#19 NullPointerException on stats.sh

[Guillaume Barreau]

Hello,
I am trying to get some stats on a scaffold for a rather large genome using stats.sh.
When I run stats.sh on the contigs (prior to the scaffolding done using bionano optical maps), the program works. When I run it on the scaffods fasta, I get:

% stats.sh final.fasta
Exception in thread "main" java.lang.NullPointerException
at jgi.AssemblyStats2.process(AssemblyStats2.java:263)
at jgi.AssemblyStats2.main(AssemblyStats2.java:38)

I could send you the file but it is rather large (352Mb).
Thanks for your help.

[renekat]

Hello Guillaume,
I am getting this "Exception in thread "main" java.lang.NullPointerException" error message too.

Exception in thread "main" java.lang.NullPointerException
at jgi.BBDuk.<init>(BBDuk.java:964)
at jgi.RQCFilter2.ktrim(RQCFilter2.java:1808)
at jgi.RQCFilter2.process(RQCFilter2.java:974)
at jgi.RQCFilter2.main(RQCFilter2.java:71)</init>

My code is:
rqcfilter2.sh \
in=Illumina_reads.fq.gz \
rqcfilterdata=/RQCFilterData path=/Results/2019.09.10 \
int=t qtrim=rl removehuman=t removedog=t removemouse=t aggressive=t removemicrobes=t copyundefined=t kapa=t clumpify=t dedupe=t opticaldupes=t khist=t \
-da -Xmx14g

The previous version that I used with success was: BBTools version 38.46
Not sure if this is a programing issue or a user issue.

Best,
René

[renekat]

Guillaume,
Turns out that I had a wrong path to some data, which was causing my NullPointer Exception error. When I removed the -da option from my code I was able to see the assertion error which told me what the exact issue was.
Not sure if this feedback will help with your error, but wanted to share.
Best,
René