BBMap Clumpify error

Question

[Tania]

Dear Everyone

Has any one come through this error in clumpify tool from BBmap?

Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: Index 0 out of bounds for length 0 at shared.PreParser.<init>(PreParser.java:71) at shared.PreParser.<init>(PreParser.java:26) at clump.Clumpify.<init>(Clumpify.java:51) at clump.Clumpify.main(Clumpify.java:37)

This is my command:

~/bbmap/clumpify.sh in1= xx.r_1.fq.gz in2=xx.r_2.fq.gz out1= xx.clumped1.fq.gz out2 = xx.clumped2.fq.gz reorder=f

I also used groups=auto, and same error.

Thanks

[GenoMax]

There should be no spaces between in1= and filename and all other file options. It looks like you have spaces in some of the options in the example above.

Answer 1

[jean.elbers]

Can you try

~/bbmap/clumpify.sh in1=xx.r_1.fq.gz in2=xx.r_2.fq.gz out1=xx.clumped1.fq.gz out2=xx.clumped2.fq.gz reorder=f

I am pretty sure the BBMap scripts don't like spaces next to the arguments.

Update @Genomax beat me to it.

[Tania]

Yes, its working now. Thanks thanks thanks so much :)