Comments (7)
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.
from phylophlan.
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)
from phylophlan.
Ok, so do you see Setting "min_num_markers=100" [..]
from the log of PhyloPhlAn?
from phylophlan.
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.
from phylophlan.
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.
from phylophlan.
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
from phylophlan.
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
from phylophlan.
Related Issues (20)
- mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64') HOT 1
- FastTreeMP returned non-zero exit status 1. HOT 8
- Phylophlan Error HOT 3
- [e] No alignments found to concatenate HOT 1
- [e] mapping file (--maas) not specified HOT 2
- How can I use my own database? HOT 2
- Restart from checkpoint function available HOT 1
- maybee update taxa2core_cpa* to recent uniprot release
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- phylophlan_metagenomic.py - offline usage HOT 1
- RAxML can't parse alignments for which there are sequences made entirely of undetermined characters HOT 1
- Can not download the phylophlan database
- [e] gene_markers_identification crashed HOT 1
- What is the difference between "phylophlan" database and "SGB.XXX"? HOT 2
- Reducing number of RAxML threads to 20, as it appears to underperform with more threads HOT 2
- broken link on wiki
- The generated phylogenetic tree is missing MAGs at the leaf nodes.
- Trouble running example 2 - Tree of Life
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