Question: BBMap Clumpify error
0
gravatar for Tania
7 months ago by
Tania130
Tania130 wrote:

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

mark duplicates • 217 views
ADD COMMENTlink written 7 months ago by Tania130
1

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.

ADD REPLYlink modified 7 months ago • written 7 months ago by GenoMax95k
2
gravatar for jean.elbers
7 months ago by
jean.elbers1.5k
jean.elbers1.5k wrote:

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.

ADD COMMENTlink modified 7 months ago • written 7 months ago by jean.elbers1.5k

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

ADD REPLYlink written 7 months ago by Tania130
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