fanxinping
commented
2 years ago @CJBgon
It's very strange. Can you provide some details of how to build it in Singularity or the def file of Singularity?
Closed CJBgon closed 2 years ago
fanxinping
commented
2 years ago @CJBgon
It's very strange. Can you provide some details of how to build it in Singularity or the def file of Singularity?
polyactis
commented
2 years ago We missed a few python3 packages during the python3 upgrade for this program and will make a new docker image ASAP.
On Fri, Sep 10, 2021 at 2:20 AM Christian Bouwens @.***> wrote:
I've ran into some errors with the docker (build in Singularity). The plotting steps require matplotlib. However, plot_cnv errors out when importing matplotlib. Interestingly, plotCPandMCP.py is written in Python3. I suspect the docker only installed matplotlib for python2.
log:
[15_1] [TaskRunner:plot_cnv] Task initiated on local node [15_1] [TaskManager] [ERROR] Failed to complete command task: 'plot_cnv' launched from master workflow, error code: 1, command: '/usr/local/Accucopy/plotCPandMCP.py -i /.../accucopy/results/cnv.output.tsv -r /mnt/refData/genome.dict --no_of_autosomes 22 -o /.../accucopy/results/plot.cnv.png' [15_1] [TaskManager] [ERROR] [plot_cnv] Error Message: [15_1] [TaskManager] [ERROR] [plot_cnv] Last 27 stderr lines from task (of 27 total lines): [15_1] [TaskManager] [ERROR] [plot_cnv] Error processing line 1 of /usr/local/lib/python3.6/dist-packages/matplotlib-3.3.4-py3.6-nspkg.pth: [15_1] [TaskManager] [ERROR] [] [] [15_1] [plot_cnv] [15_1] [TaskManager] [ERROR] [] [] [15_1] [plot_cnv] Traceback (most recent call last): [15_1] [TaskManager] [ERROR] [] [] [15_1] [plot_cnv] File "/usr/lib/python3.6/site.py", line 174, in addpackage [15_1] [TaskManager] [ERROR] [] [] [15_1] [plot_cnv] exec(line) [15_1] [TaskManager] [ERROR] [] [] [15_1] [plot_cnv] File "
", line 1, in [15_1] [TaskManager] [ERROR] [] [] [15_1] [plot_cnv] File " ", line 568, in module_from_spec [15_1] [TaskManager] [ERROR] [] [] [15_1] [plot_cnv] AttributeError: 'NoneType' object has no attribute 'loader' [15_1] [TaskManager] [ERROR] [] [] [15_1] [plot_cnv] [15_1] [TaskManager] [ERROR] [] [] [15_1] [plot_cnv] Remainder of file ignored [15_1] [TaskManager] [ERROR] [] [] [15_1] [plot_cnv] Matplotlib created a temporary config/cache directory at /tmp/matplotlib-pql0p325 because the default path (/root/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. [15_1] [TaskManager] [ERROR] [] [] [15_1] [plot_cnv] Traceback (most recent call last): [15_1] [TaskManager] [ERROR] [] [] [15_1] [plot_cnv] File "/usr/local/Accucopy/plotCPandMCP.py", line 7, in [15_1] [TaskManager] [ERROR] [] [] [15_1] [plot_cnv] from matplotlib import pyplot as plt [15_1] [TaskManager] [ERROR] [] [] [15_1] [plot_cnv] File "/usr/local/lib/python3.6/dist-packages/matplotlib/pyplot.py", line 36, in [15_1] [TaskManager] [ERROR] [] [] [15_1] [plot_cnv] import matplotlib.colorbar [15_1] [TaskManager] [ERROR] [] [] [15_1] [plot_cnv] File "/usr/local/lib/python3.6/dist-packages/matplotlib/colorbar.py", line 44, in [15_1] [TaskManager] [ERROR] [] [] [15_1] [plot_cnv] import matplotlib.contour as contour [15_1] [TaskManager] [ERROR] [] [] [15_1] [plot_cnv] File "/usr/local/lib/python3.6/dist-packages/matplotlib/contour.py", line 21, in [15_1] [TaskManager] [ERROR] [] [] [15_1] [plot_cnv] import matplotlib.texmanager as texmanager [15_1] [TaskManager] [ERROR] [] [] [15_1] [plot_cnv] File " ", line 971, in _find_and_load [15_1] [TaskManager] [ERROR] [] [] [15_1] [plot_cnv] File " ", line 955, in _find_and_load_unlocked [15_1] [TaskManager] [ERROR] [] [] [15_1] [plot_cnv] File " ", line 665, in _load_unlocked [15_1] [TaskManager] [ERROR] [] [] [15_1] [plot_cnv] File " ", line 674, in exec_module [15_1] [TaskManager] [ERROR] [] [] [15_1] [plot_cnv] File " ", line 779, in get_code [15_1] [TaskManager] [ERROR] [] [] [15_1] [plot_cnv] File " ", line 487, in _compile_bytecode [15_1] [TaskManager] [ERROR] [] [] [15_1] [plot_cnv] EOFError: marshal data too short [15_1] [TaskManager] [ERROR] Shutting down task submission. Waiting for remaining tasks to complete. In the singularity container i couldn't import matplotlib, pandas or numpy for python3 (but could for python2).
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CJBgon
commented
2 years ago @fanxinping I've build the singularity container straight from the docker:
sudo singularity build --writable accucopy.sif docker://polyactis/accucopy
I'll check with the new docker if the same issue occurs.
polyactis
commented
2 years ago The new image has been pushed to the docker hub. Please try and let us know if any problem
On Thu, Sep 16, 2021, 6:15 AM Christian Bouwens @.***> wrote:
@fanxinping https://github.com/fanxinping I've build the singularity container straight from the docker:
sudo singularity build --writable accucopy.sif docker://polyactis/accucopy
I'll check with the new docker if the same issue occurs.
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CJBgon
commented
2 years ago I can confirm the new docker has resolved the problem, thank you for the help.
I've ran into some errors with the docker (build in Singularity). The plotting steps require matplotlib. However, plot_cnv errors out when importing matplotlib. Interestingly, plotCPandMCP.py is written in Python3. I suspect the docker only installed matplotlib for python2.
log:
In the singularity container i couldn't import matplotlib, pandas or numpy for python3 (but could for python2).