Skip to content

Instantly share code, notes, and snippets.

@macmanes
Last active June 28, 2018 11:24
Show Gist options
  • Save macmanes/c3db3bcc4af9d5de99c24ffff006c00b to your computer and use it in GitHub Desktop.
Save macmanes/c3db3bcc4af9d5de99c24ffff006c00b to your computer and use it in GitHub Desktop.
error installing Albacore on Bridges
[macmanes@br018 ~]$ conda create -n albacore-2.3.1 python=3.6
-bash: conda: command not found
[macmanes@br018 ~]$ module load anaconda
[macmanes@br018 ~]$ conda create -n albacore-2.3.1 python=3.6
Fetching package metadata .........
Solving package specifications: .

Package plan for installation in environment /home/macmanes/.conda/envs/albacore-2.3.1:

The following NEW packages will be INSTALLED:

    certifi:    2016.2.28-py36_0
    openssl:    1.0.2l-0
    pip:        9.0.1-py36_1
    python:     3.6.2-0
    readline:   6.2-2
    setuptools: 36.4.0-py36_1
    sqlite:     3.13.0-0
    tk:         8.5.18-0
    wheel:      0.29.0-py36_0
    xz:         5.2.3-0
    zlib:       1.2.11-0

Proceed ([y]/n)? y

python-3.6.2-0 100% |##############################################################################################################| Time: 0:00:00  22.90 MB/s
certifi-2016.2 100% |##############################################################################################################| Time: 0:00:00  18.66 MB/s
wheel-0.29.0-p 100% |##############################################################################################################| Time: 0:00:00  14.88 MB/s
setuptools-36. 100% |##############################################################################################################| Time: 0:00:00  19.72 MB/s
pip-9.0.1-py36 100% |##############################################################################################################| Time: 0:00:00  16.44 MB/s
#
# To activate this environment, use:
# > source activate albacore-2.3.1
#
# To deactivate this environment, use:
# > source deactivate albacore-2.3.1
#

[macmanes@br018 ~]$ source activate albacore-2.3.1
(albacore-2.3.1) [macmanes@br018 ~]$ pip3 install ont_albacore-2.3.1-cp35-cp35m-manylinux1_x86_64.whl --user
(albacore-2.3.1) [macmanes@br018 ~]$ read_fast5_basecaller.py
RuntimeError: module compiled against API version 0xc but this version of numpy is 0xa
Traceback (most recent call last):
  File "/home/macmanes/.local/bin/read_fast5_basecaller.py", line 69, in <module>
    from albacore.input_utils import list_input_files
  File "/home/macmanes/.local/lib/python3.5/site-packages/albacore/input_utils.py", line 7, in <module>
    from albacore import log_utils
  File "/home/macmanes/.local/lib/python3.5/site-packages/albacore/log_utils.py", line 5, in <module>
    from albacore.pipeline_core import get_debug_level
SystemError: initialization of pipeline_core raised unreported exception
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment