Remove duplicated log messages

Resolving the duplicated messages and minimazing the deprecation issues will be best

```
INFO:root:Standard Pipeline Version 3.0 used
LOG MESSAGE: Standard Pipeline Version 3.0 used
INFO:root:2022-11-08
LOG MESSAGE: 2022-11-08
INFO:root:Analysis 'besca25_cellbender' on data located in'/gpfs/scratchfs01/site/u/albertl2/Test/besca25'
LOG MESSAGE: Analysis 'besca25_cellbender' on data located in'/gpfs/scratchfs01/site/u/albertl2/Test/besca25'
INFO:root:species: human
LOG MESSAGE: species: human
INFO:root:Batch effect to correct: None
LOG MESSAGE: Batch effect to correct: None
INFO:root:Parameters:
LOG MESSAGE: Parameters:
INFO:root: standard_min_genes = 0
LOG MESSAGE: standard_min_genes = 0
INFO:root: standard_min_cells = 30
LOG MESSAGE: standard_min_cells = 30
INFO:root: standard_min_counts = 0
LOG MESSAGE: standard_min_counts = 0
INFO:root: standard_n_genes = 15000
LOG MESSAGE: standard_n_genes = 15000
INFO:root: standard_max_counts = 300000
LOG MESSAGE: standard_max_counts = 300000
INFO:root: standard_percent_mito = 1
LOG MESSAGE: standard_percent_mito = 1
INFO:root: Time for creating all output directories and setting up logging: 0.02s
LOG MESSAGE: Time for creating all output directories and setting up logging: 0.02s
```