Closed pamelarussell closed 5 years ago
hsgweon
commented
5 years ago Hi Pam,
Can you let me know which system you are running PIPITS on? It is MacOS, Ubuntu, Debian etc.? (I only test PIPITS on Ubuntu and MacOS)
Can you please try:
source activate pipits_env
python --version
conda list numpyand let me know the outcome?
pamelarussell
commented
5 years ago Hi, thanks for your quick reply.
Here is our Linux distribution:
cat /etc/os-release
NAME="Arch Linux"
PRETTY_NAME="Arch Linux"
ID=arch
ID_LIKE=archlinux
ANSI_COLOR="0;36"
HOME_URL="https://www.archlinux.org/"
SUPPORT_URL="https://bbs.archlinux.org/"
BUG_REPORT_URL="https://bugs.archlinux.org/"Python version:
python --version
Python 3.6.6NumPy version:
conda list numpy
/software/cgeh/conda/daily/install/lib/python3.6/site-packages/requests/__init__.py:80: RequestsDependencyWarning: urllib3 (1.19.1) or chardet (3.0.4) doesn't match a supported version!
RequestsDependencyWarning)
# packages in environment at /Fingerlin/home/russellp/.conda/envs/pipits_env:
#
numpy 1.15.2 py36_blas_openblashd3ea46f_1 [blas_openblas] conda-forge
numpy-base 1.14.3 py36h0ea5e3f_1 Hmm... ok... I've tested with the latest PIPITS and dependencies on Ubuntu and I can't replicate this problem. Wondering if it's todo with Arch Linux...
Anyway, can you let me know what you get when you type:
python -c 'import sys; print(sys.path)'Essentially this should only show directories with "pipits_env" in them...
Also can you just try to update everything and see if everything works as intended (probably not...) by:
source activate pipits_env
conda update --allHere is the sys.path statement inside the pipits environment:
(09:17 > source activate pipits_env
(pipits_env) (09:17 russellp@c05 > python -c 'import sys; print(sys.path)'
['', '/usr/lib/python3.5/site-packages', '/home/russellp/Software/Python-3.5.2/lib/python3.5', '/<path omitted>/pipits_testing', '/Fingerlin/home/russellp/.conda/envs/pipits_env/lib/python36.zip', '/Fingerlin/home/russellp/.conda/envs/pipits_env/lib/python3.6', '/Fingerlin/home/russellp/.conda/envs/pipits_env/lib/python3.6/lib-dynload', '/Fingerlin/home/russellp/.local/lib/python3.6/site-packages', '/Fingerlin/home/russellp/.conda/envs/pipits_env/lib/python3.6/site-packages']I did conda update --all and then ran into an issue with vsearch. I recognized this from having a problem with it in an earlier stage of the pipeline, where I had followed the advice in issue #7 to install vsearch 2.8.0. After doing that again, I'm back to the original error.
Before installing vsearch 2.8.0:
> pipits_process -i out_funits/ITS.fasta -o out_process
pipits_process 2.2, the PIPITS Project
https://github.com/hsgweon/pipits
---------------------------------
2018-10-12 09:27:35 pipits_process started
2018-10-12 09:27:35 Generating a sample list from the input sequences
2018-10-12 09:27:36 Dereplicating and removing unique sequences prior to picking OTUs
2018-10-12 09:27:36 Error: None zero returncode: vsearch --derep_fulllength out_funits/ITS.fasta --output out_process/intermediate/input_nr.fasta --minuniquesize 2 --sizeout --threads 1After installing vsearch 2.8.0:
> pipits_process -i out_funits/ITS.fasta -o out_process
pipits_process 2.2, the PIPITS Project
https://github.com/hsgweon/pipits
---------------------------------
2018-10-12 09:32:09 pipits_process started
2018-10-12 09:32:09 Generating a sample list from the input sequences
2018-10-12 09:32:09 Dereplicating and removing unique sequences prior to picking OTUs
2018-10-12 09:32:09 Picking OTUs [VSEARCH]
2018-10-12 09:32:09 Removing chimeras [VSEARCH]
2018-10-12 09:32:14 Renaming OTUs
2018-10-12 09:32:14 Mapping reads onto centroids [VSEARCH]
2018-10-12 09:32:14 Making OTU table
2018-10-12 09:32:15 Converting classic tabular OTU into a BIOM format [BIOM]
2018-10-12 09:32:15 Error: None zero returncode: biom convert -i out_process/intermediate/otu_table_prelim.txt -o out_process/intermediate/otu_table_prelim.biom --table-type="OTU table" --to-jsonTrying the command directly:
> biom convert -i out_process/intermediate/otu_table_prelim.txt -o out_process/intermediate/otu_table_prelim.biom --table-type="OTU table" --to-json
Traceback (most recent call last):
File "/Fingerlin/home/russellp/.conda/envs/pipits_env/bin/biom", line 7, in <module>
from biom.cli import cli
File "/Fingerlin/home/russellp/.conda/envs/pipits_env/lib/python3.6/site-packages/biom/__init__.py", line 51, in <module>
from .table import Table
File "/Fingerlin/home/russellp/.conda/envs/pipits_env/lib/python3.6/site-packages/biom/table.py", line 176, in <module>
import numpy as np
File "/usr/lib/python3.5/site-packages/numpy/__init__.py", line 142, in <module>
from . import add_newdocs
File "/usr/lib/python3.5/site-packages/numpy/add_newdocs.py", line 13, in <module>
from numpy.lib import add_newdoc
File "/usr/lib/python3.5/site-packages/numpy/lib/__init__.py", line 8, in <module>
from .type_check import *
File "/usr/lib/python3.5/site-packages/numpy/lib/type_check.py", line 11, in <module>
import numpy.core.numeric as _nx
File "/usr/lib/python3.5/site-packages/numpy/core/__init__.py", line 14, in <module>
from . import multiarray
ImportError: cannot import name 'multiarray'Can you please try to remove the environment and try again, but with unset PYTHONPATH before doing so?
conda env remove --name pipits_env
unset PYTHONPATH
conda create -n pipits_env python=3.6 pipitsThen into conda env, and downgrade VSEARCH:
source activate pipits_env
conda install vsearch=2.8.0This solved the problem and it now runs through to completion. Thanks so much for your help!!
Hi,
I am working my way through the instructions in your README with your test dataset. I've made it to the final step. I am getting stuck in
pipits_processwith the following output:When I run the problem command directly from the command line I get this:
Some Googling suggests that this issue can be solved by deleting and reinstalling NumPy. However, I have not been able to change the version or reinstall NumPy due to the dependencies of PIPITS. Can you suggest a solution for this issue?
Thanks! Pam