Comments (6)
cmandreani
commented on August 11, 2024
Hi @SamWilliamsUOB , I retrieved the same error with anaconda3, and network files were properly generated but there was no tree constructed.
With docker worked fine, though.
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Sam-Will
commented on August 11, 2024
Managed to get this script to work with the --clans-off flag
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jorgecnavarrom
commented on August 11, 2024
Seems like scikit-learn's Affinity propagation was the cause.. which version do you have installed?
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Sam-Will
commented on August 11, 2024
Hi Jorge,
So looks like 1.0.2 for sklearn
>>> import sklearn
>>> print(sklearn.__version__)
1.0.2
Thanks,
Sam
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jorgecnavarrom
commented on August 11, 2024
Could you try with v0.19.2?
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zreitz
commented on August 11, 2024
FYI, I had a similar error with --mix and --cutoffs above ~0.4.
/lustre/BIF/nobackup/reitz001/mambaforge/envs/bigscape/lib/python3.6/site-packages/sklearn/cluster/_affinity_propagation.py:247: ConvergenceWarning: Affinity propagation did not converge, this model will not have any cluster centers.
"will not have any cluster centers.", ConvergenceWarning)
Traceback (most recent call last):
File "/home/reitz001/lustre/software/BiG-SCAPE/bigscape.py", line 3042, in <module>
clanCutoff=options.clan_cutoff, htmlFolder=network_html_folder)
File "/home/reitz001/lustre/software/BiG-SCAPE/bigscape.py", line 1459, in clusterJsonBatch
labels[bgcExt2Int[bgcSub2Ext_[i]]] = bgcExt2Int[bgcSub2Ext_[exemplarsSub[labelsSub[i]]]]
IndexError: list index out of range
Downgrading sklearn from v0.24.2 to v0.19.2 solved it.
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Related Issues (20)
- Don't know why the task killed, the task have finished in network? is the task finished?
- 'ascii' codec can't decode byte 0xce & No sequence extracted HOT 3
- The inconsistent results in "mix_clustering_c0.30" and "mix_c0.30.network" HOT 7
- cosine distance among BGCs HOT 2
- Singularity Read-only file system Error HOT 3
- Error while running BiG-SCAPE HOT 3
- Docker HOT 1
- Add official singularity image HOT 1
- Memory error HOT 1
- MIBiG singletons in network file
- MIBiG subnetworks not pruned
- Delete or fix the bioconda recipe HOT 2
- Filter, warn or quit if input GenBank is too large
- error: TypeError: 'NoneType' object is not subscriptable HOT 5
- BGCs missing in network HOT 2
- BiG-SCAPE recognises gbk file but does not extract sequences HOT 2
- sklearn is deprecated HOT 1
- Affinity propagation did not converge HOT 7
- The error "did not find file MIBiG_1.4_final.zip" HOT 2
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