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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
24 stars 11 forks source link

Aptasuite is running too long #109

Open EleEre opened 2 years ago

EleEre commented 2 years ago

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:

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

EleEre commented 2 years ago

error

EleEre commented 2 years ago

It tried with another Library, round and therefore files and got the same issue. Everything stuck on sorting data as on the picture above

EleEre commented 2 years ago

Could you please answer my question?

EleEre commented 2 years ago

Figured it out!

Thank you

solracTV commented 2 years ago

Hey EleEre, I'm having the same issue, could you tell me how you fixed yours?

EleEre commented 2 years ago

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

image

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