Problem running hiccups
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Yunjiang Qiu
Jul 6, 2016, 1:43:22 PM7/6/16
to 3D Genomics
Hi,
I just got an error message when I try to run hiccups. Can anyone help me with it?
Error message:
Reading file: test.hic
HiC file version: 8
Using the following configurations for HiCCUPS:
Config res: 10000 peak: 2 window: 5 fdr: 10% radius: 20000
Exception in thread "main" java.lang.NullPointerException
at juicebox.tools.clt.juicer.HiCCUPS.run(HiCCUPS.java:293)
at juicebox.tools.HiCTools.main(HiCTools.java:77)
Command line:
java -Djava.awt.headless=true -Djava.library.path=juicebox/native_launcher/natives/ -Xmx12288m -Xms12288m -jar juicebox_tools_7.0.jar hiccups -r 10000 -f .1 -p 2 -i 5 -d 20000 -c 22 test.hic hiccups_loops
Thank you!
Best,
Yunjiang
Neva Durand
Jul 6, 2016, 2:36:06 PM7/6/16
to Yunjiang Qiu, 3D Genomics
Hello Yunjiang,
It possibly has to do with the name of your chromosome. Try "chr22". If that doesn't work, we can try some other debugging steps.
Best
Neva
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Neva Cherniavsky Durand, Ph.D.
Staff Scientist, Aiden Lab
Yunjiang Qiu
Jul 6, 2016, 3:02:01 PM7/6/16
to Neva Durand, 3D Genomics
I tried with chr22, but it is not working. I still get the same error message.
Neva Durand
Jul 6, 2016, 3:12:50 PM7/6/16
to Yunjiang Qiu, 3D Genomics
Hi Yunjiang,
Is your .hic file very big? Could you post it somewhere for me to download and test?
Best
Neva
Muhammad Saad Shamim
Jul 6, 2016, 3:40:16 PM7/6/16
to Neva Durand, Yunjiang Qiu, 3D Genomics
Interesting, did you build this hic file with a custom jar and remove the 2.5MB resolution from pre?
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Yunjiang Qiu
Jul 6, 2016, 4:21:01 PM7/6/16
to Muhammad Saad Shamim, Neva Durand, 3D Genomics
Yes. We also add some other resolution such as 4Kb, 3Kb and 1Kb.
Muhammad Saad Shamim
Jul 6, 2016, 5:33:44 PM7/6/16
to Yunjiang Qiu, Neva Durand, 3D Genomics
Pushed bug fix, can you download the latest jar at http://aidenlab.org/commandlinetools/
Yunjiang Qiu
Jul 6, 2016, 6:03:37 PM7/6/16
to Muhammad Saad Shamim, Neva Durand, 3D Genomics
It works now. Thank you so much!
I also got a warning saying that Unable to assess map sparsity. Is that due to customized bin size?
Muhammad Saad Shamim
Jul 6, 2016, 6:12:55 PM7/6/16
to Yunjiang Qiu, Neva Durand, 3D Genomics
Yes, due to the missing 2.5MB resolution.
But it'll skip the sparsity check and run fine.
Yunjiang Qiu
Jul 6, 2016, 6:23:13 PM7/6/16
to Muhammad Saad Shamim, Neva Durand, 3D Genomics
I see. If I add 2.5MB back, can I use default setting with extra resolution? And is that possible to run hiccups at fragment level?
Thank you so much!
Muhammad Saad Shamim
Jul 6, 2016, 6:46:53 PM7/6/16
to Yunjiang Qiu, 3D Genomics
Not sure I understand...
It's still using the default setting (i.e. calling loops at 5, 10, and 25 KB) unless a resolution is specified (e.g. 10 KB only in the code posted above).
There are no defaults for custom resolutions (e.g. 4, 3, or 1 KB) as we don't usually run HiCCUPS for them. For new resolutions, you will need to specify the peak width (-p), window width (-i), fdr (-f), and clustering distance (-d). Note that for new resolutions, there is also no merging across resolutions.
Yunjiang Qiu
Jul 6, 2016, 8:24:10 PM7/6/16
to Muhammad Saad Shamim, 3D Genomics
Sorry, I didn’t express it clearly. Now I understand it.
Just one more question. is it possible to run hiccups at fragment level if I have fragment level maps in .hic file?
Thank you very much!
Best,
Yunjiang
Muhammad Saad Shamim
Jul 7, 2016, 1:49:06 AM7/7/16
to Yunjiang Qiu, 3D Genomics
At present it is not possible as juicebox_tools assumes it is not dealing with fragment resolutions. We could add this to our feature list though.
Yunjiang Qiu
Jul 7, 2016, 6:22:40 PM7/7/16
to Muhammad Saad Shamim, 3D Genomics
Hi Muhammad,
Sorry to bother you again, but I just got another error running hiccups. It works fine for another hit file and this hic file at 5kb, but raise the error at 10kb. It tried to adjust m to 256, but it is not helpful.
Please see the error message and commands below.
Running HiCCUPS for resolution 10000
Exception in thread "main" jcuda.CudaException: CUDA_ERROR_ILLEGAL_ADDRESS
at jcuda.utils.KernelLauncher.checkResult(KernelLauncher.java:1044)
at jcuda.utils.KernelLauncher.call(KernelLauncher.java:1030)
at juicebox.tools.utils.juicer.hiccups.GPUController.process(GPUController.java:122)
at juicebox.tools.clt.juicer.HiCCUPS.runHiccupsProcessing(HiCCUPS.java:476)
at juicebox.tools.clt.juicer.HiCCUPS.run(HiCCUPS.java:353)
at juicebox.tools.HiCTools.main(HiCTools.java:77)
java -Djava.awt.headless=true -Djava.library.path=juicebox/native_launcher/natives/ -Xmx12288m -Xms12288m -jar juicebox_tools_7.0.jar hiccups -m 256 -r 5000,10000 -k KR -f .1,.1 -p 4,2 -i 7,5 -t 0.02,1.5,1.75,2 -d 20000,20000 test.hic hiccups_loops
Thank you!
Best,
Yunjiang
Yunjiang Qiu
Jul 11, 2016, 1:05:46 PM7/11/16
to 3D Genomics, sa50...@gmail.com
Hi,
Just want to check if anyone has any idea?
Thanks,
Yunjiang
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