error with juicer: [bwt_restore_sa] SA-BWT inconsistency: seq_len is not the same

[Susan Chacko]

Hi,

I've just installed the juicer pipeline for use on our cluster here, and modified the juicer.sh script to submit jobs correctly in our environment. In my tests, the jobs all get submitted with the right dependencies. But my test job does not complete. It fails at the align1 and align2 step with:

[bwt_restore_sa] SA-BWT inconsistency: seq_len is not the same. Abort!

I'm using
BWA 0.7.13
Java 1.8.0_11
splitsize=90000000 (the default)


Any ideas what might be the problem?  Thanks for any suggestions,
Susan

[Machol, Ido]

Hi Susan,

Did you try to re-index the reference?

(bwa index <reference file>)

Best,

Ido

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[Susan C]

Ah, thanks, that fixed it. 

[Susan Chacko]

After reindexing the BWA indexes, my test job ran all the way upto the Hic calculations. The hic30 and hic error files both say:
--------------------------
[+] Loading java 1.8.0_11 ...
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)
--------------------------
Is my java version the problem, and if so, is there another version that is recommended? Or is the problem something completely different?

Susan

[Neva Durand]

Hello Susan,

This is a problem with your chromosome names in chrom.sizes or as referenced via the genome ID not being the same as the names in your file.  It also arises due to using fragment-delimited maps.  

See:  https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!topic/3d-genomics/8MPPvoHdA8g

One solution is to just not have fragment delimited maps.  Otherwise, be sure that your chromosome names are consistent with what Juicebox expects.

Best

Neva

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Neva Cherniavsky Durand, Ph.D.

Staff Scientist, Aiden Lab

www.aidenlab.org