Error executing process > 'summary (megahit)'

[hdflorezr]

Hi, Mattia.

I'm running tutorial stable for metaphage and I found this error and I actually don't know how I can fix it:

Error executing process > 'summary (megahit)'

Caused by: Process summary (megahit) terminated with an error exit status (1)

Command executed:

Rscript /media/omicas/data/apps/MetaPhage-0.3.3/bin/Rscript/summary_report.R count_table.csv megahit_vOTUs_consensus.fasta metadata.csv Infant_delivery_type /media/omicas/data/apps/MetaPhage-0.3.3/MetaPhage-output

Command exit status: 1

Command output: (empty)

Command error: Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'as.data.frame': dim(X) must have a positive length Calls: as.data.frame -> apply Ejecución interrumpida

Work dir: /media/omicas/data/apps/MetaPhage-0.3.3/work/8e/d5fbff060d20179cf69e548d02a7d4

Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run.

In the other hand, I was trying to run the pipeline for tutorial beta, but I'm having an error related to numpy and that was the log file content:

Error in rule classify_by_group: jobid: 57 output: iter-0/ssDNA/all.pdg.clf conda-env: /media/omicas/data/Datos_Hernan/MetaPhage/MetaPhage/db/virsorter/virsorter2/conda_envs/f1f2e930 shell:

Log=/media/omicas/data/Datos_Hernan/MetaPhage/MetaPhage/work/1b/6c9dcbb09335b1d01611163e3b9fdb/SRR8653218_virsorter2/log/iter-0/step3-classify/all-score-ssDNA.log
python /home/omicas/miniconda3/envs/metaphage2/lib/python3.7/site-packages/virsorter/./scripts/classify.py iter-0/ssDNA/all.pdg.ftr /media/omicas/data/Datos_Hernan/MetaPhage/MetaPhage/db/virsorter/virsorter2/group/ssDNA/model ssDNA iter-0/ssDNA/all.pdg.clf 2> $Log || { echo "See error details in $Log" | python /home/omicas/miniconda3/envs/metaphage2/lib/python3.7/site-packages/virsorter/./scripts/echo.py --level error; exit 1; }

(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

[2024-02-28 00:33 ERROR] See error details in /media/omicas/data/Datos_Hernan/MetaPhage/MetaPhage/work/1b/6c9dcbb09335b1d01611163e3b9fdb/SRR8653218_virsorter2/log/iter-0/step3-classify/all-score-dsDNAphage.log [Wed Feb 28 00:33:53 2024] Error in rule classify_by_group: jobid: 56 output: iter-0/dsDNAphage/all.pdg.clf conda-env: /media/omicas/data/Datos_Hernan/MetaPhage/MetaPhage/db/virsorter/virsorter2/conda_envs/f1f2e930 shell:

Log=/media/omicas/data/Datos_Hernan/MetaPhage/MetaPhage/work/1b/6c9dcbb09335b1d01611163e3b9fdb/SRR8653218_virsorter2/log/iter-0/step3-classify/all-score-dsDNAphage.log python /home/omicas/miniconda3/envs/metaphage2/lib/python3.7/site-packages/virsorter/./scripts/classify.py iter-0/dsDNAphage/all.pdg.ftr /media/omicas/data/Datos_Hernan/MetaPhage/MetaPhage/db/virsorter/virsorter2/group/dsDNAphage/model dsDNAphage iter-0/dsDNAphage/all.pdg.clf 2> $Log || { echo "See error details in $Log" | python /home/omicas/miniconda3/envs/metaphage2/lib/python3.7/site-packages/virsorter/./scripts/echo.py --level error; exit 1; } And the log file information is:File "/media/omicas/data/Datos_Hernan/MetaPhage/MetaPhage/db/virsorter/virsorter2/conda_envs/f1f2e930/lib/python3.8/site-packages/sklearn/linear_model/_least_angle.py", line 30, in method='lar', copy_X=True, eps=np.finfo(np.float).eps, File "/home/omicas/.local/lib/python3.8/site-packages/numpy/init.py", line 305, in getattr raise AttributeError(former_attrs[attr]) AttributeError: module 'numpy' has no attribute 'float'. np.float was a deprecated alias for the builtin float. To avoid this error in existing code, use float by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.float64 here. The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations

I really don't know how could I fix this, but I'd like to use this version instead the stable.

Thanks for your help.