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PouletAxel / SIP

SIP: Significant Interaction Peak caller
GNU General Public License v3.0
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Empty loop files #10

Closed ahmedabbas81 closed 3 years ago

ahmedabbas81 commented 3 years ago

Dear all, I run the following command:

java -jar SIP_HiC_v1.6.1.jar hic /fastscratch/ahmed/human/young_male/Juicer_home/aligned/inter_30.hic hg19.chrom.sizes ./young_male_sip /fastscratch/ahmed/human/young_male/Juicer_home/scripts/juicer_tools.jar

I get errors like this:

start dump chrX size 155270560 res 5kb
start dump chrX size 155270560 dump chrX:0:9999999 res 5kb
Exception in thread "pool-1-thread-4" java.lang.IndexOutOfBoundsException: Index: 1, Size: 1
    at java.util.ArrayList.rangeCheck(ArrayList.java:657)
    at java.util.ArrayList.get(ArrayList.java:433)
    at process.DumpData.observedMExpected(DumpData.java:109)
    at process.DumpData.dumpObservedMExpected(DumpData.java:85)
    at multiProcesing.RunnableDumpDataHiC.run(RunnableDumpDataHiC.java:91)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)

and get empty output file like this image

Any suggestions please?

Thank you

PouletAxel commented 3 years ago

Dear, Are you using the same chr size file used to make the hic file? Axel

On Mon, 8 Feb 2021 at 14:04, ahmedabbas81 notifications@github.com wrote:

Dear all, I run the following command:

java -jar SIP_HiC_v1.6.1.jar hic /fastscratch/ahmed/human/young_male/Juicer_home/aligned/inter_30.hic hg19.chrom.sizes ./young_male_sip /fastscratch/ahmed/human/young_male/Juicer_home/scripts/juicer_tools.jar

I get errors like this:

start dump chrX size 155270560 res 5kb start dump chrX size 155270560 dump chrX:0:9999999 res 5kb Exception in thread "pool-1-thread-4" java.lang.IndexOutOfBoundsException: Index: 1, Size: 1 at java.util.ArrayList.rangeCheck(ArrayList.java:657) at java.util.ArrayList.get(ArrayList.java:433) at process.DumpData.observedMExpected(DumpData.java:109) at process.DumpData.dumpObservedMExpected(DumpData.java:85) at multiProcesing.RunnableDumpDataHiC.run(RunnableDumpDataHiC.java:91) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748)

and get empty output file like this [image: image] https://user-images.githubusercontent.com/32098502/107268510-3bcc4680-6a16-11eb-9dac-04ba67ab6642.png

Any suggestions please?

Thank you

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ahmedabbas81 commented 3 years ago

Hi, I didn't use chr size file to get the hic file. I used the same reference files as here https://github.com/aidenlab/juicer/wiki/Installation

Thank you

PouletAxel commented 3 years ago

How did you make the hic file? I think the problem is, the program tries to dump some data not existing in your hic file.

On Mon, 8 Feb 2021 at 20:35, ahmedabbas81 notifications@github.com wrote:

Hi, I didn't use chr size file to get the hic file. I used the same reference files as here https://github.com/aidenlab/juicer/wiki/Installation

Thank you

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ahmedabbas81 commented 3 years ago

I am using Juicer, and using the genome id: hg19. In this case, it is not required to put chrom.sizes path

Thanks

PouletAxel commented 3 years ago

Ok great, Can you share with your hic file? I need to test what is wrong. my private email address is pouletaxel@gmail.com

Best Axel

On Mon, 8 Feb 2021 at 21:06, ahmedabbas81 notifications@github.com wrote:

I am using Juicer, and using the genome id: hg19. In this case, it is not required to put chrom.sizes path

Thanks

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ahmedabbas81 commented 3 years ago

Thank you. I tried with another slightly older version of Juicer tools and it worked. Thank you

PouletAxel commented 3 years ago

Great, could you send me the 2 first lines of your chr size file please. Did you use the latest juicer version when SIP failed?

ahmedabbas81 commented 3 years ago

sorry for the late answer. Yes the latest version of juicer failed. I will send you the two lines. Thanks

PouletAxel commented 3 years ago

Ok thanks. I need to document it so thanks to catch it.

On Fri, 12 Feb 2021 at 20:05, ahmedabbas81 notifications@github.com wrote:

sorry for the late answer. Yes the latest version of juicer failed. I will send you the two lines. Thanks

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