Getting ArrayIndexOutOfBoundsException When Running CPU HiCCUPS

[Sadman Sakib]

Hello, 

I am running into exceptions when running CPU version of HiCCUPS. I used this hic file. 

I could only find three files in the output directory: fdr_thresholds_5000, fdr_thresholds_10000, fdr_thresholds_25000. I think loop files were not produced by HiCCUPS due to the exception. I used this command: 

java -jar juicer_tools.jar hiccups --cpu data/GSE151553_A364_merged.hic a364_loops

I am using juicer_tools_1.22.01.jar file. The full error is:

     

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.

WARN [2021-07-14T19:11:45,816]  [Globals.java:138] [main]  Development mode is enabled

Reading file: data/GSE151553_A364_merged.hic

No valid configurations specified, using default settings

WARNING - You are using the CPU version of HiCCUPS.

The GPU version of HiCCUPS is the official version and has been tested extensively.

The CPU version only searches for loops within 8MB (by default) of the diagonal and is still experimental.

Using 1 CPU thread(s)

Unable to assess map sparsity; continuing with HiCCUPS

Default settings for 5kb, 10kb, and 25kb being used

Running HiCCUPS for resolution 5000

Exception in thread "pool-2-thread-1" java.lang.ArrayIndexOutOfBoundsException: Index 306 out of bounds for length 306

        at juicebox.tools.utils.juicer.hiccups.GPUController.runCPUVersion(GPUController.java:384)

        at juicebox.tools.utils.juicer.hiccups.GPUController.process(GPUController.java:141)

        at juicebox.tools.clt.juicer.HiCCUPS.runCoreCodeForHiCCUPS(HiCCUPS.java:521)

        at juicebox.tools.clt.juicer.HiCCUPS.access$200(HiCCUPS.java:158)

        at juicebox.tools.clt.juicer.HiCCUPS$1.run(HiCCUPS.java:434)

        at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)

        at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)

        at java.base/java.lang.Thread.run(Thread.java:829)

Exception in thread "pool-4-thread-1" java.lang.ArrayIndexOutOfBoundsException: Index 306 out of bounds for length 306

        at juicebox.tools.utils.juicer.hiccups.GPUController.runCPUVersion(GPUController.java:384)

        at juicebox.tools.utils.juicer.hiccups.GPUController.process(GPUController.java:141)

        at juicebox.tools.clt.juicer.HiCCUPS.runCoreCodeForHiCCUPS(HiCCUPS.java:521)

        at juicebox.tools.clt.juicer.HiCCUPS.access$200(HiCCUPS.java:158)

        at juicebox.tools.clt.juicer.HiCCUPS$1.run(HiCCUPS.java:434)

        at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)

        at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)

        at java.base/java.lang.Thread.run(Thread.java:829)

Running HiCCUPS for resolution 10000

Exception in thread "pool-6-thread-1" java.lang.ArrayIndexOutOfBoundsException: Index 153 out of bounds for length 153

        at juicebox.tools.utils.juicer.hiccups.GPUController.runCPUVersion(GPUController.java:384)

        at juicebox.tools.utils.juicer.hiccups.GPUController.process(GPUController.java:141)

        at juicebox.tools.clt.juicer.HiCCUPS.runCoreCodeForHiCCUPS(HiCCUPS.java:521)

        at juicebox.tools.clt.juicer.HiCCUPS.access$200(HiCCUPS.java:158)

        at juicebox.tools.clt.juicer.HiCCUPS$1.run(HiCCUPS.java:434)

        at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)

        at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)

        at java.base/java.lang.Thread.run(Thread.java:829)

Exception in thread "pool-8-thread-1" java.lang.ArrayIndexOutOfBoundsException: Index 153 out of bounds for length 153

        at juicebox.tools.utils.juicer.hiccups.GPUController.runCPUVersion(GPUController.java:384)

        at juicebox.tools.utils.juicer.hiccups.GPUController.process(GPUController.java:141)

        at juicebox.tools.clt.juicer.HiCCUPS.runCoreCodeForHiCCUPS(HiCCUPS.java:521)

        at juicebox.tools.clt.juicer.HiCCUPS.access$200(HiCCUPS.java:158)

        at juicebox.tools.clt.juicer.HiCCUPS$1.run(HiCCUPS.java:434)

        at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)

        at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)

        at java.base/java.lang.Thread.run(Thread.java:829)

Running HiCCUPS for resolution 25000

Exception in thread "pool-10-thread-1" java.lang.ArrayIndexOutOfBoundsException: Index 61 out of bounds for length 61

        at juicebox.tools.utils.juicer.hiccups.GPUController.runCPUVersion(GPUController.java:384)

        at juicebox.tools.utils.juicer.hiccups.GPUController.process(GPUController.java:141)

        at juicebox.tools.clt.juicer.HiCCUPS.runCoreCodeForHiCCUPS(HiCCUPS.java:521)

        at juicebox.tools.clt.juicer.HiCCUPS.access$200(HiCCUPS.java:158)

        at juicebox.tools.clt.juicer.HiCCUPS$1.run(HiCCUPS.java:434)

        at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)

        at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)

        at java.base/java.lang.Thread.run(Thread.java:829)

Exception in thread "pool-12-thread-1" java.lang.ArrayIndexOutOfBoundsException: Index 61 out of bounds for length 61

        at juicebox.tools.utils.juicer.hiccups.GPUController.runCPUVersion(GPUController.java:384)

        at juicebox.tools.utils.juicer.hiccups.GPUController.process(GPUController.java:141)

        at juicebox.tools.clt.juicer.HiCCUPS.runCoreCodeForHiCCUPS(HiCCUPS.java:521)

        at juicebox.tools.clt.juicer.HiCCUPS.access$200(HiCCUPS.java:158)

        at juicebox.tools.clt.juicer.HiCCUPS$1.run(HiCCUPS.java:434)

        at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)

        at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)

        at java.base/java.lang.Thread.run(Thread.java:829)

HiCCUPS complete

Any help or suggestions are appreciated. 

Thanks, 

Sadman 

[Muhammad Saad Shamim]

Can you try with specifying --threads 1?

--
You received this message because you are subscribed to the Google Groups "3D Genomics" group.
To unsubscribe from this group and stop receiving emails from it, send an email to 3d-genomics...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/3d-genomics/489ee9e4-4a6e-436e-a595-5cdabc1c26b6n%40googlegroups.com.

[Sadman Sakib]

Hello, 

Thanks for the quick reply! I have tried with --threads 1. Unfortunately, I'm getting the same error. 

I was able to run it with Google Colab's GPU. So, the problem is not that crucial for me now. If this problem on CPU version is difficult to troubleshoot, we can skip it I guess. 

Thanks, 

Sadman