12/16/2020 03:40:32 PM - kneaddata.knead_data - INFO: Running kneaddata v0.7.2
12/16/2020 03:40:32 PM - kneaddata.knead_data - INFO: Output files will be written to: /blue/lorca/m.torrezlamberti/NS2074/RAW2/cutadapt2/test/kneaddata_clean/S15SW3_S31_L002_R2_new.fastq
12/16/2020 03:40:32 PM - kneaddata.knead_data - DEBUG: Running with the following arguments: 
verbose = False
bmtagger_path = None
minscore = 50
bowtie2_path = /apps/kneaddata/0.7.4/bin/bowtie2
maxperiod = 500
no_discordant = False
serial = False
fastqc_start = False
bmtagger = False
cat_final_output = False
log_level = DEBUG
log = /blue/lorca/m.torrezlamberti/NS2074/RAW2/cutadapt2/test/kneaddata_clean/S15SW3_S31_L002_R2_new.fastq/S15SW3_S31_L002_R1_new_kneaddata.log
max_memory = 500m
remove_intermediate_output = False
fastqc_path = None
output_dir = /blue/lorca/m.torrezlamberti/NS2074/RAW2/cutadapt2/test/kneaddata_clean/S15SW3_S31_L002_R2_new.fastq
trf_path = None
remove_temp_output = True
reference_db = /blue/lorca/m.torrezlamberti/NS2074/RAW2/human_genome/Homo_sapiens
input = /blue/lorca/m.torrezlamberti/NS2074/RAW2/cutadapt2/test/S15SW3_S31_L002_R1_new.fastq /blue/lorca/m.torrezlamberti/NS2074/RAW2/cutadapt2/test/S15SW3_S31_L002_R2_new.fastq
pi = 10
reorder = False
pm = 80
trimmomatic_path = /apps/kneaddata/0.7.4/bin/trimmomatic-0.33.jar
store_temp_output = False
mismatch = 7
threads = 24
delta = 7
bowtie2_options = --very-sensitive --phred33
bypass_trim = False
processes = 1
trimmomatic_quality_scores = -phred33
fastqc_end = False
trf = False
trimmomatic_options = None
output_prefix = S15SW3_S31_L002_R1_new_kneaddata
match = 2

12/16/2020 03:40:32 PM - kneaddata.utilities - INFO: Reformatting file sequence identifiers ...
12/16/2020 03:43:22 PM - kneaddata.utilities - INFO: Reformatting file sequence identifiers ...
12/16/2020 03:46:35 PM - kneaddata.utilities - INFO: READ COUNT: raw pair1 : Initial number of reads ( /blue/lorca/m.torrezlamberti/NS2074/RAW2/cutadapt2/test/kneaddata_clean/S15SW3_S31_L002_R2_new.fastq/reformatted_identifiers3o4DcF_S15SW3_S31_L002_R2_new ): 17689391
12/16/2020 03:46:58 PM - kneaddata.utilities - INFO: READ COUNT: raw pair2 : Initial number of reads ( /blue/lorca/m.torrezlamberti/NS2074/RAW2/cutadapt2/test/kneaddata_clean/S15SW3_S31_L002_R2_new.fastq/reformatted_identifiersvgGKia_S15SW3_S31_L002_R1_new ): 17689391
12/16/2020 03:46:58 PM - kneaddata.utilities - DEBUG: Checking input file to Trimmomatic : /blue/lorca/m.torrezlamberti/NS2074/RAW2/cutadapt2/test/kneaddata_clean/S15SW3_S31_L002_R2_new.fastq/reformatted_identifiersvgGKia_S15SW3_S31_L002_R1_new
12/16/2020 03:46:58 PM - kneaddata.utilities - DEBUG: Checking input file to Trimmomatic : /blue/lorca/m.torrezlamberti/NS2074/RAW2/cutadapt2/test/kneaddata_clean/S15SW3_S31_L002_R2_new.fastq/reformatted_identifiers3o4DcF_S15SW3_S31_L002_R2_new
12/16/2020 03:46:58 PM - kneaddata.utilities - INFO: Running Trimmomatic ... 
12/16/2020 03:46:58 PM - kneaddata.utilities - INFO: Execute command: java -Xmx500m -jar /apps/kneaddata/0.7.4/bin/trimmomatic-0.33.jar PE -threads 24 -phred33 /blue/lorca/m.torrezlamberti/NS2074/RAW2/cutadapt2/test/kneaddata_clean/S15SW3_S31_L002_R2_new.fastq/reformatted_identifiersvgGKia_S15SW3_S31_L002_R1_new /blue/lorca/m.torrezlamberti/NS2074/RAW2/cutadapt2/test/kneaddata_clean/S15SW3_S31_L002_R2_new.fastq/reformatted_identifiers3o4DcF_S15SW3_S31_L002_R2_new /blue/lorca/m.torrezlamberti/NS2074/RAW2/cutadapt2/test/kneaddata_clean/S15SW3_S31_L002_R2_new.fastq/S15SW3_S31_L002_R1_new_kneaddata.trimmed.1.fastq /blue/lorca/m.torrezlamberti/NS2074/RAW2/cutadapt2/test/kneaddata_clean/S15SW3_S31_L002_R2_new.fastq/S15SW3_S31_L002_R1_new_kneaddata.trimmed.single.1.fastq /blue/lorca/m.torrezlamberti/NS2074/RAW2/cutadapt2/test/kneaddata_clean/S15SW3_S31_L002_R2_new.fastq/S15SW3_S31_L002_R1_new_kneaddata.trimmed.2.fastq /blue/lorca/m.torrezlamberti/NS2074/RAW2/cutadapt2/test/kneaddata_clean/S15SW3_S31_L002_R2_new.fastq/S15SW3_S31_L002_R1_new_kneaddata.trimmed.single.2.fastq ILLUMINACLIP:/apps/kneaddata/0.7.4/lib/python2.7/site-packages/kneaddata/adapters/NexteraPE-PE.fa:2:30:10:8:TRUE SLIDINGWINDOW:4:20 MINLEN:125