Error to load database: Fatal error: null

[Natacha Martins]

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!

[Bitbucket user]

Hi,

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

Thanks,

Alexandre

[Natacha Martins]

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]]

[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

[Natacha Martins]

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

[Ana Valero]

Hi, I have to report the same fatal error. My imput MLST file looks like this: Thanks, Ana

[Bitbucket user]

Hi,

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

Thanks,

@aplf

[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

[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.

[lokman galal]

hi

I have the same problem Romário Sales

[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.