Default for --min_num_markers

[biobakery]

Default for --min_num_markers

[fasnicar]

Hi,
As written in the wiki if you specify as database -d phylophlan or -d amphora2 then --min_num_markers will be automatically set to 100 or 34, respectively.
Note that you need to specify --verbose to make PhyloPhlAn print that one of the above choices was made.

The above automatic values work unless you specify --min_num_markers in the command line. The command line has higher priority over the defaults and overrides the default values.

You said that it seems that PhyloPhlAn is still using 1 when -d phylophlan, this is very strange, but if you can give an example I can have a look.

[adityabandla]

Hi Francesco, yes, I did specify --verbose. I installed phylophlan v3 from bioconda
phylophlan --version gives me PhyloPhlAn version 3.0.51 (11 May 2020)

[fasnicar]

Ok, so do you see Setting "min_num_markers=100" [..] from the log of PhyloPhlAn?

[adityabandla]

Does phylophlan produce a separate log file? My observations are based on the messages that get printed in STDOUT with --verbose which lists all the parameter values.

[fasnicar]

Sorry, no there is no separate log, the stdout is what I'm referring to.

It should print the full command line and then the progress of the analysis. Between the command line and the progress of the analysis you should see the line I wrote above.
If you want to attach the I can have a look at it.

[adityabandla]

PhyloPhlAn version 3.0.51 (11 May 2020)

Command line: /home/projects/11001755/miniconda3/envs/phylophlan/bin/phylophlan -i sp_faa -d phylophlan --diversity high --accurate -f supermatrix_aa.cfg --verbose -o phylo_tree --nproc 24

Automatically setting "input=sp_faa" and "input_folder=/home/projects/11001713/datasets/glv_mg/data/processed/5_binning/99_final_bin_set_renamed/10_phylophlan"
Creating folder "phylo_tree"
Creating folder "phylo_tree/tmp"
"high-accurate" preset
Setting "sort=True" because "database=phylophlan"
Arguments: {'input': 'sp_faa', 'clean': None, 'output': 'phylo_tree', 'database': 'phylophlan', 'db_type': None, 'config_file': 'phylophlan_configs/supermatrix_aa.cfg', 'diversity': 'high', 'accurate': True, 'fast': False, 'clean_all': False, 'database_list': False, 'submat': 'pfasum60', 'submat_list': False, 'submod_list': False, 'nproc': 24, 'min_num_proteins': 1, 'min_len_protein': 50, 'min_num_markers': 1, 'trim': 'greedy', 'gap_perc_threshold': 0.67, 'not_variant_threshold': 0.95, 'subsample': <function twentyfive at 0x2aaae5693680>, 'unknown_fraction': 0.3, 'scoring_function': <function trident at 0x2aaae56938c0>, 'sort': True, 'remove_fragmentary_entries': False, 'fragmentary_threshold': 0.75, 'min_num_entries': 4, 'maas': None, 'remove_only_gaps_entries': False, 'mutation_rates': False, 'force_nucleotides': False, 'input_folder': '/home/projects/11001713/datasets/glv_mg/data/processed/5_binning/99_final_bin_set_renamed/10_phylophlan/sp_faa', 'data_folder': 'phylo_tree/tmp', 'databases_folder': 'phylophlan_databases/', 'submat_folder': '/home/projects/11001755/miniconda3/envs/phylophlan/lib/python3.7/site-packages/phylophlan/phylophlan_substitution_matrices/', 'submod_folder': '/home/projects/11001755/miniconda3/envs/phylophlan/lib/python3.7/site-packages/phylophlan/phylophlan_substitution_models/', 'configs_folder': 'phylophlan_configs/', 'output_folder': '', 'genome_extension': '.fna', 'proteome_extension': '.faa', 'update': False, 'verbose': True}
Loading configuration file "phylophlan_configs/supermatrix_aa.cfg"
Checking configuration file

[fasnicar]

Hi, thanks for reporting this.
It is now fixed with commit ID 30117ce
This version is not yet available in Bioconda, so for the moment, you should get PhyloPhlAn directly from the repository.

Many thanks,
Francesco