CPU-HiCCUPS ERROR: Could not read hic file: null

[Kevin Lee]

Hello,

I sought to call loops from my .hic file using cpu version of HiCCUPS, but failed due to the error "Could not read hic file: null". 

I was using default parameters, which is,

java -Xmx32g -jar ./juicer_tools.1.9.9_jcuda.0.8.jar hiccups --cpu 30 my.hic ./hiccups_output/.

And the log files looks like

Reading file: 30

ERROR [2020-06-06 23:30:30,635]  [MessageUtils.java:64] [main]  File could not be found

(30)

java.io.FileNotFoundException: 30 (No such file or directory)

        at java.io.FileInputStream.open0(Native Method)

        at java.io.FileInputStream.open(FileInputStream.java:195)

        at java.io.FileInputStream.<init>(FileInputStream.java:138)

        at java.io.FileInputStream.<init>(FileInputStream.java:93)

        at juicebox.data.DatasetReaderV2.getMagicString(DatasetReaderV2.java:99)

        at juicebox.data.HiCFileTools.extractDatasetForCLT(HiCFileTools.java:57)

        at juicebox.tools.clt.juicer.HiCCUPS.readJuicerArguments(HiCCUPS.java:220)

        at juicebox.tools.clt.JuicerCLT.readArguments(JuicerCLT.java:64)

        at juicebox.tools.HiCTools.main(HiCTools.java:95)

ERROR [2020-06-06 23:30:30,638]  [MessageUtils.java:74] [main]  File could not be found

(30)

Could not read hic file: null

Does anyone has any idea how to solve this? 

Thank you in advance!

Kevin Lee

2020-06-06

[Neva Durand]

It’s trying to read a file named “30” 

What is that 30 there for?

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Neva Cherniavsky Durand, Ph.D.

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[Kevin Lee]

Sorry for the stupid question. "30" is the number of threads I want to use. I forgot the tag "--threads".

Thank you for quick reply!

Best wishes,

Kevin Lee
2020-06-08
在 2020年6月7日星期日 UTC+8上午12:08:22，Kevin Lee写道：