juicebox pre - troubleshooting - .java.io.IOException: No such file or directory

Vivek

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Mar 26, 2016, 4:55:29 PM3/26/16

to 3D Genomics

Hi all,

I am running the juicer pipeline with the AWS image. I am able to run the pipeline with the image provided. It is giving me the following error. Any suggestions would be helpful.

sudo /opt/juicer/scripts/juicebox pre -f /hi_c/references/dme3_DpnII.txt -s /next_seq_data/orer_2_4h_1/aligned/inter.txt -g /next_seq_data/orer_2_4h_1/aligned/inter_hists.m -q 1 /next_seq_data/orer_2_4h_1/aligned/merged_nodups.txt /next_seq_data/orer_2_4h_1/aligned/inter.hic /hi_c/references/flybase_dm3.txt ;

Start preprocess

Writing header

Writing body

.java.io.IOException: No such file or directory

at java.io.UnixFileSystem.createFileExclusively(Native Method)

at java.io.File.createTempFile(File.java:2001)

at java.io.File.createTempFile(File.java:2047)

at juicebox.tools.utils.original.Preprocessor$MatrixZoomDataPP.incrementCount(Preprocessor.java:1308)

at juicebox.tools.utils.original.Preprocessor$MatrixPP.incrementCount(Preprocessor.java:1129)

at juicebox.tools.utils.original.Preprocessor.writeBody(Preprocessor.java:375)

at juicebox.tools.utils.original.Preprocessor.preprocess(Preprocessor.java:216)

at juicebox.tools.clt.old.PreProcessing.run(PreProcessing.java:94)

at juicebox.tools.HiCTools.main(HiCTools.java:79)

I got this output from the lsf.out file. I get the same error when I try to run it separately in the command line.

Thanks,

Vivek

Machol, Ido

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Mar 26, 2016, 10:53:04 PM3/26/16

to Vivek, 3D Genomics

Hi Vivek.

Happy to hear you get to use our software.

Can you check all files in your inputs are actually accessible? Did you get any output file created?

Ido

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Vivek

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Mar 28, 2016, 2:29:01 PM3/28/16

to 3D Genomics, albertm...@gmail.com, Ido.M...@bcm.edu

Hi Ido,

My inputs are accessible. I figured out that it is trying to write to /opt/juicer/tmp directory which does not exist in the AMI image. Once I created the tmp directory, it is working fine.