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ERROR: Disentangling failed: Failed in 'from scipy import stats, inf, log'! #315

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andreasmorales opened this issue Mar 4, 2024 · 3 comments
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ERROR: Disentangling failed: Failed in 'from scipy import stats, inf, log'! #315

andreasmorales opened this issue Mar 4, 2024 · 3 comments
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@andreasmorales
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I used get_organelle_from_reads.py with the folowing parameters: -t 64 -R 100 -k 21,35,45,65,85,105,127 -F embplant_mt,embplant_pt -P 1000000 --target-genome-size 350000,160000 --spades-options "-m 120" and after sliming assembly I get the following error:

2024-03-04 08:25:37,314 - INFO: Extracting embplant_mt from the assemblies ...
2024-03-04 08:25:37,318 - INFO: Disentangling /home/amorales/scratch/Asa-genoma-mitochondriale/getorganelle_out/extended_spades/K127/assembly_graph.fastg.extend-embplant_mt-embplant_pt.fastg as a circular genome ... 
2024-03-04 08:25:37,418 - ERROR: Disentangling failed: Failed in 'from scipy import stats, inf, log'!
2024-03-04 08:25:37,420 - INFO: Extracting embplant_mt from the assemblies failed.

2024-03-04 08:25:37,420 - INFO: Extracting embplant_pt from the assemblies ...
2024-03-04 08:25:37,421 - INFO: Disentangling /home/amorales/scratch/Asa-genoma-mitochondriale/getorganelle_out/extended_spades/K127/assembly_graph.fastg.extend-embplant_mt-embplant_pt.fastg as a circular genome ... 
2024-03-04 08:25:37,517 - ERROR: Disentangling failed: Failed in 'from scipy import stats, inf, log'!
2024-03-04 08:25:37,518 - INFO: Extracting embplant_pt from the assemblies failed.

I'm using a fresh anaconda3 environment with GetOrganelle v1.7.7.0 (build pyh7cba7a3_0, channel bioconda)

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@JianjunJin
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Thanks for reaching out!
Please downgrade scipy from 1.12 to 1.11.3. See here for more.

Let me know.

@JianjunJin JianjunJin added the bug label Mar 5, 2024
@andreasmorales
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It works like a charm! Thanks! Sorry for not finding that issue, since the output differs I thought mine was a different bug.

JianjunJin added a commit that referenced this issue Apr 3, 2024
@JianjunJin
1.7.7.1 - bug fixes
1949437 
1. fix a import bug of 'from scipy import stat, log, inf' issue (issue #132 #315)
2. fix a ZeroDivisionError bug when the estimated coverage is 0 (issue #311)
3. Disentangling failed -> Disentangling unsuccessful to avoid panic (issue #308)
4. fix a bug in parsing options when '-F anonym' is used (issue #319)
5. have max_multiplicity passed to no-slim case
6. minor adjustment
@JianjunJin
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As a follow-up, GetOrganelle v1.7.7.1 can now be installed using conda/mamba.

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@JianjunJin @andreasmorales