APA error

[kate]

Hello,

I am trying APA with the latest jar (1.22.01) on SLURM.

However, I got the following err:

Processing APA for resolution 20000

Exception in thread "main" java.lang.IllegalArgumentException

at java.util.concurrent.ThreadPoolExecutor.<init>(ThreadPoolExecutor.java:1307)

at java.util.concurrent.ThreadPoolExecutor.<init>(ThreadPoolExecutor.java:1195)

at java.util.concurrent.Executors.newFixedThreadPool(Executors.java:89)

at juicebox.tools.clt.juicer.APA.runWithReturn(APA.java:298)

at juicebox.tools.clt.juicer.APA.run(APA.java:223)

at juicebox.tools.HiCTools.main(HiCTools.java:94)

Would you please help me figure out the problem? I'm using java/jdk-11.0.11 and  cuda/8.0.

Thank you,

Kate

[Neva Durand]

What is your command?

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Neva Cherniavsky Durand, Ph.D. | she, her, hers

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[Muhammad Saad Shamim]

You may want to use --threads 1 or an older jar. 

To view this discussion on the web visit https://groups.google.com/d/msgid/3d-genomics/CAF1CciUPwVsw%3DYXLsAxvoK%3DsxkX-kMDv3J_bTt%3D_b3pJdB6oKg%40mail.gmail.com.

[Kate]

Hello,

--threads1 is working! Can I ask you one more question? 

I want to use CenterNormedAPA and APA to compare the strength of looping interaction at the specific loop anchors between control and treated sample. 

To do this, I export the values to R and draw heat map with the same scale (color)-range for two samples.

But I'm not sure if I really need to adjust the scale-range to the same for comparison. Do I need to do that or P2LL score tells everything (significance >1)? The original png files show all different color scales. 

Thank you!

Kate

2021년 9월 5일 (일) 오후 1:39, Muhammad Saad Shamim <sa50...@gmail.com>님이 작성:

[Ashley S Doane]

Thanks I had the same error and this solved it.   Is this a java version issue?  Would be great to add this to documentation somewhere as it took awhile to track down solution.