Error: Could not find or load main class jgi.BBMerge

[sjfleck]

Hello,
I'm using BBmerge to determine which adapter sequences on my short reads (as suggested on http://seqanswers.com/forums/showthread.php?t=63537). I was wondering if you could help with an error I'm getting. When I run this line from my SLURM script:

scripts="/gpfs/scratch/sjfleck/modulefiles/BBMap/sh"
fastq="/gpfs/scratch/sjfleck/MaSuRCA/my_species"
$scripts/bbmerge.sh $fastq/in1=forward_reads_1.fq.gz $fastq/in2=reverse_reads_2.fq.gz outa=my_species_adapters.fa

Here is the error file I get (I'm separating some lines for clarity):

java -Djava.library.path=/gpfs/scratch/sjfleck/modulefiles/BBMap/sh/jni/ -ea -Xmx1000m -cp /gpfs/scratch/sjfleck/modulefiles/BBMap/sh/current/
in1=forward_reads_1.fq.gz
in2=reverse_reads_2.fq.gz
outa=Ping_moct_adapters.fa

Error: Could not find or load main class jgi.BBMerge

There are a few things I'm immediately noticing:

1. there is no file named "jgi.BBMerge" in "/gpfs/scratch/sjfleck/modulefiles/BBMap/sh/current/"

• There is a folder called "jgi" in this directory, but no files.
• within the "jgi" directory, the closest thing to "jgi.BBMerge" is "BBMerge.java" and "BBMergeOverlapper.java"

2. " jgi.BBMerge" starts with a space in the script. Is this by design?

Any help you could offer would be greatly appreciated. Thank you,
Steve