The bioBakery help forum

FileNotFoundError when installing 16s databases

Hello,
I followed the instructions to install the dependencies and databases for the 16s workflow. I am getting the following error:
“”"
Traceback (most recent call last):
File “/cluster/tufts/bio/tools/conda_envs/biobakery/bin/biobakery_workflows_databases”, line 10, in
sys.exit(main())
File “/cluster/tufts/bio/tools/conda_envs/biobakery/lib/python3.7/site-packages/biobakery_workflows/biobakery_workflows_databases.py”, line 244, in main
run_command([“download_picrust_files.py”])
File “/cluster/tufts/bio/tools/conda_envs/biobakery/lib/python3.7/site-packages/biobakery_workflows/biobakery_workflows_databases.py”, line 73, in run_command
id=subprocess.check_call(command, shell=shell)
File “/cluster/tufts/bio/tools/conda_envs/biobakery/lib/python3.7/subprocess.py”, line 342, in check_call
retcode = call(*popenargs, **kwargs)
File “/cluster/tufts/bio/tools/conda_envs/biobakery/lib/python3.7/subprocess.py”, line 323, in call
with Popen(*popenargs, **kwargs) as p:
File “/cluster/tufts/bio/tools/conda_envs/biobakery/lib/python3.7/subprocess.py”, line 775, in init
restore_signals, start_new_session)
File “/cluster/tufts/bio/tools/conda_envs/biobakery/lib/python3.7/subprocess.py”, line 1522, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: ‘download_picrust_files.py’: ‘download_picrust_files.py’
“”"
I have picrust2 installed:
picrust2 2.0.3_b py_0 bioconda

but I was unable to install picrust (1) because of unresolvable conda conflicts between picrust and biobakery_workflows.

I would appreciate any help on resolving this.

Thank you,
Rebecca

In addition, I get the same error when using the Docker container. Apologies if I’m doing something basic wrong and thanks for your help.
“”"
root@e8ebf633d935:/# biobakery_workflows_databases --install 16s_usearch
Downloading green genes database files
Downloading ftp://greengenes.microbio.me/greengenes_release/gg_13_8_otus/rep_set/97_otus.fasta
Downloading file of size: 136.58 MB

136.59 MB 100.00 % 5.19 MB/sec 0 min -0 sec

Downloading ftp://greengenes.microbio.me/greengenes_release/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt
Downloading file of size: 9.61 MB

9.61 MB 100.01 % 4.66 MB/sec 0 min -0 sec

Traceback (most recent call last):
File “/usr/local/bin/biobakery_workflows_databases”, line 11, in
sys.exit(main())
File “/usr/local/lib/python3.6/dist-packages/biobakery_workflows/biobakery_workflows_databases.py”, line 244, in main
run_command([“download_picrust_files.py”])
File “/usr/local/lib/python3.6/dist-packages/biobakery_workflows/biobakery_workflows_databases.py”, line 73, in run_command
id=subprocess.check_call(command, shell=shell)
File “/usr/lib/python3.6/subprocess.py”, line 306, in check_call
retcode = call(*popenargs, **kwargs)
File “/usr/lib/python3.6/subprocess.py”, line 287, in call
with Popen(*popenargs, **kwargs) as p:
File “/usr/lib/python3.6/subprocess.py”, line 729, in init
restore_signals, start_new_session)
File “/usr/lib/python3.6/subprocess.py”, line 1364, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: ‘download_picrust_files.py’: ‘download_picrust_files.py’
“”"

Hi Rebecca, The workflows use the PICRUSt v1 script to install its databases. The workflows have the option to run either PICRUSt 1 or 2. If you install PICRUSt v1 it will have the script that the workflows are looking for and it should resolve the error you are seeing.

Thank you,
Lauren

Thank you for your quick and helpful reply. I would like to install picrust 1 but I seem to have dependency conflicts. I’ve tried with both python 2.7 and python 3.9, and can’t seem to get both biobakery_workflows and picrust 1 installed in a conda env. This is what I see:

(/cluster/tufts/bio/tools/conda_envs/biobakery) rbator01@c1cmp047:~$ conda install -c bioconda picrust
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: - 
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abor\ 
failed                                                                                                                       

UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:

Specifications:

  - picrust -> python[version='2.7.*|>=2.7,<2.8.0a0']

Your python: python=3.7

If python is on the left-most side of the chain, that's the version you've asked for.
When python appears to the right, that indicates that the thing on the left is somehow
not available for the python version you are constrained to. Note that conda will not
change your python version to a different minor version unless you explicitly specify
that.

Thank you for the detailed error messages. I am not sure if PICRUSt v1 is python3 compatible so you might want to use python 2.7. If there are no compatible conda packages for PICRUSt v1 you might consider installing it from source as it is a easy and straightforward process that is well documented (and only a couple commands). Installing PICRUSt — PICRUSt 1.1.4 documentation

Thank you,
Lauren

Hello,
I have the same problem. Missing file download_picrust_files.py after insatling conda biobackery environment.
Cant have biobackery workflow and picrust v1 in a same environment (python version).
I cant install from source picrust v1 on my cluster. Is there alternative solution? I want to try biockary 16s workflow (dada2 and usearch).

Thanks in advance for the help.

Regards