Error to load database: Fatal error: null

Issue #7 new
Natacha Martins created an issue

I am trying to load a MLST database for E. coli (.txt file) to start my analysis, however a bug with Fatal error: null message keeps coming up. Could you please help me? Thanks!

Comments (10)

  1. Bitbucket user

    Hi,

    Can you describe the content of that file or just attach the first 3 lines?

    Thanks,

    Alexandre

  2. Natacha Martins reporter

    Thank you Alexandre! I am sending below the information about the error:

    WARNING [org.netbeans.modules.autoupdate.ui.actions.AutoupdateSettings]: The property "netbeans.default_userdir_root" was not set! INFO [org.netbeans.core.startup.NbEvents]: Ativando módulos: org.openide.util.lookup [8.25.1 201408251540] org.openide.util [8.39.1 201408251540] org.openide.modules [7.43.1 201408251540] org.netbeans.api.annotations.common/1 [1.24.1 201408251540] org.openide.filesystems [8.12.1 201408251540] org.openide.awt [7.62.1 201408251540] org.netbeans.api.progress/1 [1.38.1 201408251540] org.openide.dialogs [7.38.1 201408251540] org.openide.nodes [7.39.1 201408251540] org.openide.windows [6.71.1 201408251540] org.netbeans.modules.editor.mimelookup/1 [1.36.1 201408251540] org.openide.text [6.62.2 201410071419] org.netbeans.swing.tabcontrol [1.51.1 201408251540] org.netbeans.swing.outline [1.30.1 201408251540] org.openide.explorer [6.57.1 201408251540] org.openide.actions [6.35.1 201408251540] org.netbeans.modules.queries/1 [1.39.1 201408251540] org.openide.loaders [7.57.2 201410071419] org.openide.io [1.45.1 201408251540] org.netbeans.swing.plaf [1.37.1 201408251540] org.netbeans.spi.quicksearch [1.23.1 201408251540] org.netbeans.modules.templates/1 [1.3.1 201408251540] org.netbeans.bootstrap/1 [2.69.1 201408251540] org.netbeans.core.startup/1 [1.55.1 201408251540] org.netbeans.modules.settings/1 [1.45.1 201408251540] org.netbeans.modules.sendopts/2 [2.31.1 201408251540] org.netbeans.modules.sampler [1.10.1 201408251540] org.netbeans.modules.progress.ui [1.29.2 201410071419] org.netbeans.modules.keyring [1.20.1 201408251540] org.netbeans.core/2 [3.46.1 201408251540] org.netbeans.modules.options.api/1 [1.41.1 201408251540] org.netbeans.modules.options.keymap [1.31.1 201408251540] org.netbeans.modules.masterfs/2 [2.48.2 201410071419] org.netbeans.modules.masterfs.nio2 [1.12.1 201408251540] org.netbeans.libs.jna/1 [1.38.1 201408251540] org.netbeans.modules.masterfs.macosx [1.10.1 201408251540] org.netbeans.modules.keyring.fallback [1.4.1 201408251540] org.netbeans.modules.keyring.impl [1.20.1 201408251540] org.netbeans.modules.autoupdate.services [1.47.2 201410071419] org.netbeans.modules.autoupdate.ui [1.41.1 201408251540] org.netbeans.modules.autoupdate.cli [1.9.1 201408251540] org.netbeans.core.windows/2 [2.77.1 201408251540] org.netbeans.modules.applemenu/1 [1.33.1 201408251540] org.netbeans.libs.osgi [1.18.1 201408251540] org.netbeans.libs.jna.platform/1 [1.8.1 201408251540] org.netbeans.libs.felix [2.12.1 201408251540] org.netbeans.core.ui/1 [1.41.1 201408251540] org.netbeans.core.output2/1 [1.37.1 201408251540] org.netbeans.core.network [1.6.1 201408251540] org.netbeans.core.netigso [1.27.1 201408251540] org.netbeans.core.nativeaccess/1 [1.27.1 201408251540] org.netbeans.core.multitabs/1 [1.8.1.1 1 201408251540] org.netbeans.core.io.ui/1 [1.26.1 201408251540] net.phyloviz.core/1 [1.4.2 2 141109] net.phyloviz.welcome/1 [1.0.4 4 141109] net.phyloviz.algo/1 [1.2.0 0 141109] net.phyloviz.mlva/1 [1.1.3 3 141109] net.phyloviz.goeburst/1 [1.2.3 3 150915] net.phyloviz.weightdistance/1 [1.0.1 1 141109] net.phyloviz.category/1 [1.0.5 5 141109] net.phyloviz.tview/1 [1.0.8 8 141109] net.phyloviz.stats/1 [1.0.6 6 141109] net.phyloviz.snp/1 [1.0.6 6 141109] net.phyloviz.slvgraph/1 [1.0.0 0 141109] net.phyloviz.mlst/1 [1.0.8 8 141109] net.phyloviz.pubmlst/1 [1.0.7 7 141109] net.phyloviz.mstsstatistics/1 [1.1.2 2 141109] net.phyloviz.mlvadist/1 [1.0.4 4 141109] net.phyloviz.alseq/1 [1.0.10 10 141109] net.phyloviz.loadmlst/1 [1.0.7 7 141109] net.phyloviz.gtview/1 [1.3.1 1 150401] INFO [org.netbeans.core.network.proxy.NetworkProxyReloader]: System network proxy resolver: Mac INFO [org.netbeans.core.network.proxy.NetworkProxyReloader]: System network proxy reloading failed! Trying fallback resolver. INFO [org.netbeans.core.network.proxy.fallback.FallbackNetworkProxy]: Fallback system proxy resolver: no http_proxy variable found INFO [org.netbeans.core.network.proxy.NetworkProxyReloader]: System network proxy reloading succeeded. Fallback provider was successful. INFO [org.netbeans.core.network.proxy.NetworkProxyReloader]: System network proxy - mode: direct INFO [org.netbeans.core.network.proxy.NetworkProxyReloader]: System network proxy: fell to default (correct if direct mode went before) INFO [org.netbeans.ui.metrics.laf]: USG_LOOK_AND_FEEL Diagnostic information Input arguments: -Djdk.home=/Library/Internet Plug-Ins/JavaAppletPlugin.plugin/Contents/Home -Dnetbeans.dirs=/Applications/phyloviz.app/Contents/Resources/phyloviz/phyloviz: -Dnetbeans.home=/Applications/phyloviz.app/Contents/Resources/phyloviz/platform -Dcom.apple.mrj.application.apple.menu.about.name=phyloviz -Xss32M -Xms32m -Xmx1024M -XX:+HeapDumpOnOutOfMemoryError -XX:HeapDumpPath=/Users/Natacha/Library/Application Support/phyloviz/1.0/var/log/heapdump.hprof Compiler: HotSpot 64-Bit Tiered Compilers Heap memory usage: initial 32,0MB maximum 910,5MB Non heap memory usage: initial 2,4MB maximum -1b Garbage collector: PS Scavenge (Collections=11 Total time spent=0s) Garbage collector: PS MarkSweep (Collections=1 Total time spent=0s) Classes: loaded=4785 total loaded=4785 unloaded 0 INFO [org.netbeans.core.ui.warmup.DiagnosticTask]: Total memory 4.294.967.296 INFO [null]: Memória física total 4.294.967.296 WARNING [net.phyloviz.mlst.MLSTypingFactory]: Incompatible length: {\fonttbl\f0\fnil\fcharset0 has length1(!=0) WARNING [net.phyloviz.mlst.MLSTypingFactory]: Duplicated profile: \paperw11900\paperh16840\margl1440\margr1440\vieww10800\viewh8400\viewkind0 aka {\colortbl;\red255\green255\blue255;} (frequency updated) WARNING [net.phyloviz.mlst.MLSTypingFactory]: Duplicated profile: \deftab720 aka {\colortbl;\red255\green255\blue255;} (frequency updated) WARNING [net.phyloviz.mlst.MLSTypingFactory]: Duplicated profile: \pard\pardeftab720\ri720\partightenfactor0 aka {\colortbl;\red255\green255\blue255;} (frequency updated) WARNING [net.phyloviz.mlst.MLSTypingFactory]: Duplicated profile: aka {\colortbl;\red255\green255\blue255;} (frequency updated) WARNING [net.phyloviz.mlst.MLSTypingFactory]: Incompatible length: {\fonttbl\f0\fnil\fcharset0 has length1(!=0) WARNING [net.phyloviz.mlst.MLSTypingFactory]: Duplicated profile: \paperw11900\paperh16840\margl1440\margr1440\vieww10800\viewh8400\viewkind0 aka {\colortbl;\red255\green255\blue255;} (frequency updated) WARNING [net.phyloviz.mlst.MLSTypingFactory]: Duplicated profile: \deftab720 aka {\colortbl;\red255\green255\blue255;} (frequency updated) WARNING [net.phyloviz.mlst.MLSTypingFactory]: Duplicated profile: \pard\pardeftab720\ri720\partightenfactor0 aka {\colortbl;\red255\green255\blue255;} (frequency updated) WARNING [net.phyloviz.mlst.MLSTypingFactory]: Duplicated profile: aka {\colortbl;\red255\green255\blue255;} (frequency updated) WARNING [org.openide.filesystems.Ordering]: Found same position 10 for both Actions/PHYLOViZ/GOeBurst/net-phyloviz-goeburst-ui-OutputViewAction.instance and Actions/PHYLOViZ/GOeBurst/net-phyloviz-gtview-action-SLVGraphViewAction.instance WARNING [org.openide.filesystems.Ordering]: Found same position 10 for both Actions/PHYLOViZ/GOeBurst/net-phyloviz-goeburst-ui-OutputViewAction.instance and Actions/PHYLOViZ/GOeBurst/net-phyloviz-mstsstatistics-ui-ViewAction.instance WARNING [org.openide.filesystems.Ordering]: Found same position 10 for both Actions/PHYLOViZ/GOeBurst/net-phyloviz-gtview-action-SLVGraphViewAction.instance and Actions/PHYLOViZ/GOeBurst/net-phyloviz-mstsstatistics-ui-ViewAction.instance WARNING [org.netbeans.modules.options.keymap.LayersBridge]: Invalid shortcut: org.openide.loaders.BrokenDataShadow@31050114[MultiFileObject@7fb3c555[Shortcuts/CM-F5.shadow]] WARNING [org.netbeans.modules.options.keymap.LayersBridge]: Invalid shortcut: org.openide.loaders.BrokenDataShadow@31050114[MultiFileObject@7fb3c555[Shortcuts/CM-F5.shadow]]

  3. Bitbucket user

    Hi,

    That file seems to have some problem. As far as I can check in the log above, it seems that the first profile has length 0. Can you attach the database file or just part of it?

    Thanks,

    Alexandre

  4. Natacha Martins reporter

    Hi Alexandre! Below is the image of my database file. Thank you again for helping me!

    Captura de Tela 2016-03-08 às 09.29.09.png

  5. Bitbucket user

    Hi,

    Can you attach the file instead of the screenshot so we can try to reproduce the error?

    Thanks,

    @aplf

  6. jacarrico

    Hello, I suspect that the error has to do with extra blank lines after the profile/metadata or an extra column in any of the profiles. Check your data for this and please report back to us.

    With my very best regards

  7. Romário Sales

    Hi,

    How do I solve this question Duplicated profile: 111 aka 108 (frequency updated); Duplicated profile: 115 aka 108 (frequency updated)? I have some strains that have the same profile and they are being excluded from the analysis when I do the spanning tree. I am using phyloviz 2.

  8. ramirma

    Please check if you have extra blank lines after the profile/metadata or an extra column in any of the profiles as suggested by jcarrico.

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