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davidhwyllie / findNeighbour4

A server delivering large scale, incrementable, bacterial relatedness monitoring
MIT License
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When rendering phylogenetic trees with ete3, a core dump sometimes occurs #127

Open davidhwyllie opened 2 years ago

davidhwyllie commented 2 years ago

Scenario:

A phylogenetic tree is being rendered. https://github.com/davidhwyllie/findNeighbour4/blob/d42e10711e59e93ebf0e798fbb1598929f662c9c/tree/tree_utils.py#L320

Expected result: A tree is exported, e.g. to svg format

Intermittent result: A core dump occurs due to QT5 issues. Stack trace is below. Trace is produce with QT_DEBUG_PLUGINS="1"

[121 rows x 7 columns]
INFO:root:Generation depictions for each population
Generation depictions for each population
INFO:root:Using iqTree version at {0}
Using iqTree version at {0}
INFO:root:Population # 1: Selected expanding population (max 1000 samples) for tree build n = 1000
Population # 1: Selected expanding population (max 1000 samples) for tree build n = 1000
INFO:root:iqTree command: /data/software/iqtree-2.1.3-Linux/bin/iqtree2  -nt 8 -st DNA -s  /data/data/pca/fn4_pca6/1/1/tree_no_controls/alignment.fa -m GTR+I -blmin 3.344146072300438e-06 -fconst 8748,5117,5546,9414
iqTree command: /data/software/iqtree-2.1.3-Linux/bin/iqtree2  -nt 8 -st DNA -s  /data/data/pca/fn4_pca6/1/1/tree_no_controls/alignment.fa -m GTR+I -blmin 3.344146072300438e-06 -fconst 8748,5117,5546,9414
QFactoryLoader::QFactoryLoader() checking directory path "/home/ubuntu/.local/share/virtualenvs/fn4_atp_test-Ori3-jj9/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms" ...
QFactoryLoader::QFactoryLoader() looking at "/home/ubuntu/.local/share/virtualenvs/fn4_atp_test-Ori3-jj9/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqeglfs.so"
Found metadata in lib /home/ubuntu/.local/share/virtualenvs/fn4_atp_test-Ori3-jj9/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqeglfs.so, metadata=
{
    "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",
    "MetaData": {
        "Keys": [
            "eglfs"
        ]
    },
    "archreq": 0,
    "className": "QEglFSIntegrationPlugin",
    "debug": false,
    "version": 331520
}

Got keys from plugin meta data ("eglfs")
QFactoryLoader::QFactoryLoader() looking at "/home/ubuntu/.local/share/virtualenvs/fn4_atp_test-Ori3-jj9/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqlinuxfb.so"
Found metadata in lib /home/ubuntu/.local/share/virtualenvs/fn4_atp_test-Ori3-jj9/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqlinuxfb.so, metadata=
{
    "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",
    "MetaData": {
        "Keys": [
            "linuxfb"
        ]
    },
    "archreq": 0,
    "className": "QLinuxFbIntegrationPlugin",
    "debug": false,
    "version": 331520
}

Got keys from plugin meta data ("linuxfb")
QFactoryLoader::QFactoryLoader() looking at "/home/ubuntu/.local/share/virtualenvs/fn4_atp_test-Ori3-jj9/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqminimal.so"
Found metadata in lib /home/ubuntu/.local/share/virtualenvs/fn4_atp_test-Ori3-jj9/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqminimal.so, metadata=
{
    "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",
    "MetaData": {
        "Keys": [
            "minimal"
        ]
    },
    "archreq": 0,
    "className": "QMinimalIntegrationPlugin",
    "debug": false,
    "version": 331520
}

Got keys from plugin meta data ("minimal")
QFactoryLoader::QFactoryLoader() looking at "/home/ubuntu/.local/share/virtualenvs/fn4_atp_test-Ori3-jj9/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqminimalegl.so"
Found metadata in lib /home/ubuntu/.local/share/virtualenvs/fn4_atp_test-Ori3-jj9/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqminimalegl.so, metadata=
{
    "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",
    "MetaData": {
        "Keys": [
            "minimalegl"
        ]
    },
    "archreq": 0,
    "className": "QMinimalEglIntegrationPlugin",
    "debug": false,
    "version": 331520
}

Got keys from plugin meta data ("minimalegl")
QFactoryLoader::QFactoryLoader() looking at "/home/ubuntu/.local/share/virtualenvs/fn4_atp_test-Ori3-jj9/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqoffscreen.so"
Found metadata in lib /home/ubuntu/.local/share/virtualenvs/fn4_atp_test-Ori3-jj9/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqoffscreen.so, metadata=
{
    "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",
    "MetaData": {
        "Keys": [
            "offscreen"
        ]
    },
    "archreq": 0,
    "className": "QOffscreenIntegrationPlugin",
    "debug": false,
    "version": 331520
}

Got keys from plugin meta data ("offscreen")
QFactoryLoader::QFactoryLoader() looking at "/home/ubuntu/.local/share/virtualenvs/fn4_atp_test-Ori3-jj9/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqvnc.so"
Found metadata in lib /home/ubuntu/.local/share/virtualenvs/fn4_atp_test-Ori3-jj9/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqvnc.so, metadata=
{
    "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",
    "MetaData": {
        "Keys": [
            "vnc"
        ]
    },
    "archreq": 0,
    "className": "QVncIntegrationPlugin",
    "debug": false,
    "version": 331520
}

Got keys from plugin meta data ("vnc")
QFactoryLoader::QFactoryLoader() looking at "/home/ubuntu/.local/share/virtualenvs/fn4_atp_test-Ori3-jj9/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqwayland-egl.so"
Found metadata in lib /home/ubuntu/.local/share/virtualenvs/fn4_atp_test-Ori3-jj9/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqwayland-egl.so, metadata=
{
    "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",
    "MetaData": {
        "Keys": [
            "wayland-egl"
        ]
    },
    "archreq": 0,
    "className": "QWaylandEglPlatformIntegrationPlugin",
    "debug": false,
    "version": 331520
}

Got keys from plugin meta data ("wayland-egl")
QFactoryLoader::QFactoryLoader() looking at "/home/ubuntu/.local/share/virtualenvs/fn4_atp_test-Ori3-jj9/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqwayland-generic.so"
Found metadata in lib /home/ubuntu/.local/share/virtualenvs/fn4_atp_test-Ori3-jj9/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqwayland-generic.so, metadata=
{
    "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",
    "MetaData": {
        "Keys": [
            "wayland"
        ]
    },
    "archreq": 0,
    "className": "QWaylandIntegrationPlugin",
    "debug": false,
    "version": 331520
}

Got keys from plugin meta data ("wayland")
QFactoryLoader::QFactoryLoader() looking at "/home/ubuntu/.local/share/virtualenvs/fn4_atp_test-Ori3-jj9/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqwayland-xcomposite-egl.so"
Found metadata in lib /home/ubuntu/.local/share/virtualenvs/fn4_atp_test-Ori3-jj9/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqwayland-xcomposite-egl.so, metadata=
{
    "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",
    "MetaData": {
        "Keys": [
            "wayland-xcomposite-egl"
        ]
    },
    "archreq": 0,
    "className": "QWaylandXCompositeEglPlatformIntegrationPlugin",
    "debug": false,
    "version": 331520
}

Got keys from plugin meta data ("wayland-xcomposite-egl")
QFactoryLoader::QFactoryLoader() looking at "/home/ubuntu/.local/share/virtualenvs/fn4_atp_test-Ori3-jj9/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqwayland-xcomposite-glx.so"
Found metadata in lib /home/ubuntu/.local/share/virtualenvs/fn4_atp_test-Ori3-jj9/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqwayland-xcomposite-glx.so, metadata=
{
    "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",
    "MetaData": {
        "Keys": [
            "wayland-xcomposite-glx"
        ]
    },
    "archreq": 0,
    "className": "QWaylandXCompositeGlxPlatformIntegrationPlugin",
    "debug": false,
    "version": 331520
}

Got keys from plugin meta data ("wayland-xcomposite-glx")
QFactoryLoader::QFactoryLoader() looking at "/home/ubuntu/.local/share/virtualenvs/fn4_atp_test-Ori3-jj9/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqwebgl.so"
Found metadata in lib /home/ubuntu/.local/share/virtualenvs/fn4_atp_test-Ori3-jj9/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqwebgl.so, metadata=
{
    "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",
    "MetaData": {
        "Keys": [
            "webgl"
        ]
    },
    "archreq": 0,
    "className": "QWebGLIntegrationPlugin",
    "debug": false,
    "version": 331520
}

Got keys from plugin meta data ("webgl")
QFactoryLoader::QFactoryLoader() looking at "/home/ubuntu/.local/share/virtualenvs/fn4_atp_test-Ori3-jj9/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqxcb.so"
Found metadata in lib /home/ubuntu/.local/share/virtualenvs/fn4_atp_test-Ori3-jj9/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqxcb.so, metadata=
{
    "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",
    "MetaData": {
        "Keys": [
            "xcb"
        ]
    },
    "archreq": 0,
    "className": "QXcbIntegrationPlugin",
    "debug": false,
    "version": 331520
}

Got keys from plugin meta data ("xcb")
QFactoryLoader::QFactoryLoader() checking directory path "/usr/bin/platforms" ...
loaded library "/home/ubuntu/.local/share/virtualenvs/fn4_atp_test-Ori3-jj9/lib/python3.8/site-packages/PyQt5/Qt5/plugins/platforms/libqxcb.so"
qt.qpa.xcb: could not connect to display localhost:11.0
qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found.
This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.

Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, wayland-xcomposite-egl, wayland-xcomposite-glx, webgl, xcb.

Aborted (core dumped)