Re: File name too long with --per_sequence_contrib
Robyn Wright
Hi all,Hope you all are well. I'm trying to run the picrust2 full pipeline with picrust2 v2.5.3 using my Uni's clustered computing system (using Unix).I had included --per_sequence_contrib in the command as I was interested in what proportion of the specified function is contributed by that particular taxon in the sample, however I was faced with osError "file name too long". I could only bypass the error by specifying --skip_minpath, however my understanding is that apparently it is important to have the minpath as it is more accurate (please correct me if I'm wrong in this as I'm a newbie to metagenomics).Therefore, is there anyway I can fix this issue?Thanks!Kind regards,Timothy
Misbah Tubassam
LibMambaUnsatisfiableError: Encountered problems while solving:
- nothing provides requested dendropy 4.5.2**
- nothing provides fonts-conda-ecosystem needed by pango-1.50.10-h1f197d0_0
- nothing provides tzdata needed by python-3.10.0-h1248fe1_1_cpython
Could not solve for environment specs
The following packages are incompatible
├─ dendropy 4.5.2** does not exist (perhaps a typo or a missing channel);
├─ pytest-cov >=2.6.1 is installable with the potential options
│ ├─ pytest-cov 2.6.1 would require
│ │ └─ python >=2.7,<2.8.0a0 , which can be installed;
│ ├─ pytest-cov 2.6.1 would require
│ │ └─ python >=3.6,<3.7.0a0 with the potential options
│ │ ├─ python [3.6.0|3.6.1|...|3.6.7] would require
│ │ │ └─ python_abi * *_cp36m, which can be installed;
│ │ ├─ python [3.6.10|3.6.11|...|3.6.9] would require
│ │ │ └─ python_abi 3.6.* *_cp36m, which can be installed;
│ │ └─ python [3.6.10|3.6.12|...|3.6.9], which can be installed;
│ ├─ pytest-cov 2.6.1 would require
│ │ └─ python >=3.7,<3.8.0a0 with the potential options
│ │ ├─ python [3.7.0|3.7.1|3.7.2|3.7.3|3.7.6] would require
│ │ │ └─ python_abi * *_cp37m, which can be installed;
│ │ ├─ python [3.7.0|3.7.1|...|3.7.9], which can be installed;
│ │ └─ python [3.7.10|3.7.12|...|3.7.9] would require
│ │ └─ python_abi 3.7.* *_cp37m, which can be installed;
│ ├─ pytest-cov [4.0.0|4.1.0|6.0.0] would require
│ │ └─ python [>=3.10,<3.11.0a0 |>=3.11,<3.12.0a0 |>=3.12,<3.13.0a0 |>=3.13,<3.14.0a0 ], which requires
│ │ ├─ pypy3.9 [7.3.11.* |7.3.12.* |7.3.13.* |7.3.15.* ], which requires
│ │ │ └─ tzdata, which does not exist (perhaps a missing channel);
│ │ └─ tzdata, which does not exist (perhaps a missing channel);
│ ├─ pytest-cov [4.0.0|4.1.0] would require
│ │ └─ python >=3.8,<3.9.0a0 with the potential options
│ │ ├─ python [3.8.0|3.8.1] would require
│ │ │ └─ python_abi * *_cp38, which can be installed;
│ │ ├─ python [3.8.10|3.8.12|...|3.8.8] would require
│ │ │ └─ python_abi 3.8.* *_cp38, which can be installed;
│ │ └─ python [3.8.0|3.8.1|...|3.8.8], which can be installed;
│ └─ pytest-cov [4.0.0|4.1.0|6.0.0] would require
│ └─ toml with the potential options
│ ├─ toml [0.10.0|0.9.4] would require
│ │ └─ python >=2.7,<2.8.0a0 , which can be installed;
│ ├─ toml [0.10.0|0.9.4] would require
│ │ └─ python >=3.6,<3.7.0a0 with the potential options
│ │ ├─ python [3.6.0|3.6.1|...|3.6.7], which can be installed (as previously explained);
│ │ ├─ python [3.6.10|3.6.11|...|3.6.9], which can be installed (as previously explained);
│ │ └─ python [3.6.10|3.6.12|...|3.6.9], which can be installed;
│ ├─ toml [0.10.0|0.9.4] would require
│ │ └─ python >=3.7,<3.8.0a0 with the potential options
│ │ ├─ python [3.7.0|3.7.1|3.7.2|3.7.3|3.7.6], which can be installed (as previously explained);
│ │ ├─ python [3.7.0|3.7.1|...|3.7.9], which can be installed;
│ │ └─ python [3.7.10|3.7.12|...|3.7.9], which can be installed (as previously explained);
│ └─ toml 0.9.4 would require
│ └─ python >=3.5,<3.6.0a0 with the potential options
│ ├─ python [3.5.1|3.5.2|3.5.3|3.5.4|3.5.5] would require
│ │ └─ python_abi * *_cp35m, which can be installed;
│ └─ python [3.5.4|3.5.5|3.5.6], which can be installed;
├─ r-castor >=1.7.2 is not installable because there are no viable options
│ ├─ r-castor [1.7.2|1.7.3] would require
│ │ ├─ r-base >=4.0,<4.1.0a0 with the potential options
│ │ │ ├─ r-base [4.0.0|4.0.1|4.0.2|4.0.3|4.0.5], which can be installed;
│ │ │ └─ r-base [4.0.5|4.1.3|...|4.4.2] would require
│ │ │ ├─ fonts-conda-ecosystem, which does not exist (perhaps a missing channel);
│ │ │ └─ pango [>=1.50.11,<2.0a0 |>=1.50.12,<2.0a0 |>=1.50.14,<2.0a0 |>=1.50.8,<1.51.0a0 |>=1.54.0,<2.0a0 ], which requires
│ │ │ └─ fonts-conda-ecosystem, which does not exist (perhaps a missing channel);
│ │ └─ r-naturalsort but there are no viable options
│ │ ├─ r-naturalsort 0.1.3 would require
│ │ │ └─ r-base 3.3.2* but there are no viable options
│ │ │ ├─ r-base 3.3.2 conflicts with any installable versions previously reported;
│ │ │ └─ r-base [3.3.2|3.4.1] would require
│ │ │ └─ icu 54.* , which does not exist (perhaps a missing channel);
│ │ ├─ r-naturalsort 0.1.3 would require
│ │ │ └─ r-base 3.4.1* but there are no viable options
│ │ │ ├─ r-base [3.3.2|3.4.1], which cannot be installed (as previously explained);
│ │ │ └─ r-base 3.4.1 conflicts with any installable versions previously reported;
│ │ └─ r-naturalsort 0.1.3 would require
│ │ └─ r-base >=3.5.1,<3.5.2.0a0 , which conflicts with any installable versions previously reported;
│ ├─ r-castor [1.7.10|1.7.2|...|1.7.9] would require
│ │ ├─ r-base >=4.1,<4.2.0a0 with the potential options
│ │ │ ├─ r-base [4.0.5|4.1.3|...|4.4.2], which cannot be installed (as previously explained);
│ │ │ └─ r-base [4.1.0|4.1.1|4.1.2|4.1.3], which can be installed;
│ │ └─ r-naturalsort, which cannot be installed (as previously explained);
│ └─ r-castor [1.7.10|1.7.11|...|1.8.3] would require
│ └─ r-base [>=4.2,<4.3.0a0 |>=4.3,<4.4.0a0 |>=4.4,<4.5.0a0 ], which cannot be installed (as previously explained);
└─ sepp 4.4.0** is not installable because it requires
├─ python >=3.9,<3.10.0a0 but there are no viable options
│ ├─ python [3.9.10|3.9.12] conflicts with any installable versions previously reported;
│ └─ python [3.10.0|3.10.1|...|3.9.9], which cannot be installed (as previously explained);
└─ python_abi 3.9.* *_cp39, which conflicts with any installable versions previously reported.
EnvironmentNameNotFound: Could not find conda environment: picrust-v2.5.3_2
You can list all discoverable environments with `conda info --envs`.
Obtaining file:///Users/misbahtubassam/picrust2-2.5.3
Installing build dependencies ... done
Checking if build backend supports build_editable ... done
Getting requirements to build editable ... done
Preparing editable metadata (pyproject.toml) ... done
Collecting numpy (from PICRUSt2==2.5.3)
Using cached numpy-2.0.2-pp39-pypy39_pp73-macosx_14_0_x86_64.whl.metadata (60 kB)
Collecting h5py (from PICRUSt2==2.5.3)
Using cached h5py-3.12.1.tar.gz (411 kB)
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Collecting joblib (from PICRUSt2==2.5.3)
Using cached joblib-1.4.2-py3-none-any.whl.metadata (5.4 kB)
Collecting biom-format (from PICRUSt2==2.5.3)
Using cached biom-format-2.1.16.tar.gz (11.7 MB)
Installing build dependencies ... done
Getting requirements to build wheel ... error
error: subprocess-exited-with-error
× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> [75 lines of output]
<string>:15: SetuptoolsDeprecationWarning: The test command is disabled and references to it are deprecated.
!!
********************************************************************************
Please remove any references to `setuptools.command.test` in all supported versions of the affected package.
This deprecation is overdue, please update your project and remove deprecated
calls to avoid build errors in the future.
********************************************************************************
!!
Traceback (most recent call last):
File "/private/var/folders/pr/gtvp6nsn0zl5sbz8xh589w8h0000gn/T/pip-build-env-jajcud1f/overlay/lib/pypy3.9/site-packages/numpy/_core/__init__.py", line 23, in <module>
from . import multiarray
File "/private/var/folders/pr/gtvp6nsn0zl5sbz8xh589w8h0000gn/T/pip-build-env-jajcud1f/overlay/lib/pypy3.9/site-packages/numpy/_core/multiarray.py", line 10, in <module>
from . import overrides
File "/private/var/folders/pr/gtvp6nsn0zl5sbz8xh589w8h0000gn/T/pip-build-env-jajcud1f/overlay/lib/pypy3.9/site-packages/numpy/_core/overrides.py", line 8, in <module>
from numpy._core._multiarray_umath import (
ImportError: dlopen(/private/var/folders/pr/gtvp6nsn0zl5sbz8xh589w8h0000gn/T/pip-build-env-jajcud1f/overlay/lib/pypy3.9/site-packages/numpy/_core/_multiarray_umath.pypy39-pp73-darwin.so, 0x0006): symbol not found in flat namespace '_PyPyObject_CallOneArg'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/private/var/folders/pr/gtvp6nsn0zl5sbz8xh589w8h0000gn/T/pip-build-env-jajcud1f/overlay/lib/pypy3.9/site-packages/numpy/__init__.py", line 114, in <module>
from numpy.__config__ import show as show_config
File "/private/var/folders/pr/gtvp6nsn0zl5sbz8xh589w8h0000gn/T/pip-build-env-jajcud1f/overlay/lib/pypy3.9/site-packages/numpy/__config__.py", line 4, in <module>
from numpy._core._multiarray_umath import (
File "/private/var/folders/pr/gtvp6nsn0zl5sbz8xh589w8h0000gn/T/pip-build-env-jajcud1f/overlay/lib/pypy3.9/site-packages/numpy/_core/__init__.py", line 49, in <module>
raise ImportError(msg)
ImportError:
IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!
Importing the numpy C-extensions failed. This error can happen for
many reasons, often due to issues with your setup or how NumPy was
installed.
We have compiled some common reasons and troubleshooting tips at:
https://numpy.org/devdocs/user/troubleshooting-importerror.html
Please note and check the following:
* The Python version is: Python3.9 from "/Users/misbahtubassam/opt/anaconda3/envs/myenv1/bin/python"
* The NumPy version is: "2.0.2"
and make sure that they are the versions you expect.
Please carefully study the documentation linked above for further help.
Original error was: dlopen(/private/var/folders/pr/gtvp6nsn0zl5sbz8xh589w8h0000gn/T/pip-build-env-jajcud1f/overlay/lib/pypy3.9/site-packages/numpy/_core/_multiarray_umath.pypy39-pp73-darwin.so, 0x0006): symbol not found in flat namespace '_PyPyObject_CallOneArg'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/Users/misbahtubassam/opt/anaconda3/envs/myenv1/lib/pypy3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
main()
File "/Users/misbahtubassam/opt/anaconda3/envs/myenv1/lib/pypy3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
File "/Users/misbahtubassam/opt/anaconda3/envs/myenv1/lib/pypy3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 118, in get_requires_for_build_wheel
return hook(config_settings)
File "/private/var/folders/pr/gtvp6nsn0zl5sbz8xh589w8h0000gn/T/pip-build-env-jajcud1f/overlay/lib/pypy3.9/site-packages/setuptools/build_meta.py", line 334, in get_requires_for_build_wheel
return self._get_build_requires(config_settings, requirements=[])
File "/private/var/folders/pr/gtvp6nsn0zl5sbz8xh589w8h0000gn/T/pip-build-env-jajcud1f/overlay/lib/pypy3.9/site-packages/setuptools/build_meta.py", line 304, in _get_build_requires
self.run_setup()
File "/private/var/folders/pr/gtvp6nsn0zl5sbz8xh589w8h0000gn/T/pip-build-env-jajcud1f/overlay/lib/pypy3.9/site-packages/setuptools/build_meta.py", line 522, in run_setup
super().run_setup(setup_script=setup_script)
File "/private/var/folders/pr/gtvp6nsn0zl5sbz8xh589w8h0000gn/T/pip-build-env-jajcud1f/overlay/lib/pypy3.9/site-packages/setuptools/build_meta.py", line 320, in run_setup
exec(code, locals())
File "<string>", line 16, in <module>
File "/private/var/folders/pr/gtvp6nsn0zl5sbz8xh589w8h0000gn/T/pip-build-env-jajcud1f/overlay/lib/pypy3.9/site-packages/numpy/__init__.py", line 119, in <module>
raise ImportError(msg) from e
ImportError: Error importing numpy: you should not try to import numpy from
its source directory; please exit the numpy source tree, and relaunch
your python interpreter from there.
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error
× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> See above for output.
note: This error originates from a subprocess, and is likely not a problem with pip.
Thanks in Advance.