aptasuite
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drivenbyentropy
Aptasuite is running too long
The analysis of my data is taking too much time. I run the program for almost 24h and nothing appeared. I started the analysis from a trial of only one round of SELEX and 1 library, that has 2 files, forward and reverse sequences after MiSeq NGS sequencing.
Is it normal?
Here is my logs data: 3:26:33 | CONFIG | JavaFX Application Thread: aptasuite.Aptasuite System Information: Java Version: 1.8.0_333 JavaFX Version: null OS Name: Windows 10 OS Version: 10.0 OS Architecture: amd64 OS Architecture Model: 64 CPU cores: 8 System Memory: 257425408 Mb
AptaSuite version read from file. Version is 0.9.8
Starting New Experiment Wizard
Written Configuration file to C:\Users\eremeeve\Dropbox@QUT\Sequencing\NGS_sequencing\2022_05_07\Trial\configuration.aptasuite
Reading configuration from file.
Creating Database
Instantiating MapDBAptamerPool
Created new file C:\Users\eremeeve\Dropbox@QUT\Sequencing\NGS_sequencing\2022_05_07\Trial\pooldata\data0000.mapdb
Created new bounds file C:\Users\eremeeve\Dropbox@QUT\Sequencing\NGS_sequencing\2022_05_07\Trial\pooldata\bounds_data0000.mapdb
Created new inverse file C:\Users\eremeeve\Dropbox@QUT\Sequencing\NGS_sequencing\2022_05_07\Trial\pooldata\data_inverse.mapdb
AptamerPool instantiation took 51.399 seconds
Processing selection cycle Lib40-VHH-MTX
Creating new file 'C:\Users\eremeeve\Dropbox@QUT\Sequencing\NGS_sequencing\2022_05_07\Trial\cycledata\8_Lib40-VHH-MTX.mapdb' for selection cycle Lib40-VHH-MTX.
Creating new Metadata instance.
Loading took 60894 milliseconds
Initializing Experiment
Initializing parser AptaplexParser
Starting AptaPlex:
Opened forward file in fastq format C:\Users\eremeeve\Dropbox@QUT\Sequencing\NGS_sequencing\2022_05_07\Amplicon-Elena-R8-3_S18_L001_R1_001.fastq
Opened forward reverse in fastq format C:\Users\eremeeve\Dropbox@QUT\Sequencing\NGS_sequencing\2022_05_07\Amplicon-Elena-R8-3_S18_L001_R2_001.fastq
Added poison pill to parsing queue
Encountered poison pill. Exiting thread.
Encountered poison pill. Exiting thread.
Encountered poison pill. Exiting thread.
Encountered poison pill. Exiting thread.
Encountered poison pill. Exiting thread.
Encountered poison pill. Exiting thread.
Encountered poison pill. Exiting thread.
Closing pool file handles.
Reopened as read only file C:\Users\eremeeve\Dropbox@QUT\Sequencing\NGS_sequencing\2022_05_07\Trial\pooldata\data0000.mapdb
Reopened as read only file C:\Users\eremeeve\Dropbox@QUT\Sequencing\NGS_sequencing\2022_05_07\Trial\pooldata\inverse_data0000.mapdb
Reopened as read only file C:\Users\eremeeve\Dropbox@QUT\Sequencing\NGS_sequencing\2022_05_07\Trial\pooldata\bounds_data0000.mapdb
Reopened as read only file C:\Users\eremeeve\Dropbox@QUT\Sequencing\NGS_sequencing\2022_05_07\Trial\cycledata\8_Lib40-VHH-MTX.mapdb
Saved metadata to file 'C:\Users\eremeeve\Dropbox@QUT\Sequencing\NGS_sequencing\2022_05_07\Trial\metadata.mapdb
Parsing Completed, Data storage set to read-only and metadata written to file
Parsing Completed in 6.121 seconds.
Written Configuration file to C:\Users\eremeeve\Dropbox@QUT\Sequencing\NGS_sequencing\2022_05_07\Trial\configuration.aptasuite
javafx.fxml.LoadException: file:/C:/Users/eremeeve/Dropbox/@QUT/$Programs/aptasuite-0.9.8/aptasuite-0.9.8/aptasuite-0.9.8.jar!/gui/core/experiment/overview/ExperimentOverviewRandomizedRegionSizeDistribution.fxml file:/C:/Users/eremeeve/Dropbox/@QUT/$Programs/aptasuite-0.9.8/aptasuite-0.9.8/aptasuite-0.9.8.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)
at com.sun.glass.ui.win.WinApplication._runLoop(Native Method)
at com.sun.glass.ui.win.WinApplication.lambda$null$4(WinApplication.java:185)
at java.lang.Thread.run(Unknown Source)
Caused by: java.lang.reflect.InvocationTargetException at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) at java.lang.reflect.Method.invoke(Unknown Source) at sun.reflect.misc.Trampoline.invoke(Unknown Source) at sun.reflect.GeneratedMethodAccessor1.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) at java.lang.reflect.Method.invoke(Unknown Source) at sun.reflect.misc.MethodUtil.invoke(Unknown Source) at javafx.fxml.FXMLLoader.loadImpl(FXMLLoader.java:2566) ... 22 more Caused by: java.util.NoSuchElementException: No value present at java.util.Optional.get(Unknown Source) at gui.core.experiment.overview.ExperimentOverviewRandomizedRegionSizeDistributionController.computeStatistics(ExperimentOverviewRandomizedRegionSizeDistributionController.java:90) at gui.core.experiment.overview.ExperimentOverviewRandomizedRegionSizeDistributionController.initialize(ExperimentOverviewRandomizedRegionSizeDistributionController.java:55) ... 32 more
Initializing data structures
Preparing to sort data
Retrieving data for selection cycle Lib40-VHH-MTX
Prioritizing data
Sorting data
Initializing data structures
Preparing to sort data
Retrieving data for selection cycle Lib40-VHH-MTX
Prioritizing data
Sorting data
Initializing data structures
Preparing to sort data
Retrieving data for selection cycle Lib40-VHH-MTX
Prioritizing data
Sorting data
Initializing data structures
Preparing to sort data
Retrieving data for selection cycle Lib40-VHH-MTX
Prioritizing data
Sorting data
Initializing data structures
Preparing to sort data
Retrieving data for selection cycle Lib40-VHH-MTX
Prioritizing data
Sorting data
Initializing Motif Analysis Content
Initializing data structures
Preparing to sort data
Retrieving data for selection cycle Lib40-VHH-MTX
Prioritizing data
Sorting data
Initializing data structures
Preparing to sort data
Retrieving data for selection cycle Lib40-VHH-MTX
Prioritizing data
Sorting data
Initializing data structures
Preparing to sort data
Retrieving data for selection cycle Lib40-VHH-MTX
Prioritizing data
Sorting data
Initializing Motif Analysis Content
Initializing data structures
Preparing to sort data
Retrieving data for selection cycle Lib40-VHH-MTX
Prioritizing data
Sorting data
Initializing data structures
Preparing to sort data
Retrieving data for selection cycle Lib40-VHH-MTX
Prioritizing data
Sorting data
Initializing data structures
Preparing to sort data
Retrieving data for selection cycle Lib40-VHH-MTX
Prioritizing data
Sorting data
Initializing data structures
Preparing to sort data
Retrieving data for selection cycle Lib40-VHH-MTX
Prioritizing data
Sorting data
Initializing data structures
Preparing to sort data
Retrieving data for selection cycle Lib40-VHH-MTX
Prioritizing data
Sorting data
Initializing data structures
Preparing to sort data
Retrieving data for selection cycle Lib40-VHH-MTX
Prioritizing data
Sorting data
Initializing data structures
Preparing to sort data
Retrieving data for selection cycle Lib40-VHH-MTX
Prioritizing data
Sorting data
Checking for cluster information
Reading from file 'C:\Users\eremeeve\Dropbox@QUT\Sequencing\NGS_sequencing\2022_05_07\Trial\clusterdata\clusters.mapdb' for cluster storage.
Error invoking construtor of ClusterContainer backend
Error invoking ClusterContainer backend
Did not find cluster information
Initializing data structures
Preparing to sort data
Retrieving data for selection cycle Lib40-VHH-MTX
Prioritizing data
Sorting data
Initializing data structures
Preparing to sort data
Retrieving data for selection cycle Lib40-VHH-MTX
Prioritizing data
Sorting data
It tried with another Library, round and therefore files and got the same issue. Everything stuck on sorting data as on the picture above
Hey EleEre, I'm having the same issue, could you tell me how you fixed yours?
Hey solracTV, You should use only one read type at a time, so only forward or only reverse one for all sequences uploaded.
here I found an example
