Bigscape error

[mabouelk]

After I ran "snakemake -j 16 --use-conda"

Finished job 5. 6 of 28 steps (21%) done Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: .snakemake/log/2024-09-23T134546.119120.snakemake.log WorkflowError: At least one job did not complete successfully.

[kevinbretscher]

Hi, could you share the complete log/error message from .snakemake/log/2024-09-23T134546.119120.snakemake.log

[mabouelk]

2024-09-26T154556.598497.snakemake.log

[kevinbretscher]

For bigscape it can help to run the command manually to see what causes the error. Activate the bigscape_bacLIFE enviroment and run the following command. Please share the output / errors.

python ./intermediate_files/BiG-SCAPE/bigscape.py -i intermediate_files/antismash -o intermediate_files/BiG-SCAPE/bigscape_output/ --pfam_dir intermediate_files/PFAM/ --mode glocal --mibig --cutoffs 0.3 0.7 --include_singletons --cores 24 --mix

See https://github.com/Carrion-lab/bacLIFE/issues/16 on how to resolve some potential issues.

[mabouelk]

I did and the networkx module was not installed. After installing it and re-run the code i got this

raceback (most recent call last): File "./intermediate_files/BiG-SCAPE/bigscape.py", line 63, in from sklearn.cluster import AffinityPropagation File "/home/exouser/miniconda3/envs/bigscape_bacLIFE/lib/python3.6/site-packages/sklearn/cluster/init.py", line 6, in from .spectral import spectral_clustering, SpectralClustering File "/home/exouser/miniconda3/envs/bigscape_bacLIFE/lib/python3.6/site-packages/sklearn/cluster/spectral.py", line 15, in from ..metrics.pairwise import pairwise_kernels File "/home/exouser/miniconda3/envs/bigscape_bacLIFE/lib/python3.6/site-packages/sklearn/metrics/init.py", line 33, in from . import cluster File "/home/exouser/miniconda3/envs/bigscape_bacLIFE/lib/python3.6/site-packages/sklearn/metrics/cluster/init.py", line 20, in from .unsupervised import silhouette_samples File "/home/exouser/miniconda3/envs/bigscape_bacLIFE/lib/python3.6/site-packages/sklearn/metrics/cluster/unsupervised.py", line 12, in from ..pairwise import pairwise_distances File "/home/exouser/miniconda3/envs/bigscape_bacLIFE/lib/python3.6/site-packages/sklearn/metrics/pairwise.py", line 30, in from .pairwise_fast import _chi2_kernel_fast, _sparse_manhattan ImportError: libgfortran.so.3: cannot open shared object file: No such file or directory [Tue Oct 1 20:43:46 2024] Error in rule bigscape_exe: jobid: 15 input: intermediate_files/antismash/Bacillus_licheniformis_X00001_O/Bacillus_licheniformis_X00001_O.gbk, intermediate_files/PFAM/Pfam-A.hmm output: intermediate_files/BiG-SCAPE/bigscape_output/index.html, intermediate_files/BiG-SCAPE/bigscape_output/network_files/hybrids_glocal/mix/mix_clustering_c0.70.tsv, intermediate_files/BiG-SCAPE/bigscape_output/network_files/hybrids_glocal/mix/mix_c0.70.network, intermediate_files/BiG-SCAPE/bigscape_output/network_files/hybrids_glocal/Network_Annotations_Full.tsv conda-env: bigscape_bacLIFE shell: python ./intermediate_files/BiG-SCAPE/bigscape.py -i intermediate_files/antismash/ -o intermediate_files/BiG-SCAPE/bigscape_output/ --pfam_dir intermediate_files/PFAM/ --mode glocal --mibig --cutoffs 0.3 0.7 --include_singletons --cores 24 --mix; rm -r intermediate_files/BiG-SCAPE/bigscape_output/network_files/hybrids_glocal; mv intermediate_files/BiG-SCAPE/bigscape_output/network_files/*hybrids_glocal intermediate_files/BiG-SCAPE/bigscape_output/network_files/hybrids_glocal (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: .snakemake/log/2024-10-01T204343.508978.snakemake.log WorkflowError: At least one job did not complete successfully.

[kevinbretscher]

You can maybe try the solution proposed in #16 of downgrading scikit-learn. The issue seems the be the specific bigscape install as on our side it all still works.

[mabouelk]

Yes I tried but I got this

Solving environment: - warning libmamba Added empty dependency for problem type SOLVER_RULE_UPDATE failed

LibMambaUnsatisfiableError: Encountered problems while solving:

• package scikit-learn-0.19.2-py27_blas_openblas_200 requires python 2.7*, but none of the providers can be installed

Could not solve for environment specs The following packages are incompatible ?? pin-1 is installable and it requires ? ?? python 3.12.* , which can be installed; ?? scikit-learn 0.19.2* is not installable because there are no viable options ?? scikit-learn 0.19.2 would require ? ?? python [2.7 |>=2.7,<2.8.0a0 ], which conflicts with any installable versions previously reported; ?? scikit-learn 0.19.2 would require ? ?? python [3.5 |>=3.5,<3.6.0a0 ], which conflicts with any installable versions previously reported; ?? scikit-learn 0.19.2 would require ? ?? python 3.6 , which conflicts with any installable versions previously reported; ?? scikit-learn 0.19.2 would require ? ?? python >=3.6,<3.7.0a0 , which conflicts with any installable versions previously reported; ?? scikit-learn 0.19.2 would require ?? python >=3.7,<3.8.0a0 , which conflicts with any installable versions previously reported.

[kevinbretscher]

@gguerr001 Is working on a docker for Baclife that hopefully will solve any install issues with bigscape. We hope it will be available soon.

For now you could try to reinstall the enviroment with Conda instead of mamba as it seems this can sometimes solve issues.

[Hu-jiayu]

Dear authors and users,Hello, I'm a loyal fan of the baclife tool from China. This tool is simply great！ But I also encountered the same problem in the process of operation. Did you solve it in the end? Can you tell me how to solve this error problem?I can't wait to solve this problem and analyze my data. I would appreciate it if you could tell me how to solve this problem.

[anilchauhanhp9]

I Installed gcc-6-base 1st and then ibgfortran3. After that I installed networkx in the bacLIFE env, and pipeline works without any errors.

Information on how to install gcc-6-base and ibgfortran3 can be found at (https://gist.github.com/sakethramanujam/faf5b677b6505437dbdd82170ac55322)