enrichM database

[fanlu-f]

I want to download the database. I used the command that "enrichm data" .but the database not download automatically.

(enrichm) user@user-X11DPi-N-T:~/Desktop$ enrichm data usage: enrichm data [-h] [--log LOG] [--verbosity VERBOSITY] [--output OUTPUT] [--force] [--uninstall] [--create CREATE] [--dry]

optional arguments: -h, --help show this help message and exit

Logging options: --log LOG Output logging information to this file. --verbosity VERBOSITY Level of verbosity (1 - 5 - default = 4) 5 = Very verbose, 1 = Silent

Output options: --output OUTPUT Output directory --force Overwrite previous run

Uninstall: --uninstall Remove enrichm database --create CREATE create enrichm database --dry Download an empty database (debug) None

[jsgounot]

Same problem. I think the current conda version did not include the last commit(s) (I only looked at the data.py file).

Running enrichm, it says version 0.6.3

I tried to run this command line : enrichm data --create new (there are no informations about what the --create value should be), which gave me this error message :

ModuleNotFoundError: No module named 'IPython'

And indeed, I did not install IPython on this conda env. I looked up a bit and I guess the last current conda version does not include the last commits, since this import has been removed here.

Is it possible to update the current conda version with the last commits ? It's a shame that this bugs make the whole software completly unusable.

[Lucas-Maciel]

Tried v 0.5.0 but the script is not finding the db

enrichm data
[2021-05-26 17:06:18 PM] INFO: Command: ~/miniconda3/envs/enrichm_5/bin/enrichm data
[2021-05-26 17:06:18 PM] INFO: Running the data pipeline
Traceback (most recent call last):
  File "~/miniconda3/envs/enrichm_5/lib/python3.6/site-packages/enrichm/data.py", line 114, in do
    version_remote = urllib.request.urlopen(self.ftp + self.VERSION).readline().strip().decode("utf-8")
AttributeError: module 'urllib' has no attribute 'request'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "~/miniconda3/envs/enrichm_5/bin/enrichm", line 342, in <module>
    run.run_enrichm(args, sys.argv)
  File "~/miniconda3/envs/enrichm_5/lib/python3.6/site-packages/enrichm/run.py", line 288, in run_enrichm
    d.do(args.uninstall, args.dry)
  File "~/miniconda3/envs/enrichm_5/lib/python3.6/site-packages/enrichm/data.py", line 117, in do
    "Unable to find most current EnrichM database VERSION in ftp. Please complain at https://github.com/geronimp/enrichM")
Exception: Unable to find most current EnrichM database VERSION in ftp. Please complain at https://github.com/geronimp/enrichM

Tried the v 0.6.3 and even when you install iPython something weird happens:

enrichm data --create new
[2021-05-26 17:02:19 PM] INFO: Command: ~/miniconda3/envs/enrichm/bin/enrichm data --create new
[2021-05-26 17:02:19 PM] INFO: Running the data pipeline
Python 3.6.13 | packaged by conda-forge | (default, Feb 19 2021, 05:36:01) 
Type 'copyright', 'credits' or 'license' for more information
IPython 7.16.1 -- An enhanced Interactive Python. Type '?' for help.
In [1]: 

[jsgounot]

For your first error with v.0.5, is it possible that it's a python version error ?

AttributeError: module 'urllib' has no attribute 'request'

This has changed between python 2 and 3.

[Lucas-Maciel]

@jsgounot the version 0.5.0 came with Python 3.6.13 in the conda env.

I manually modified the script data.py as indicated by #103 but I'm worried that something else might be wrong due to a different version. For example, my script is clustering 2K proteins with 16 threads and 48GB for over 8 hours and still running.

[2021-05-27 01:02:38 AM] INFO: Command: ~/miniconda3/envs/enrichm_5/bin/enrichm annotate --protein_files Bacteroides_vulgatus/GCF_000012825.1_ASM1282v1_protein.faa --ko --ko_hmm --pfam --tigrfam --orthologs --cazy --ec --threads 16 --parallel 16 --output Bacteroides_vulgatus/GCF_000012825.1_ASM1282v1_protein.enrichm
[2021-05-27 01:02:38 AM] INFO: Running the annotate pipeline
[2021-05-27 01:02:38 AM] INFO: Running pipeline: annotate
[2021-05-27 01:02:38 AM] INFO: Setting up for genome annotation
[2021-05-27 01:02:38 AM] INFO: Using provided proteins
[2021-05-27 01:02:38 AM] INFO: Preparing genomes for annotation
[2021-05-27 01:02:38 AM] INFO: Starting annotation:
[2021-05-27 01:02:38 AM] INFO:     - Annotating genomes with hypothetical clusters
[2021-05-27 01:02:38 AM] INFO:     - Generating MMSeqs2 database
[2021-05-27 01:02:39 AM] INFO:     - Clustering genome proteins

[mengyuan09876]

I try to update the database, but it shows me unable to locate enrichM database. I open the envs folder in anaconda, but I didn't find a file named like "database", could you please tell me the name of this database ， I would like to see if I can export it， thanks!