Comments (4)
Hi!
-
the scripts in the
examples
folders contain the.py
because they assume you got PhyloPhlAn by cloning the repo and through the conda package (which will not provide the examples). -
Apologies. The script is not updated with the latest version of the
phylophlan_metagenomic.py
script. Updated now (136f2f1) in the repo. Basically, the-d
is now a required parameter, this to ensure no different database version are used to process batches of samples of the same project. -
This shouldn't happen if you already have the
phylophlan_metagenomic.txt
file. Is the file in the correct folder?
from phylophlan.
As we all known (laugh cry), we cannot download from dropbox directly.
And my bash history is like this:
(phylophlan) [clsxx@cas556 ~/Work/2020-09-MgAffect/Analyze/phylophlan]$phylophlan \
> -i ${bin_dir} \
> -d phylophlan --diversity high -f supertree_aa.cfg \
> --genome_extension .fa \
> --nproc 4 \
> --maas phylophlan_substitution_models/phylophlan.tsv \
> --verbose\
> 2>&1 | tee tmp2.log
PhyloPhlAn version 3.0.59 (10 November 2020)
Command line: /lustre/home/acct-clsxx/clsxx/software/anaconda3/envs/phylophlan/bin/phylophlan -i /lustre/home/acct-clsxx/clsxx/Work/2020-09-MgAffect//F-06-MAG/03_modify/7_final/ -d phylophlan --diversity high -f supertree_aa.cfg --genome_extension .fa --nproc 4 --maas phylophlan_substitution_models/phylophlan.tsv --verbose
Automatically setting "input=7_final" and "input_folder=/lustre/home/acct-clsxx/clsxx/Work/2020-09-MgAffect/F-06-MAG/03_modify"
[e] "/lustre/home/acct-clsxx/clsxx/software/anaconda3/envs/phylophlan/lib/python3.9/site-packages/PhyloPhlAn-3.0.1-py3.9.egg/phylophlan/phylophlan_configs/" folder does not exists
Creating folder "7_final_phylophlan"
Creating folder "7_final_phylophlan/tmp"
"high-accurate" preset
Setting "sort=True" because "database=phylophlan"
Setting "min_num_markers=100" since no value has been specified and the "database=phylophlan"
Arguments: {'input': '7_final', 'clean': None, 'output': '7_final_phylophlan', 'database': 'phylophlan', 'db_type': None, 'config_file': 'supertree_aa.cfg', 'diversity': 'high', 'accurate': True,
'fast': False, 'clean_all': False, 'database_list': False, 'submat': 'pfasum60', 'submat_list': False, 'submod_list': False, 'nproc': 4, 'min_num_proteins': 1, 'min_len_protein': 50, 'min_num_markers': 100, 'trim': 'greedy', 'gap_perc_threshold': 0.67, 'not_variant_threshold': 0.95, 'subsample': <function twentyfive at 0x2b6080061f70>, 'unknown_fraction': 0.3, 'scoring_function': <function trident at 0x2b60800621f0>, 'sort': True, 'remove_fragmentary_entries': False, 'fragmentary_threshold': 0.75, 'min_num_entries': 4, 'maas': 'phylophlan_substitution_models/phylophlan.tsv', 'remove_only_gaps_entries': False, 'mutation_rates': False, 'force_nucleotides': False, 'input_folder':
'/lustre/home/acct-clsxx/clsxx/Work/2020-09-MgAffect/F-06-MAG/03_modify/7_final', 'data_folder': '7_final_phylophlan/tmp', 'databases_folder': 'phylophlan_databases/', 'submat_folder': '/lustre/home/acct-clsxx/clsxx/software/anaconda3/envs/phylophlan/lib/python3.9/site-packages/PhyloPhlAn-3.0.1-py3.9.egg/phylophlan/phylophlan_substitution_matrices/', 'submod_folder': 'phylophlan_substitution_models/', 'configs_folder': None, 'output_folder': '', 'genome_extension': '.fa', 'proteome_extension': '.faa', 'update': False, 'verbose': True}
Loading configuration file "supertree_aa.cfg"
Checking configuration file
Checking "/lustre/home/acct-clsxx/clsxx/software/anaconda3/envs/phylophlan/bin/diamond"
Checking "/lustre/home/acct-clsxx/clsxx/software/anaconda3/envs/phylophlan/bin/mafft"
Checking "/lustre/home/acct-clsxx/clsxx/software/anaconda3/envs/phylophlan/bin/trimal"
Checking "/lustre/home/acct-clsxx/clsxx/software/anaconda3/envs/phylophlan/bin/FastTree"
Checking "/lustre/home/acct-clsxx/clsxx/software/anaconda3/envs/phylophlan/bin/raxmlHPC"
Checking "java"
File "phylophlan_databases/phylophlan_databases.txt" present
Downloading "https://zenodo.org/record/4005620/files/phylophlan.tar?download=1" to "phylophlan_databases/phylophlan.tar"
Downloading file of size: 64.05 MB
^C03 MB 4.73 % 0.37 MB/sec 2 min 47 sec
(phylophlan) [clsxx@cas556 ~/Work/2020-09-MgAffect/Analyze/phylophlan]$ls -l phylophlan_databases/
total 3112
-rw-rw-r-- 1 clsxx clsxx 323 Nov 13 16:47 phylophlan_databases.txt
-rw-rw-r-- 1 clsxx clsxx 3027 Nov 13 16:47 phylophlan_metagenomic.txt
-rw-rw-r-- 1 clsxx clsxx 3178496 Nov 13 16:51 phylophlan.tar
(phylophlan) [clsxx@cas556 ~/Work/2020-09-MgAffect/Analyze/phylophlan]$phylophlan_metagenomic
-i ${bin_dir} -d SGB.Jul20 --database_folder ~/software/phylophlan/phylophlan_databases
--nproc 4 --verbose 2>&1 | tee tmp1.log
phylophlan_metagenomic.py version 3.0.34 (18 August 2020)
Command line: /lustre/home/acct-clsxx/clsxx/software/anaconda3/envs/phylophlan/bin/phylophlan_metagenomic -i /lustre/home/acct-clsxx/clsxx/Work/2020-09-MgAffect//F-06-MAG/03_modify/7_final/ -d SGB.Jul20 --database_folder /lustre/home/acct-clsxx/clsxx/software/phylophlan/phylophlan_databases --nproc 4 --verbose
Setting --database_folder to "/lustre/home/acct-clsxx/clsxx/software/phylophlan/phylophlan_databases"
Setting input extension to ".fa"
Setting output prefix to "/lustre/home/acct-clsxx/clsxx/Work/2020-09-MgAffect/F-06-MAG/03_modify/7_final"
Output prefix is a folder, setting it to "/lustre/home/acct-clsxx/clsxx/Work/2020-09-MgAffect/F-06-MAG/03_modify/7_final/7_final"
Folder "/lustre/home/acct-clsxx/clsxx/Work/2020-09-MgAffect/F-06-MAG/03_modify/7_final/7_final_sketches" already present
Folder "/lustre/home/acct-clsxx/clsxx/Work/2020-09-MgAffect/F-06-MAG/03_modify/7_final/7_final_sketches/inputs" already present
Folder "/lustre/home/acct-clsxx/clsxx/Work/2020-09-MgAffect/F-06-MAG/03_modify/7_final/7_final_dists" already present
Arguments: {'input': '/lustre/home/acct-clsxx/clsxx/Work/2020-09-MgAffect//F-06-MAG/03_modify/7_final/', 'output_prefix': '/lustre/home/acct-clsxx/clsxx/Work/2020-09-MgAffect/F-06-MAG/03_modify/7_final/7_final', 'database': 'SGB.Jul20', 'database_list': False, 'database_update': False, 'input_extension': '.fa', 'how_many': 10, 'nproc': 4, 'database_folder': '/lustre/home/acct-clsxx/clsxx/software/phylophlan/phylophlan_databases', 'only_input': False, 'add_ggb': False, 'add_fgb': False, 'overwrite': False, 'verbose': True, 'mapping': 'SGB.Jul20.txt.bz2'}
Checking "mash"
Downloading "https://www.dropbox.com/s/xdqm836d2w22npb/phylophlan_metagenomic.txt?dl=1" to "phylophlan_metagenomic.txt"
[e] unable to download "https://www.dropbox.com/s/xdqm836d2w22npb/phylophlan_metagenomic.txt?dl=1"
(phylophlan) [clsxx@cas556 ~/Work/2020-09-MgAffect/Analyze/phylophlan]$
from phylophlan.
Hi and thanks for the log.
As you can see phylophlan_metagenomic.py
set as database_folder
the path /lustre/home/acct-clsxx/clsxx/software/phylophlan/phylophlan_databases
.
Arguments: {'input': '/lustre/home/acct-clsxx/clsxx/Work/2020-09-MgAffect//F-06-MAG/03_modify/7_final/', 'output_prefix': '/lustre/home/acct-clsxx/clsxx/Work/2020-09-MgAffect/F-06-MAG/03_modify/7_final/7_final', 'database': 'SGB.Jul20', 'database_list': False, 'database_update': False, 'input_extension': '.fa', 'how_many': 10, 'nproc': 4, 'database_folder': '/lustre/home/acct-clsxx/clsxx/software/phylophlan/phylophlan_databases', 'only_input': False, 'add_ggb': False, 'add_fgb': False, 'overwrite': False, 'verbose': True, 'mapping': 'SGB.Jul20.txt.bz2'}
which is not the location where you downloaded the phylophlan_metagenomic.txt
file (appears to be ~/Work/2020-09-MgAffect/Analyze/phylophlan/phylophlan_databases/
).
Se, when running phylophlan_metagenomic.py
you can specify as database folder the path to the folder containing the phylophlan_metagenomic.txt
file you downloaded, using the --database_folder
param, and this should solve the download issue.
Many thanks,
Francesco
from phylophlan.
Now I found the bug:
In phylophlan.py
, you modified database_download
:
phylophlan/phylophlan/phylophlan.py
Lines 3206 to 3207 in 136f2f1
However, in
phylophlan_metagenomic.py
, file will be downloaded to current path:phylophlan/phylophlan/phylophlan_metagenomic.py
Lines 715 to 716 in 136f2f1
from phylophlan.
Related Issues (20)
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from phylophlan.