sip stalling

[avramiaharonoff]

Hello,

Thanks for your tool! It's great. I'm running into a snag where the program stalls during the loop calling step.

For example, it stalls here, or at a later time.

Start loop detction step ./5kb/chrI/ ./5kb/normVector/chrI.normnormVector end loading file: chrI.norm 5kb 2 ./5kb/chrI/chrI_2500000_4999999.txt 1 ./5kb/chrI/chrI_1250000_3749999.txt

I'm not really sure why, and no error pops up, just stalls until the time I requested runs out.

I am using v1.6.2 and juicer tools v1.13.01 like recommended. The weird thing is it was working for a while before it started stalling.

Thank you,

Avrami

[PouletAxel]

Hi Avrami, Could you send me the command line or the parameters you used please? Best Axel

[jiangshan529]

Hi Avrami, Could you send me the command line or the parameters you used please? Best Axel

Hi, I meet the same problem, it stalls: Start loop detction step ./WT_SIP/5kb/chr9/ ./WT_SIP/5kb/normVector/chr9.normnormVector end loading file: chr9.norm 5kb 12 ./WT_SIP/5kb/chr9/chr9_60000000_69999999.txt 2 ./WT_SIP/5kb/chr9/chr9_10000000_19999999.txt 10 ./WT_SIP/5kb/chr9/chr9_50000000_59999999.txt 0 ./WT_SIP/5kb/chr9/chr9_0_9999999.txt,

the command I used is: java -jar ~/biosoft/SIP_HiC_v1.6.1.jar hic HEK_WT1_merge_UU_dedup.pairs.hic /genome_sequence/human/hg38/hg38.clean.chrom.sizes ./WT_SIP ~/juicer/CPU/common/juicer_tools.jar

[PouletAxel]

Hi, Could you send me the version of juicer_tools that you are using please? Best

Axel

[jiangshan529]

~/juicer/CPU/common/juicer_tools.jar

hi, it is juicer_tools.1.9.9_jcuda.0.8.jar

[PouletAxel]

Thanks, I will run SIP on HiC data with the same parameter, I will come back to you later

[PouletAxel]

can you try to run: SIP_HiC_v1.6.1.jar version please. It is working for me. So if you need result now you can use this version. I will work on a new version as soon as possible sorry about that

Best Axel

[PouletAxel]

jiangshan529 could you test the new version of SIP I just pre-released (https://github.com/PouletAxel/SIP/releases). I tested on my laptop, running different datasets and it didn't stale and I obtain the usual output.

I will wait your feedback before to made this version a real release

[jiangshan529]

jiangshan529 could you test the new version of SIP I just pre-released (https://github.com/PouletAxel/SIP/releases). I tested on my laptop, running different datasets and it didn't stale and I obtain the usual output.

I will wait your feedback before to made this version a real release

Hi, Thank you! I downloaded the jar file and it reports some error: $ java -jar SIP-1.6.4.jar Exception in thread "main" java.awt.HeadlessException: No X11 DISPLAY variable was set, but this program performed an operation which requires it. at java.desktop/java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:208) at java.desktop/java.awt.Window.(Window.java:548) at java.desktop/java.awt.Frame.(Frame.java:423) at java.desktop/java.awt.Frame.(Frame.java:388) at java.desktop/javax.swing.JFrame.(JFrame.java:180) at plop.gui.GuiAnalysis.(GuiAnalysis.java:136) at plop.sipMain.Hic_main.main(Hic_main.java:186)

[PouletAxel]

Did you only run java -jar SIP-1.6.4.jar in the terminal? If yes he is trying to open a graphical user interface, can you run: java -jar SIP-1.6.4.jar -h

[jiangshan529]

Did you only run java -jar SIP-1.6.4.jar in the terminal? If yes he is trying to open a graphical user interface, can you run: java -jar SIP-1.6.4.jar -h

thanks. there are some other problems:

End dump chr14 10kb

start dump chr17 size 83257441 dump chr17:70000000:83257441 res 10kb

End dump chr17 10kb

########### End of the dump Step Start loop detection step ./HCT_SIP/10kb/chr9/ ./HCT_SIP/10kb/normVector/chr9.normnormVector end loading file: chr9.norm 10kb ./HCT_SIP/10kb/chr7/ ./HCT_SIP/10kb/normVector/chr7.normnormVector end loading file: chr7.norm 10kb ./HCT_SIP/10kb/chr8/ ./HCT_SIP/10kb/normVector/chr8.normnormVector end loading file: chr8.norm 10kb ./HCT_SIP/10kb/chr5/ ./HCT_SIP/10kb/normVector/chr5.normnormVector end loading file: chr5.norm 10kb ./HCT_SIP/10kb/chr6/ ./HCT_SIP/10kb/normVector/chr6.normnormVector end loading file: chr6.norm 10kb ./HCT_SIP/10kb/chr21/ ./HCT_SIP/10kb/normVector/chr21.normnormVector end loading file: chr21.norm 10kb ./HCT_SIP/10kb/chr3/ ./HCT_SIP/10kb/normVector/chr3.normnormVector end loading file: chr3.norm 10kb ./HCT_SIP/10kb/chr22/ ./HCT_SIP/10kb/normVector/chr22.normnormVector end loading file: chr22.norm 10kb 2 ./HCT_SIP/10kb/chr8/chr8_20000000_39999999.txt 0 ./HCT_SIP/10kb/chr22/chr22_0_19999999.txt 7 ./HCT_SIP/10kb/chr3/chr3_70000000_89999999.txt 0 ./HCT_SIP/10kb/chr21/chr21_0_19999999.txt 1 ./HCT_SIP/10kb/chr9/chr9_10000000_29999999.txt 11 ./HCT_SIP/10kb/chr6/chr6_110000000_129999999.txt 10 ./HCT_SIP/10kb/chr7/chr7_100000000_119999999.txt 1 ./HCT_SIP/10kb/chr5/chr5_10000000_29999999.txt Exception in thread "pool-2-thread-6" java.lang.NoClassDefFoundError: Could not initialize class ij.plugin.frame.Recorder at ij.ImagePlus.getProcessor(ImagePlus.java:986) at ij.ImagePlus.createLut(ImagePlus.java:1679) at ij.ImagePlus.getFileInfo(ImagePlus.java:2436) at ij.io.FileSaver.(FileSaver.java:36) at plop.process.CallLoops.saveFile(CallLoops.java:171) at plop.process.CallLoops.makeImage(CallLoops.java:157) at plop.process.CallLoops.detectLoops(CallLoops.java:96) at plop.multiProcesing.RunnableDetectLoops.run(RunnableDetectLoops.java:87) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:834) Exception in thread "pool-2-thread-8" java.lang.ExceptionInInitializerError at ij.ImagePlus.getProcessor(ImagePlus.java:986) at ij.ImagePlus.createLut(ImagePlus.java:1679) at ij.ImagePlus.getFileInfo(ImagePlus.java:2436) at ij.io.FileSaver.(FileSaver.java:36) at plop.process.CallLoops.saveFile(CallLoops.java:171) at plop.process.CallLoops.makeImage(CallLoops.java:157) at plop.process.CallLoops.detectLoops(CallLoops.java:96) at plop.multiProcesing.RunnableDetectLoops.run(RunnableDetectLoops.java:87) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:834) Caused by: java.awt.HeadlessException: No X11 DISPLAY variable was set, but this program performed an operation which requires it. at java.desktop/java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:208) at java.desktop/java.awt.TextComponent.(TextComponent.java:134) at java.desktop/java.awt.TextArea.(TextArea.java:258) at java.desktop/java.awt.TextArea.(TextArea.java:162) at ij.plugin.frame.Recorder.(Recorder.java:33) ... 11 more this is the command I used: java -jar SIP-1.6.4.jar hic dedup_941M.hic hg38.clean.chrom.sizes ./HCT_SIP juicer_tools.jar -cpu 8 -res 10000. and in the output folder I did not see the loop file

[PouletAxel]

Can you share with me your hic file, and your chr file Because I am not able to reproduce your error.

Thanks

[jiangshan529]

Can you share with me your hic file, and your chr file Because I am not able to reproduce your error.

Thanks

Hi, this hic file is 2.9Gb, how should I share it with you?

[PouletAxel]

Via Google drive  my email is @. or @. from my iPhoneOn Jul 2, 2024, at 6:13 PM, jiangshan529 @.***> wrote:

Can you share with me your hic file, and your chr file Because I am not able to reproduce your error. Thanks

Hi, this hic file is 2.9Gb, how should I share it with you?

—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you commented.Message ID: @.***>

[PouletAxel]

you can find the email address here: https://github.com/PouletAxel/SIP