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PouletAxel / SIP

SIP: Significant Interaction Peak caller
GNU General Public License v3.0
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fail to read hic file #6

Closed xiaowenchenjax closed 4 years ago

xiaowenchenjax commented 4 years ago

Hi, I used the command line to run HIC file java -jar /home/c-chenx/SIP_HiC_v1.5/SIP_HiC.jar hic /projects/li-lab/chenx/hic/juicer_mm/juicer_mm_TET2_wt1/aligned/inter_30.hic /home/c-chenx/juicer/references/mm10.chrom.sizes /projects/li-lab/chenx/hic/juicer_mm/juicer_mm_TET2_wt1/aligned/inter_30_loops /home/c-chenx/juicer/scripts/juicer_tools.jar but there is an error: Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 1 at sipMain.Hic_main.readChrSizeFile(Hic_main.java:277) at sipMain.Hic_main.main(Hic_main.java:209)

Could you give me some suggestion? Thank you

jordrow commented 4 years ago

It sounds like there is an issue reading in your chromosome size file. Can you paste the contents of the size file that you are using?

PouletAxel commented 4 years ago

Can you run it with the last version please and tell me if you have the same error please? here

xiaowenchenjax commented 4 years ago

1.6 version ？

Xiaowen Chen

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On 04/20/2020 21:50, PouletAxel wrote:

Can you run it with the last version please and tell me if you have the same error please? here

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PouletAxel commented 4 years ago

yes

xiaowenchenjax commented 4 years ago

sure!

在 2020-04-21 09:50:50，"PouletAxel" notifications@github.com 写道：

Can you run it with the last version please and tell me if you have the same error please? here

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

PouletAxel commented 4 years ago

And send me then the command line you are running and the error if you still have the error please

xiaowenchenjax commented 4 years ago

Hi, still same error.

java -jar /home/c-chenx/script/SIP-SIP_HiC_v1.6/SIP_HiC_v1.6.jar hic /projects/li-lab/chenx/hic/juicer_mm/juicer_mm_TET2_wt1/aligned/inter_30.hic /home/c-chenx/juicer/references/mm10.chrom.sizes /projects/li-lab/chenx/hic/juicer_mm/juicer_mm_TET2_wt1/aligned/inter_30_loops /home/c-chenx/juicer/scripts/juicer_tools.jar

Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 1

at sipMain.Hic_main.readChrSizeFile(Hic_main.java:336)

at sipMain.Hic_main.main(Hic_main.java:231)

At 2020-04-21 09:54:57, "PouletAxel" notifications@github.com wrote:

And send me then the command line you are running and the error if you still have the error please

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

PouletAxel commented 4 years ago

Can you test with the file join : mm10.chrom.sizes.txt

xiaowenchenjax commented 4 years ago

It is running, what you change to make it work? Do i need to dump the hic file, if it is created from juicer pipeline? Thank you!!

At 2020-04-21 10:08:10, "PouletAxel" notifications@github.com wrote:

Can you test with the file join : mm10.chrom.sizes.txt

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

PouletAxel commented 4 years ago

it is because you have some spaces and not tabulation in your chr file: between the name of chr and the size you one tabulation and not several spaces.

Yes because SIP i doing some computation to obtain the value and work with them. When you have run one time SIP after you can use the processed command to refine the other parameter and refine the detection of loop

Thanks And thanks to use SIP