#73 AssociationViewer and score file

[Aldi]

Hi, I am testing AssociationViewer with a score file similar to what you have provided in the example, then only thing is that my file is with 2.5 million SNPs with tab delimited format. Followed these steps: Add track, track type=score, selected the file type as txt, delimiter-tab, text delimiter=' (left the default), start at line 1, which has column names: snpID chromID position and score (which is -log10(p). Selected chromID and position and ticked all four variables mentioned.
The software says that something wrong happened when loading data and provided the following details.
at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at javax.swing.SwingWorker.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
Do you known what does this mean, and what is the solution?
Thank you in advance,

Aldi

[Olivier Martin]

Hello,

I think that you may have ticked more columns than required, since only the score columns should be selected. If I am right, your file looks like this:

snpID chromID position score
rs3094315 1 792429 0.82
[....]

The 5th column (and any other score column) can be ticked, but not the other columns. Otherwise the viewer will get confused.
Talking about error, the details you've provided is probably only a subset of the whole error details. The dialog window should display a scroll panel containing the full stack trace. To see the whole details, you'll have to scroll up or down. You can also use keyboard shortcut CTRL+A (replace CTRL with the relevant key on your operating system) to copy panel content and paste it somewhere else. The only informative lines for me starts with "ch.isbsib.viewer".

Let me know if it helps,

Olivier