Erorr running hiccups
97 views
Skip to first unread message
Yunjiang Qiu
Jun 29, 2016, 1:20:59 AM6/29/16
to 3D Genomics
Hi,
I just got an error below when running hiccups. It seems to be a problem only when I run in chr1 but not other chromosomes.
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: -1
at juicebox.tools.utils.juicer.hiccups.HiCCUPSUtils.calculateThresholdAndFDR(HiCCUPSUtils.java:535)
at juicebox.tools.clt.juicer.HiCCUPS.runHiccupsProcessing(HiCCUPS.java:455)
at juicebox.tools.clt.juicer.HiCCUPS.run(HiCCUPS.java:283)
at juicebox.tools.HiCTools.main(HiCTools.java:79)
Thank you very much!
Best,
Yunjiang
Muhammad Saad Shamim
Jun 29, 2016, 1:25:46 AM6/29/16
to Yunjiang Qiu, 3D Genomics
Hi Yunjiang,
Can you paste the command and parameters used?
--
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/d7df97c6-be0e-4419-9c8f-394602a1db7c%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.
Yunjiang Qiu
Jun 29, 2016, 1:54:55 AM6/29/16
to Muhammad Saad Shamim, 3D Genomics
Sure. Here is the command I used.
java -Djava.awt.headless=true -Djava.library.path=$$HOME/juicebox/native_launcher/natives/ -Xmx24576m -Xms24576m -jar $HOME/.local/bin/juicebox_tools.jar hiccups -c chr1 test.hic test.chr1.hiccups_loops.txt
Muhammad Saad Shamim
Jun 29, 2016, 1:56:32 AM6/29/16
to Yunjiang Qiu, 3D Genomics
Can you try running with "-c 1" instead of "-c chr1"?
(I'll also add this to our bug list)
Muhammad Saad Shamim
Jun 29, 2016, 2:18:00 AM6/29/16
to Yunjiang Qiu, 3D Genomics
Yunjiang Qiu
Jun 29, 2016, 2:22:50 AM6/29/16
to Muhammad Saad Shamim, 3D Genomics
I tried with 1 instead of chr1, and I got the same error.
Yes. I am using gpu nodes in a super computer.
I don’t think that it’s something wrong systematically, since I run hiccups for each chromosomes separately, and the error is only reported in chr1 while all other chromosomes are fine.
Muhammad Saad Shamim
Jun 29, 2016, 2:26:45 AM6/29/16
to Yunjiang Qiu, 3D Genomics
Do you get this bug when running without the -c flag? And do you encounter any issues when opening chr1 in Juicebox?
Yunjiang Qiu
Jun 29, 2016, 3:04:06 AM6/29/16
to Muhammad Saad Shamim, 3D Genomics
I run without -c first, but I still got the same error.
Chr1 looks totally fine in juicebox, and I tried to dump chr1 matrix, it is also fine. I also attached a picture for chr1.
Best,
Yunjiang
Message has been deleted
Muhammad Saad Shamim
Jun 29, 2016, 8:32:00 PM6/29/16
to Yunjiang Qiu, 3D Genomics
For reference, the newest jar is here:
On Wed, Jun 29, 2016 at 2:28 PM, Yunjiang Qiu <sere...@gmail.com> wrote:
It turned out to be problem of an old jar file. The bug is resolved in new jar file.
Reply all
Reply to author
Forward
0 new messages