Troubleshooting

Several potential fix for issues we encounter.

m2m_analysis: “Can’t connect to X11 window server using…”

Issue encountered when using m2m_analysis on a HPC:

<II> Create SVG ... Exception in thread "main" java.awt.AWTError: Can't connect to X11 window server using ':0' as the value of the DISPLAY variable.
    at sun.awt.X11GraphicsEnvironment.initDisplay(Native Method)
    at sun.awt.X11GraphicsEnvironment.access$200(X11GraphicsEnvironment.java:65)
    at sun.awt.X11GraphicsEnvironment$1.run(X11GraphicsEnvironment.java:115)
    at java.security.AccessController.doPrivileged(Native Method)
    at sun.awt.X11GraphicsEnvironment.<clinit>(X11GraphicsEnvironment.java:74)
    at java.lang.Class.forName0(Native Method)
    at java.lang.Class.forName(Class.java:264)
    at java.awt.GraphicsEnvironment.createGE(GraphicsEnvironment.java:103)
    at java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment(GraphicsEnvironment.java:82)
    at java.awt.image.BufferedImage.createGraphics(BufferedImage.java:1181)
    at org.apache.batik.svggen.SVGGraphics2D.<init>(Unknown Source)
    at org.apache.batik.svggen.SVGGraphics2D.<init>(Unknown Source)
    at org.mattlab.eaglevista.ui.GraphImageFactory.getSVGGraphicsOfGraph(GraphImageFactory.java:157)
    at org.mattlab.eaglevista.ui.GraphImageFactory.createImage(GraphImageFactory.java:80)
    at org.mattlab.eaglevista.ui.EvCommandLineInterpreter.runImpl(EvCommandLineInterpreter.java:466)
    at org.mattlab.eaglevista.ui.EvCommandLineInterpreter.main(EvCommandLineInterpreter.java:81)

One potential fix is to unset DISPLAY before launching m2m:

unset DISPLAY
m2m_analysys workflow...

UnicodeDecodeError when running m2m_analysis with Singularity

Error encountered when using m2m_analysis in a Singularity:

######### Creation of the powergraph website accessible at results_m2m_analysis_scfa/html/metabolic_targets_scfa #########
Traceback (most recent call last):
File "/usr/local/bin/m2m_analysis", line 8, in <module>
    sys.exit(main())
File "/usr/local/lib/python3.6/dist-packages/metage2metabo/__main_analysis__.py", line 289, in main
    args.oog, new_arg_modelhost, args.level)
File "/usr/local/lib/python3.6/dist-packages/metage2metabo/__main_analysis__.py", line 303, in main_analysis_workflow
    run_analysis_workflow(*allargs)
File "/usr/local/lib/python3.6/dist-packages/metage2metabo/m2m_analysis/m2m_analysis_workflow.py", line 48, in run_analysis_workflow
    powergraph_analysis(gml_output, output_dir, oog_jar, taxon_file, taxonomy_level)
File "/usr/local/lib/python3.6/dist-packages/metage2metabo/m2m_analysis/graph_compression.py", line 174, in powergraph_analysis
    merge_html_css_js(html_target +'_taxon', output_html_merged)
File "/usr/local/lib/python3.6/dist-packages/metage2metabo/m2m_analysis/graph_compression.py", line 473, in merge_html_css_js
    cytoscape_min_js_str =  input_cytoscape_min_js.read()
File "/usr/lib/python3.6/encodings/ascii.py", line 26, in decode
    return codecs.ascii_decode(input, self.errors)[0]
UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 234868: ordinal not in range(128)

This is an issue with the encodign standard used. A solution is to set the local codec to LC_ALL=C.UTF-8:

LC_ALL=C.UTF-8 && srun singularity exec -B....