Python: command not found

[Erin-Chee]

Hi, thank you for making the pipeline!

I am currently trying to run concat_by_homology_multiple_species.nf with some sample data but have been getting an error, (command.sh: line 2: python: command not found) and am not sure what is causing it.

Error message

N E X T F L O W  ~  version 21.10.6
Launching `concat_by_homology_multiple_species.nf` [happy_koch] - revision: c3fd4fa590

===========================================================


Cross-species integration and assessment - nextflow pipeline
Use singularity containers for cluster execution
- check inout format
- concatenate input anndata
Author: ysong@ebi.ac.uk
Initial date: Mar 2022
Latest date: Oct 2023

===========================================================

[-        ] process > validate_adata_input           -
[-        ] process > concat_by_homology             -
[-        ] process > concat_by_homology_rliger_u... -
[-        ] process > convert_format_h5ad            -

[-        ] process > validate_adata_input           [  0%] 0 of 1
[-        ] process > concat_by_homology             [  0%] 0 of 1
[-        ] process > concat_by_homology_rliger_u... [  0%] 0 of 1
[-        ] process > convert_format_h5ad            -
[-        ] process > convert_format_rliger_uinmf    -

executor >  slurm (1)
[-        ] process > validate_adata_input           [  0%] 0 of 1
[-        ] process > concat_by_homology             [  0%] 0 of 1
[60/8f2d67] process > concat_by_homology_rliger_u... [  0%] 0 of 1
[-        ] process > convert_format_h5ad            -
[-        ] process > convert_format_rliger_uinmf    -

executor >  slurm (3)
[03/5858c5] process > validate_adata_input (1)       [  0%] 0 of 1
[57/d3ceef] process > concat_by_homology (1)         [  0%] 0 of 1
[60/8f2d67] process > concat_by_homology_rliger_u... [  0%] 0 of 1
[-        ] process > convert_format_h5ad            -
[-        ] process > convert_format_rliger_uinmf    -

executor >  slurm (3)
[03/5858c5] process > validate_adata_input (1)       [  0%] 0 of 1
[57/d3ceef] process > concat_by_homology (1)         [  0%] 0 of 1
[60/8f2d67] process > concat_by_homology_rliger_u... [  0%] 0 of 1
[-        ] process > convert_format_h5ad            -
[-        ] process > convert_format_rliger_uinmf    -

executor >  slurm (3)
[03/5858c5] process > validate_adata_input (1)       [  0%] 0 of 1
[57/d3ceef] process > concat_by_homology (1)         [  0%] 0 of 1
[60/8f2d67] process > concat_by_homology_rliger_u... [  0%] 0 of 1
[-        ] process > convert_format_h5ad            -
[-        ] process > convert_format_rliger_uinmf    -
Error executing process > 'validate_adata_input (1)'

Caused by:
  Process `validate_adata_input (1)` terminated with an error exit status (127)

Command executed:

  python /mnt/storage/nobackup/proj/scbsu/nec181/BENGAL/BENGAL-main/bin/validate_input.py metadata_nf.tsv --batch_key species_key --species_key species_key --cluster_key cluster_key

Command exit status:
  127

Command output:
  (empty)

Command error:
  WARNING: passwd file doesn't exist in container, not updating
  WARNING: group file doesn't exist in container, not updating
  .command.sh: line 2: python: command not found

Work dir:
  /mnt/storage/nobackup/proj/scbsu/nec181/BENGAL/BENGAL-main/work/03/5858c5a3afb6b260e13f26e552e982

I tried redownloading the bengal_py.sif container but the error hasn't changed. I tried using a Singularity Shell to access the container and check python with python --version but it returns bash: python: command not found

[Erin-Chee]

Small update: I tried python3 --version which did return python3.9, but after an attempt changing the concat_by_homology_multiple_species.nf script from python to python3 it returned a ModuleNotFoundError instead.

I changed the bengal_py.sif container to sandbox format and the modules are there now, and the pipeline runs when I use the container in sandbox format.