Program crashing when parsing FASTQ

[JeremyWearO]

I've been trying to get started with 0.9.4. I can run AptaSim and then perform all the applicable analysis on the simulated aptamer pools. However, I run into problems whenever I try to parse FASTQ files - the program crashes when I try to import the data. The log is as follows:

System Information:
Java Version: 1.8.0_291
JavaFX Version: null
OS Name: Windows 10
OS Version: 10.0
OS Architecture: x86
OS Architecture Model: 32
CPU cores: 8
System Memory: 16252928 Mb

AptaSuite version read from file. Version is 0.9.4

Error checking for newer version

java.lang.NumberFormatException: For input string: "5b"
at java.lang.NumberFormatException.forInputString(Unknown Source)
at java.lang.Integer.parseInt(Unknown Source)
at java.lang.Integer.parseInt(Unknown Source)
at utilities.Version.newerVersionAvailable(Version.java:124)
at gui.core.RootClass.start(RootClass.java:55)
at com.sun.javafx.application.LauncherImpl.lambda$launchApplication1$8(LauncherImpl.java:863)
at com.sun.javafx.application.PlatformImpl.lambda$runAndWait$7(PlatformImpl.java:326)
at com.sun.javafx.application.PlatformImpl.lambda$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)

Starting New Experiment Wizard

Written Configuration file to C:\Users\path\to\folder\configuration.aptasuite

Reading configuration from file.

Creating Database

Error invoking construtor of AptamerPool backend

Error invoking AptamerPool backend

If there is anything obviously wrong here that would be good to know. I've tried it on multiple FASTQ files including real NGS files, self-made sample files, and those generated by AptaSim.

Thanks in advance for your help.

[drivenbyentropy]

I looks like you are trying to set the selection cycle number to an invalid input (5b). The selection cycle should be a single integer number (e.g. 5). If you have multiple pools for a particular selection round, you can distinguish between these by giving them different names and giving them all the same selection cycle integer.

Let me know if this solves the issue.

[JeremyWearO]

No, I don't think this is the case.

As you can see, I'm setting the selection cycle number to an integer in the GUI.

In all my logs (for all FASTQ files) I do get:

java.lang.NumberFormatException: For input string: "5b"

Plus the block that goes with it. I'm not sure where this would be coming from. There is nowhere that I am inputting '5b'.

Thanks for your help so far. Please let me know if you have any other insights.

[drivenbyentropy]

Could you please share your configuration file? It could help getting to the bottom of this. Thanks!

[JeremyWearO]

Here are the Config parameters:

Experiment.name = test
Experiment.description = test
Experiment.projectPath = C:\Users\user\Documents\AptaSuite\verify\trying again\testingagain\test
Experiment.primer5 = GGAGGCTCTCGGGACGAC
Experiment.primer3 = CGTCCCGATGCTGCAATCGTAA
Experiment.randomizedRegionSize = 32
AptaplexParser.isPerFile = true
AptaplexParser.reader = FastqReader
SelectionCycle.name = 1
SelectionCycle.round = 1
SelectionCycle.isControlSelection = false
SelectionCycle.isCounterSelection = false
AptaplexParser.forwardFiles = C:\\Users\\user\\Documents\\AptaSuite\\verify\\trying again\\testingagain\\Cycle0.fastq

I don't see anything wrong myself. Maybe you can see something. I might try installing and running the software on another PC.

Thanks again for your help

[drivenbyentropy]

Has this been fixed? Please feel free to reopen if the issue persists.