Hi all,

I am trying to run BBDuk to quality trim and filter my illumina whole genome sequences. I have used this program before and haven't had any problems. However when I run the command:

bbduk.sh -Xmx80g in1=17198wC1_Sample_3_1_trimmed.fastq  in2=17198wC1_Sample_3_2_trimmed.fastq out1=~/comp_genomics/bb_qc_30/bb30_17198wC1_Sample_3_1_trimmed.fastq out2=~/comp_genomics/bb_qc_30/bb30_17198wC1_Sample_3_2_trimmed.fastq qtrim=rl trimq=30 maq= 30 t=16

Or if I run the command in a forloop:

for i in ~/comp_genomics/raw_genomes/scalp_genomereads/*_1_trimmed.fastq; do bbduk.sh -Xmx80g in1=$i in2=${i%%_1_trimmed.fastq}_2_trimmed.fastq out1=~/comp_genomics/bb_qc_30/$i out2=~/comp_genomics/bb_qc_30/${i%%_1_trimmed.fastq}_2_trimmed.fastq qtrim=rl trimq=30 maq= 30 t=16; done

I get the error message:

Version 38.22 Exception in thread "main" java.lang.NullPointerException
    at shared.Parser.parseTrim(Parser.java:317)
    at jgi.BBDukF.<init>(BBDukF.java:163)
    at jgi.BBDukF.main(BBDukF.java:67)

I have run this both in a conda environment and using the downloaded program, however I still get the same error and no output. I have also made sure that the versions I have are updated.

If anyone could help, I would be very grateful!

Thank you!!