Entering edit mode
4.2 years ago
seta
★
1.9k
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
Did you move any folder contents after you downloaded and uncompressed BBMap code?
No, I just put the program at the PATH.
Which version of Java are you using? BBMap needs Java 8 and above.
And as I tested,
jni
doesn't work withopen-jdk
.Use
conda
to install if you can.