan.py", line 1205, in fit
) = hdbscan(cleandata, **kwargs)
File "/home/metac/anaconda3/envs/snakemake/envs/lrbinner/lib/python3.10/site-packages/hdbscan/hdbscan.py", line 884, in hdbscan
_tree_tolabels(
File "/home/metac/anaconda3/envs/snakemake/envs/lrbinner/lib/python3.10/site-packages/hdbscan/hdbscan.py", line 80, in _tree_to_labels
labels, probabilities, stabilities = get_clusters(
File "hdbscan/_hdbscan_tree.pyx", line 659, in hdbscan._hdbscan_tree.get_clusters
File "hdbscan/_hdbscan_tree.pyx", line 733, in hdbscan._hdbscan_tree.get_clusters
TypeError: 'numpy.float64' object cannot be interpreted as an integer
Could you give me some insight on what may be happening?
Thank you in advance, Pablo