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drivenbyentropy / aptasuite

A full-featured bioinformatics software collection for the comprehensive analysis of aptamers in HT-SELEX experiments.
https://drivenbyentropy.github.io/
GNU General Public License v3.0
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aptamer pool tab hanging #81

Open nl82 opened 4 years ago

nl82 commented 4 years ago

Hello,

I was able to parse the fastq files in aptasuite v.0.9.4. (the gui) but afterwards, the aptamer pool tab keeps calculating without showing any data. I got the following log in return. Any help is much appreciated.

Starting New Experiment Wizard

Written Configuration file to /Users/m/Desktop/Aptasuit HT-SELEX/sel_N_4/selexN4/configuration.aptasuite

Reading configuration from file.

Creating Database

Instantiating MapDBAptamerPool

Created new file /Users/m/Desktop/Aptasuit HT-SELEX/sel_N_4/selexN4/pooldata/data0000.mapdb

Created new bounds file /Users/m/Desktop/Aptasuit HT-SELEX/sel_N_4/selexN4/pooldata/bounds_data0000.mapdb

Created new inverse file /Users/m/Desktop/Aptasuit HT-SELEX/sel_N_4/selexN4/pooldata/data_inverse.mapdb

AptamerPool instantiation took 9.356 seconds

Processing selection cycle sel_N_4_r1

Creating new file '/Users/m/Desktop/Aptasuit HT-SELEX/sel_N_4/selexN4/cycledata/1_sel_N_4_r1.mapdb' for selection cycle sel_N_4_r1.

Processing selection cycle sel_N_4_r2

Creating new file '/Users/m/Desktop/Aptasuit HT-SELEX/sel_N_4/selexN4/cycledata/2_sel_N_4_r2.mapdb' for selection cycle sel_N_4_r2.

Creating new Metadata instance.

Loading took 15996 milliseconds

Initializing Experiment

Initializing parser AptaplexParser

Starting AptaPlex:

Opened forward file in fastq format /Users/m/Desktop/Aptasuit HT-SELEX/sel_N_4/sel_N_4_r1.fastq

Written Configuration file to /Users/m/Desktop/Aptasuit HT-SELEX/sel_N_4/selexN4/configuration.aptasuite

javafx.fxml.LoadException: file:/Users/m/Downloads/aptasuite-0.9.4/aptasuite-0.9.4.jar!/gui/core/experiment/overview/ExperimentOverviewRandomizedRegionSizeDistribution.fxml file:/Users/m/Downloads/aptasuite-0.9.4/aptasuite-0.9.4.jar!/gui/core/experiment/overview/ExperimentOverviewRoot.fxml:328

at javafx.fxml.FXMLLoader.constructLoadException(FXMLLoader.java:2601)
at javafx.fxml.FXMLLoader.loadImpl(FXMLLoader.java:2571)
at javafx.fxml.FXMLLoader.loadImpl(FXMLLoader.java:2441)
at javafx.fxml.FXMLLoader.access$2700(FXMLLoader.java:103)
at javafx.fxml.FXMLLoader$IncludeElement.constructValue(FXMLLoader.java:1143)
at javafx.fxml.FXMLLoader$ValueElement.processStartElement(FXMLLoader.java:746)
at javafx.fxml.FXMLLoader.processStartElement(FXMLLoader.java:2707)
at javafx.fxml.FXMLLoader.loadImpl(FXMLLoader.java:2527)
at javafx.fxml.FXMLLoader.loadImpl(FXMLLoader.java:2441)
at javafx.fxml.FXMLLoader.loadImpl(FXMLLoader.java:3214)
at javafx.fxml.FXMLLoader.loadImpl(FXMLLoader.java:3175)
at javafx.fxml.FXMLLoader.loadImpl(FXMLLoader.java:3148)
at javafx.fxml.FXMLLoader.loadImpl(FXMLLoader.java:3124)
at javafx.fxml.FXMLLoader.loadImpl(FXMLLoader.java:3104)
at javafx.fxml.FXMLLoader.load(FXMLLoader.java:3097)
at gui.core.RootLayoutController.addExperimentOverviewTab(RootLayoutController.java:607)
at gui.core.RootLayoutController.lambda$showInitialTabs$5(RootLayoutController.java:313)
at com.sun.javafx.application.PlatformImpl.lambda$null$5(PlatformImpl.java:295)
at java.security.AccessController.doPrivileged(Native Method)
at com.sun.javafx.application.PlatformImpl.lambda$runLater$6(PlatformImpl.java:294)
at com.sun.glass.ui.InvokeLaterDispatcher$Future.run(InvokeLaterDispatcher.java:95)

Caused by: java.lang.reflect.InvocationTargetException at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at sun.reflect.misc.Trampoline.invoke(MethodUtil.java:71) at sun.reflect.GeneratedMethodAccessor1.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at sun.reflect.misc.MethodUtil.invoke(MethodUtil.java:275) at javafx.fxml.FXMLLoader.loadImpl(FXMLLoader.java:2566) ... 19 more Caused by: java.util.NoSuchElementException: No value present at java.util.Optional.get(Optional.java:135) at gui.core.experiment.overview.ExperimentOverviewRandomizedRegionSizeDistributionController.computeStatistics(ExperimentOverviewRandomizedRegionSizeDistributionController.java:90) at gui.core.experiment.overview.ExperimentOverviewRandomizedRegionSizeDistributionController.initialize(ExperimentOverviewRandomizedRegionSizeDistributionController.java:55) ... 29 more

Initializing data structures

Preparing to sort data

Retrieving data for selection cycle sel_N_4_r2

Prioritizing data

Sorting data

Initializing data structures

Preparing to sort data

Retrieving data for selection cycle sel_N_4_r2

Prioritizing data

Sorting data

Bioanalytica commented 4 years ago

(User, not a dev) The last error "ExperimentOverviewRandomizedRegionSizeDistributionController.java:55" looks like an issue with the input value for the length of your aptamer library: a) pseudo-random region of recombinatorial synthesis (n) or b) mismatch between input maximum value for primers and/or n

In the GUI these values are specified in the "advanced" settings, I prefer to use a range because reads usually can have snp of +/- ~1nt (so I use a range of +/- 3, the most I've seen is 2) so my config file has the following:

AptaplexParser.randomizedRegionSizeLowerBound = (n) - 3 AptaplexParser.randomizedRegionSizeUpperBound = (n) + 3

The default value is 55, it looks like the program is reading 90? Not sure, Java isn't my forte.

What operating system and version of Java JDK, Java JRE, & JavaFX are installed? I don't know what the optimal/maximum is but I'm running jdk-8u251, jre-8u251, & javafx_sdk-1_3_1-b05a.

Edit: After rummaging through the log files I saw an error thrown so apparently I'm sub-optimal, no surprise there:

WARNING: Loading FXML document with JavaFX API of version 9 by JavaFX runtime of version >8.0.251

I got the following output:

Parsing Completed in 1050.158 seconds.

Selection Cycle Statistics RME-AptaLib RME-Round1-Pos RME-Round2-Pos RME-Round2-Neg RME-Round3-Pos RME-Round3-NegB RME-Round4-Pos RME-Round5-Pos Starting Structure Predition Using existing sequencing data Instantiating MapDBStructurePool Starting Structure Prediction using 24 threads: Predicting...

This was all done in Ubuntu v20 but I've used Win7 and Win10 to do similar analyses using the command line, if you need the GUI it will generate a config file and you can kill the process and run it in cmd/terminal, fixed many issues I had running the GUI.