Java class error message when using BBDuk

Question

[milewski]

I am trying to run BBDuk to quality trim and filter my illumina whole genome sequences. I have used other trimming scripts before and have not had a problem. Although this is my first time preprocessing sequencing data from Quantseq samples. I have cloned the bbmap Git Hub and made a path to it on the server. However, when I run the following command:

for fileName in *.fastq; do sample=${fileName%.*.*}; bbduk.sh -Xmx5g in=${fileName} out=cleaned/${sample}.fq ref=/stor/work//processing_tools_rnaseq/BBMap/resources/polyA.fa.gz,/stor/work/processing_tools_rnaseq/BBMap/resources/truseq_rna.fa.gz t=4 k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 &>> bbduk_log.txt; done

I get the following error:

  java -ea -Xmx5g -Xms5g -cp /stor/work/processing_tools_rnaseq/BBMap/sh/current/ jgi.BBDuk
    -Xmx5g in=1488303_S4_R1_001.fastq out=cleaned/1488303_S4_R1_001.fastq.fq ref=/stor/work/processing_tools_rnaseq/BBMap/resources/polyA.fa.gz,/stor/work/processing_tools_rnaseq/BBMap/resources/truseq_rna.fa.gz t=4 k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 Error: Could not find or load main class jgi.BBDuk Caused by: java.lang.ClassNotFoundException: jgi.BBDuk

Any idea what might be the problem? My java version is 11 and up to date.

Thank you in advance for all the help.

[GenoMax]

I have cloned the bbmap Git Hub

You are not using official repository then.

BBMap is available from SourceForge or Bitbucket. Simply download the zip archive and uncompress. Do not move any of the files around in the uncompressed folder.