When I run a command as follows
mkdir -p $OUTPUT_DIR
for i in {2…45}
do
if [ $i -eq 6 ] || [ $i -eq 30 ]; then
continue
fi
INPUT1=“./${i}_1.fq.gz”
INPUT2=“./${i}_2.fq.gz”
kneaddata --input1 $INPUT1 --input2 $INPUT2
–reference-db ./hostgenome/
–output ${OUTPUT_DIR}/Sample_${i}
–trimmomatic-options=“MINLEN:90”
–threads 120
done
Then, an error message like below returned
Decompressing gzipped file …
Decompressing gzipped file …
Reformatting file sequence identifiers …
Reformatting file sequence identifiers …
Reordering read identifiers …
Initial number of reads ( /data/jwhuh/CRC_metagenome_raw/fastq/kneaddataOutputPairedEnd/Sample_2/reordered_4078pz9p_reformatted_identifiersp9uic1je_decompressed_6begby74_2_1 ): 41168182.0
Initial number of reads ( /data/jwhuh/CRC_metagenome_raw/fastq/kneaddataOutputPairedEnd/Sample_2/reordered_e8o17fuu_reformatted_identifiers5oezloh1_decompressed_of0gd9pz_2_2 ): 41168182.0
Running Trimmomatic …
CRITICAL ERROR: Error executing: java -Xmx500m -jar /home/jwhuh/.conda/envs/kneaddata/bin/trimmomatic PE -threads 120 -phred33 /data/jwhuh/CRC_metagenome_raw/fastq/kneaddataOutputPairedEnd/Sample_2/reordered_4078pz9p_reformatted_identifiersp9uic1je_decompressed_6begby74_2_1 /data/jwhuh/CRC_metagenome_raw/fastq/kneaddataOutputPairedEnd/Sample_2/reordered_e8o17fuu_reformatted_identifiers5oezloh1_decompressed_of0gd9pz_2_2 /data/jwhuh/CRC_metagenome_raw/fastq/kneaddataOutputPairedEnd/Sample_2/2_1_kneaddata.trimmed.1.fastq /data/jwhuh/CRC_metagenome_raw/fastq/kneaddataOutputPairedEnd/Sample_2/2_1_kneaddata.trimmed.single.1.fastq /data/jwhuh/CRC_metagenome_raw/fastq/kneaddataOutputPairedEnd/Sample_2/2_1_kneaddata.trimmed.2.fastq /data/jwhuh/CRC_metagenome_raw/fastq/kneaddataOutputPairedEnd/Sample_2/2_1_kneaddata.trimmed.single.2.fastq MINLEN:90
Error message returned from Trimmomatic :
Error: Invalid or corrupt jarfile /home/jwhuh/.conda/envs/kneaddata/bin/trimmomatic
I set a proper path but it doesn’t fix the problem.
Thank you for your time