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Rounge-lab / VirMake

VirMake is a Snakemake based pipeline that offers viral metagenic data analysis on paired-end data. It offers taxonomic and functional annotation, supports offline running and support for HPC cluster execution. It is made for Linux based systems and has been tested on SLURM cluster execution.
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Installing Issue #13

Closed o-enric closed 3 weeks ago

o-enric commented 7 months ago

Operating System: Linux horizon 5.15.0-91-generic CPU: AMD Epyc 7763 processors Memory: DDR4 RAM Storage: SSD (Solid State Drive) Graphics Accelerator: Tesla A40 GPU

Steps to Reproduce:

Activate the base environment: conda activate base

Clone the VirMake repository: git clone https://github.com/uio-bmi/VirMake.git

Navigate to the VirMake directory: cd VirMake

Run the setup script: python setup.py -y

Description: Initially, I successfully installed Virmake, but it crashed at 61%. Now, I am unable to reinstall it.

Activating conda environment: .snakemake/conda/6c72fc1cbcaf2ae14237d0977e6eb871 Traceback (most recent call last): File "/str1/home/otavio.henrique/VirMake/workflow/.snakemake/conda/6c72fc1cbcaf2ae14237d0977e6eb871/bin/DRAM-setup.py", line 5, in from mag_annotator.database_processing import (prepare_databases, update_dramforms, File "/str1/home/otavio.henrique/VirMake/workflow/.snakemake/conda/6c72fc1cbcaf2ae14237d0977e6eb871/lib/python3.10/site-packages/mag_annotator/database_processing.py", line 13, in from skbio import read as readsequence File "/str1/home/otavio.henrique/VirMake/workflow/.snakemake/conda/6c72fc1cbcaf2ae14237d0977e6eb871/lib/python3.10/site-packages/skbio/init.py", line 11, in import skbio.io # noqa File "/str1/home/otavio.henrique/VirMake/workflow/.snakemake/conda/6c72fc1cbcaf2ae14237d0977e6eb871_/lib/python3.10/site-packages/skbio/io/init.py", line 248, in importmodule('skbio.io.format.lsmat') File "/str1/home/otavio.henrique/VirMake/workflow/.snakemake/conda/6c72fc1cbcaf2ae14237d0977e6eb871/lib/python3.10/importlib/init.py", line 126, in import_module return _bootstrap._gcdimport(name[level:], package, level) File "/str1/home/otavio.henrique/VirMake/workflow/.snakemake/conda/6c72fc1cbcaf2ae14237d0977e6eb871/lib/python3.10/site-packages/skbio/io/format/lsmat.py", line 77, in from skbio.stats.distance import DissimilarityMatrix, DistanceMatrix File "/str1/home/otavio.henrique/VirMake/workflow/.snakemake/conda/6c72fc1cbcaf2ae14237d0977e6eb871_/lib/python3.10/site-packages/skbio/stats/distance/init.py", line 197, in from .mantel import mantel, pwmantel File "/str1/home/otavio.henrique/VirMake/workflow/.snakemake/conda/6c72fc1cbcaf2ae14237d0977e6eb871/lib/python3.10/site-packages/skbio/stats/distance/mantel.py", line 16, in from scipy.stats import ConstantInputWarning ImportError: cannot import name 'ConstantInputWarning' from 'scipy.stats' (/str1/home/otavio.henrique/VirMake/workflow/.snakemake/conda/6c72fc1cbcaf2ae14237d0977e6eb871/lib/python3.10/site-packages/scipy/stats/init.py) [Thu Mar 28 02:53:01 2024] Error in rule DRAMv: jobid: 2 output: /str1/home/otavio.henrique/VirMake/databases/DRAM/DRAMdata conda-env: /str1/home/otavio.henrique/VirMake/workflow/.snakemake/conda/6c72fc1cbcaf2ae14237d0977e6eb871 shell: DRAM-setup.py prepare_databases --output_dir /str1/home/otavio.henrique/VirMake/databases/DRAM/DRAM_data --verbose --skip_uniref --threads 24;DRAM-setup.py export_config --output_file /str1/home/otavio.henrique/VirMake/databases/DRAM/DRAM_data/DRAM.config (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/2024-03-28T025258.574203.snakemake.log ERROR conda.cli.main_run:execute(124): conda run snakemake --snakefile utils/setup_db.smk --cores 24 --configfile /str1/home/otavio.henrique/VirMake/workflow/config.yaml --use-conda --nolock --rerun-incomplete --directory /str1/home/otavio.henrique/VirMake/workflow failed. (See above for error)

setup.log virsorter2_pass2.log

torognes commented 6 months ago

Hi!

Sorry for the late reply.

The problems you have experienced probably stems from conflicts in the environment used during setup of the DRAM databases. We have made many changes to VirMake recently, including the database setup. We have also tested the database setup and the rest of the pipeline from scratch, and the it seemed to work well.

I would therefore recommend that you try installing VirMake again from scratch.

torognes commented 3 weeks ago

A new version of VirMake has now been merged into the main branch of VirMake. It has been extensively tested with several different real datasets.

I am closing this issue now.