trouble creating hic files - java.lang.NullPointerException

[Vivek]

Hi all,

I am running the juicer pipeline with the AWS image. I am able to run the pipeline with the image provided. I runs fine till it creates merged.nodups.txt file. It just stops doing anything once it reaches the hic file creation step. It is giving me the following error. Any suggestions would be helpful.

/opt/juicer/scripts/juicebox pre -f /hi_c/references/dme3_DpnII.txt -q 30 /my_data/run_2016_03_01/aligned/merged_nodups.txt /my_data/run_2016_03_01/aligned/inter_30.hic /hi_c/references/chrom.sizes.txt

Picked up _JAVA_OPTIONS: -Xmx8192m

java.lang.NullPointerException

at juicebox.tools.utils.original.ExpectedValueCalculation.<init>(ExpectedValueCalculation.java:109)

at juicebox.tools.utils.original.Preprocessor.preprocess(Preprocessor.java:201)

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

[Vivek]

I think I have figured out what is the problem. It seems like the names of the chromosomes from chrom.sizes file and the fasta file are different as they from UCSC and flybase. Changing that fixed the problem, I think. I am running the code again and no errors so far!

[Neva Durand]

This looks like an error with your restriction site file. Is your chrom.sizes file corresponding correctly to the restriction site file?  When you ran the pipeline did you run into any trouble with the fragment assignment?

--
You received this message because you are subscribed to the Google Groups "3D Genomics" group.
To unsubscribe from this group and stop receiving emails from it, send an email to 3d-genomics...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/3d-genomics/748c7f41-cc77-4874-93f6-ad7b2ea87481%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

--

Neva Cherniavsky Durand, Ph.D.

Staff Scientist, Aiden Lab

www.aidenlab.org