ERROR ~ Error executing process > 'VIROPROFILER:VIBRANT'

[JJJIKING]

Description of the bug

Based on the error log, the VIBRANT module failed to run, with the following main reasons:

VIBRANT's dependent sklearn contains NumPy warnings, i.e. NP.float is already deprecated.

During the execution of VIBRANT, the output file failed to be generated: "VIBRANT_contigs/VIBRANT_results_contigs/VIBRANT_genome_quality_contigs.tsv"

Command used and terminal output

executor >  local (22)
[01/afca51] process > VIROPROFILER:FASTQC (UC21)               [100%] 5 of 5 ✔
[4a/376dcb] process > VIROPROFILER:FASTP (UC20)                [100%] 5 of 5 ✔
[ca/3aa1cc] process > VIROPROFILER:SPADES (UC20)               [100%] 5 of 5 ✔
[c4/b2a5bf] process > VIROPROFILER:CONTIGLIB                   [100%] 1 of 1 ✔
[f1/d4b8c0] process > VIROPROFILER:CHECKV                      [100%] 1 of 1 ✔
[95/af3d36] process > VIROPROFILER:CONTIGLIB_CLUSTER           [100%] 1 of 1 ✔[7d/8ed314] process > VIROPROFILER:GENEPRED4CTG                [100%] 1 of 1 ✔
[e8/7e42c9] process > VIROPROFILER:NRPROT                      [100%] 1 of 1 ✔
[a7/ea14bb] process > VIROPROFILER:NRGENE                      [100%] 1 of 1 ✔
[-        ] process > VIROPROFILER:CONTIGINDEX                 -[-        ] process > VIROPROFILER:MAPPING2CONTIGS2            -
[-        ] process > VIROPROFILER:ABUNDANCE                   -
[43/97cc95] process > VIROPROFILER:VIBRANT                     [100%] 1 of 1, failed: 1 ✘
[-        ] process > VIROPROFILER:DVF                         -[-        ] process > VIROPROFILER:VIRCONTIGS_PRE              -
[-        ] process > VIROPROFILER:VIRSORTER2                  -
[-        ] process > VIROPROFILER:DRAMV                       -
[-        ] process > VIROPROFILER:TAXONOMY_VCONTACT           -[-        ] process > VIROPROFILER:TAXONOMY_MMSEQS             -
[-        ] process > VIROPROFILER:TAXONOMY_MERGE              -
[-        ] process > VIROPROFILER:VIRALHOST_IPHOP             -
[-        ] process > VIROPROFILER:BACPHLIP                    -[-        ] process > VIROPROFILER:RESULTS_TSE                 -
[-        ] process > VIROPROFILER:CUSTOM_DUMPSOFTWAREVERSIONS -
[-        ] process > VIROPROFILER:MULTIQC                     -
-[ViroProfiler] Pipeline completed with errors-ERROR ~ Error executing process > 'VIROPROFILER:VIBRANT'

Caused by:
  Missing output file(s) `VIBRANT_contigs/VIBRANT_results_contigs/VIBRANT_genome_quality_contigs.tsv` expected by process `VIROPROFILER:VIBRANT`

Command executed:

  ln -s contigs_nrclib.fasta contigs.fasta  VIBRANT_run.py -i contigs.fasta -d /home/zhangliji/viroprofiler/vibrant/databases -m /home/zhangliji/viroprofiler/vibrant/files -t 2 -virome

Command exit status:
  0

Command output:
  (empty)
Command error:
  /opt/conda/lib/python3.7/site-packages/sklearn/linear_model/least_angle.py:30: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, 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.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    method='lar', copy_X=True, eps=np.finfo(np.float).eps,
  /opt/conda/lib/python3.7/site-packages/sklearn/linear_model/least_angle.py:167: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, 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.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    method='lar', copy_X=True, eps=np.finfo(np.float).eps,
  /opt/conda/lib/python3.7/site-packages/sklearn/linear_model/least_angle.py:284: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, 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.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    eps=np.finfo(np.float).eps, copy_Gram=True, verbose=0,
  /opt/conda/lib/python3.7/site-packages/sklearn/linear_model/least_angle.py:862: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, 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.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    eps=np.finfo(np.float).eps, copy_X=True, fit_path=True,
  /opt/conda/lib/python3.7/site-packages/sklearn/linear_model/least_angle.py:1101: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, 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.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    eps=np.finfo(np.float).eps, copy_X=True, fit_path=True,
  /opt/conda/lib/python3.7/site-packages/sklearn/linear_model/least_angle.py:1127: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, 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.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    eps=np.finfo(np.float).eps, positive=False):
  /opt/conda/lib/python3.7/site-packages/sklearn/linear_model/least_angle.py:1362: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, 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.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    max_n_alphas=1000, n_jobs=None, eps=np.finfo(np.float).eps,
  /opt/conda/lib/python3.7/site-packages/sklearn/linear_model/least_angle.py:1602: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, 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.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    max_n_alphas=1000, n_jobs=None, eps=np.finfo(np.float).eps,
  /opt/conda/lib/python3.7/site-packages/sklearn/linear_model/least_angle.py:1738: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, 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.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    eps=np.finfo(np.float).eps, copy_X=True, positive=False):
  /opt/conda/lib/python3.7/site-packages/sklearn/decomposition/online_lda.py:29: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, 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.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    EPS = np.finfo(np.float).eps

Work dir:
  /home/zhangliji/workspace/testviro/work/43/97cc956a63ad9f50bfd5e8e36de556

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

 -- Check '.nextflow.log' file for details

Relevant files

No response

System information

No response