Please help about java error of BBDuk
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21 months ago
seta ★ 1.7k

Dear all,

I'm using BBDuk from bbmap package (last version) for the trimming of RNA-seq reads. I used the below code:

bbduk.sh in=file_1.fastq.gz  out=trimmed_1.fastq.gz  ref=/opt/BBMap/resources/adapters.fa ktrim=r k=23 mink=11 hdist=1  qtrim=rl trimq=20

But it gave the error:

java -Djava.library.path=/opt/BBMap/sh/jni/ -ea -Xmx11756m -Xms11756m -cp /opt/BBMap/sh/current/ jgi.BBDukF in=file_1.fastq.gz out=trimmed_1.fastq.gz ref=/opt/BBMap/resources/adapters.fa ktrim=r k=23 mink=11 hdist=1 qtrim=rl trimq=20
Error: Could not find or load main class jgi.BBDukF

From the net, I tried the below solution code:

java -ea -Xmx5g -Xms5g -cp /opt/BBMap/current/jgi.BBDukF in=file_1.fastq.gz  out=trimmed_1.fastq.gz  ref=/opt/BBMap/resources/adapters.fa ktrim=r k=23 mink=11 hdist=1  qtrim=rl trimq=20
Error: Could not find or load main class in=file_1.fastq.gz

I'm totally confused. Could you please let me know how I can fix the error?

Thanks

bbmap bbduk java brian bushnel • 950 views
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Did you move any folder contents after you downloaded and uncompressed BBMap code?

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No, I just put the program at the PATH.

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Which version of Java are you using? BBMap needs Java 8 and above.

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And as I tested, jni doesn't work with open-jdk.

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Use conda to install if you can.

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