10/05/2022 04:31:12 PM - kneaddata.knead_data - INFO: Running kneaddata v0.12.0
10/05/2022 04:31:12 PM - kneaddata.knead_data - INFO: Output files will be written to: /home/lliu/ZhangJ/try/demoo9
10/05/2022 04:31:12 PM - kneaddata.knead_data - DEBUG: Running with the following arguments: 
verbose = False
input1 = examples/demoR_1.fastq
input2 = examples/demoR_2.fastq
unpaired = None
output_dir = /home/lliu/ZhangJ/try/demoo9
scratch_dir = 
reference_db = /data1/projects/liullab/metagenome/kneaddata_database/human_genome/hg37dec_v0.1 /data1/projects/liullab/metagenome/kneaddata_database/human_transcriptome/human_hg38_refMrna /data1/projects/liullab/metagenome/kneaddata_database/mouse_C57BL/mouse_C57BL_6NJ
bypass_trim = False
output_prefix = demoR_1_kneaddata
threads = 1
processes = 1
trimmomatic_quality_scores = -phred33
bmtagger = False
bypass_trf = False
run_trf = False
fastqc_start = True
fastqc_end = True
store_temp_output = False
remove_intermediate_output = False
cat_final_output = True
log_level = DEBUG
log = /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata.log
trimmomatic_path = /home/lliu/software/miniconda3/envs/biobakery/share/trimmomatic-0.33-0/trimmomatic-0.33.jar
run_trim_repetitive = False
max_memory = 500m
trimmomatic_options = ILLUMINACLIP:/home/lliu/software/miniconda3/envs/biobakery/share/trimmomatic-0.33-0/adapters/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:15 MINLEN:36
sequencer_source = NexteraPE
bowtie2_path = /home/lliu/software/miniconda3/envs/biobakery/bin/bowtie2
bowtie2_options = --very-sensitive-local --phred33
decontaminate_pairs = strict
reorder = False
serial = True
bmtagger_path = None
trf_path = /home/lliu/software/miniconda3/envs/biobakery/bin/trf
match = 2
mismatch = 7
delta = 7
pm = 80
pi = 10
minscore = 50
maxperiod = 500
fastqc_path = /home/lliu/software/miniconda3/envs/biobakery/bin/fastqc
remove_temp_output = True
input = /home/lliu/ZhangJ/try/examples/demoR_1.fastq /home/lliu/ZhangJ/try/examples/demoR_2.fastq
discordant = True

10/05/2022 04:31:12 PM - kneaddata.utilities - INFO: Reformatting file sequence identifiers ...
10/05/2022 04:31:12 PM - kneaddata.utilities - INFO: Reformatting file sequence identifiers ...
10/05/2022 04:31:12 PM - kneaddata.utilities - INFO: READ COUNT: raw pair1 : Initial number of reads ( /home/lliu/ZhangJ/try/demoo9/reformatted_identifiersykhe7w0i_demoR_1 ): 400.0
10/05/2022 04:31:12 PM - kneaddata.utilities - INFO: READ COUNT: raw pair2 : Initial number of reads ( /home/lliu/ZhangJ/try/demoo9/reformatted_identifierskc1mw0eo_demoR_2 ): 400.0
10/05/2022 04:31:12 PM - kneaddata.utilities - DEBUG: Creating output directory: /home/lliu/ZhangJ/try/demoo9/fastqc
10/05/2022 04:31:12 PM - kneaddata.utilities - DEBUG: Checking input file to fastqc : /home/lliu/ZhangJ/try/examples/demoR_1.fastq
10/05/2022 04:31:12 PM - kneaddata.utilities - DEBUG: Checking input file to fastqc : /home/lliu/ZhangJ/try/examples/demoR_2.fastq
10/05/2022 04:31:12 PM - kneaddata.utilities - INFO: Running fastqc ... 
10/05/2022 04:31:12 PM - kneaddata.utilities - INFO: Execute command: /home/lliu/software/miniconda3/envs/biobakery/bin/fastqc /home/lliu/ZhangJ/try/examples/demoR_1.fastq /home/lliu/ZhangJ/try/examples/demoR_2.fastq --threads 1 --outdir /home/lliu/ZhangJ/try/demoo9/fastqc --extract
10/05/2022 04:31:21 PM - kneaddata.utilities - DEBUG: b'Started analysis of demoR_1.fastq\nAnalysis complete for demoR_1.fastq\nStarted analysis of demoR_2.fastq\nAnalysis complete for demoR_2.fastq\n'
10/05/2022 04:31:21 PM - kneaddata.utilities - DEBUG: Checking input file to Trimmomatic : /home/lliu/ZhangJ/try/demoo9/reformatted_identifiersykhe7w0i_demoR_1
10/05/2022 04:31:21 PM - kneaddata.utilities - DEBUG: Checking input file to Trimmomatic : /home/lliu/ZhangJ/try/demoo9/reformatted_identifierskc1mw0eo_demoR_2
10/05/2022 04:31:21 PM - kneaddata.utilities - INFO: Running Trimmomatic ... 
10/05/2022 04:31:21 PM - kneaddata.utilities - INFO: Execute command: java -Xmx500m -jar /home/lliu/software/miniconda3/envs/biobakery/share/trimmomatic-0.33-0/trimmomatic-0.33.jar PE -threads 1 -phred33 /home/lliu/ZhangJ/try/demoo9/reformatted_identifiersykhe7w0i_demoR_1 /home/lliu/ZhangJ/try/demoo9/reformatted_identifierskc1mw0eo_demoR_2 /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata.trimmed.1.fastq /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata.trimmed.single.1.fastq /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata.trimmed.2.fastq /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata.trimmed.single.2.fastq ILLUMINACLIP:/home/lliu/software/miniconda3/envs/biobakery/share/trimmomatic-0.33-0/adapters/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:15 MINLEN:36
10/05/2022 04:31:21 PM - kneaddata.utilities - DEBUG: b"TrimmomaticPE: Started with arguments: -threads 1 -phred33 /home/lliu/ZhangJ/try/demoo9/reformatted_identifiersykhe7w0i_demoR_1 /home/lliu/ZhangJ/try/demoo9/reformatted_identifierskc1mw0eo_demoR_2 /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata.trimmed.1.fastq /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata.trimmed.single.1.fastq /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata.trimmed.2.fastq /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata.trimmed.single.2.fastq ILLUMINACLIP:/home/lliu/software/miniconda3/envs/biobakery/share/trimmomatic-0.33-0/adapters/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:15 MINLEN:36\nUsing PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT'\nILLUMINACLIP: Using 1 prefix pairs, 0 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences\nInput Read Pairs: 400 Both Surviving: 387 (96.75%) Forward Only Surviving: 1 (0.25%) Reverse Only Surviving: 11 (2.75%) Dropped: 1 (0.25%)\nTrimmomaticPE: Completed successfully\n"
10/05/2022 04:31:21 PM - kneaddata.utilities - DEBUG: Checking output file from Trimmomatic : /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata.trimmed.1.fastq
10/05/2022 04:31:21 PM - kneaddata.utilities - DEBUG: Checking output file from Trimmomatic : /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata.trimmed.single.1.fastq
10/05/2022 04:31:21 PM - kneaddata.utilities - DEBUG: Checking output file from Trimmomatic : /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata.trimmed.2.fastq
10/05/2022 04:31:21 PM - kneaddata.utilities - DEBUG: Checking output file from Trimmomatic : /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata.trimmed.single.2.fastq
10/05/2022 04:31:21 PM - kneaddata.utilities - INFO: READ COUNT: trimmed pair1 : Total reads after trimming ( /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata.trimmed.1.fastq ): 387.0
10/05/2022 04:31:21 PM - kneaddata.utilities - INFO: READ COUNT: trimmed pair2 : Total reads after trimming ( /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata.trimmed.2.fastq ): 387.0
10/05/2022 04:31:21 PM - kneaddata.utilities - INFO: READ COUNT: trimmed orphan1 : Total reads after trimming ( /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata.trimmed.single.1.fastq ): 1.0
10/05/2022 04:31:21 PM - kneaddata.utilities - INFO: READ COUNT: trimmed orphan2 : Total reads after trimming ( /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata.trimmed.single.2.fastq ): 11.0
10/05/2022 04:31:21 PM - kneaddata.utilities - DEBUG: Checking input file to trf : /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata.trimmed.1.fasta
10/05/2022 04:31:21 PM - kneaddata.utilities - INFO: Running trf ... 
10/05/2022 04:31:21 PM - kneaddata.utilities - INFO: Execute command: kneaddata_trf_parallel --input /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata.trimmed.1.fasta --output /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata.trimmed.1.fasta.trf.parameters.2.7.7.80.10.50.500.dat --trf-path /home/lliu/software/miniconda3/envs/biobakery/bin/trf --trf-options '2 7 7 80 10 50 500 -h -ngs' --nproc 1
10/05/2022 04:31:21 PM - kneaddata.utilities - DEBUG: 0
10/05/2022 04:31:21 PM - kneaddata.utilities - DEBUG: Checking output file from trf : /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata.trimmed.1.fasta.trf.parameters.2.7.7.80.10.50.500.dat
10/05/2022 04:31:21 PM - kneaddata.utilities - DEBUG: Checking input file to trf : /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata.trimmed.2.fasta
10/05/2022 04:31:21 PM - kneaddata.utilities - INFO: Running trf ... 
10/05/2022 04:31:21 PM - kneaddata.utilities - INFO: Execute command: kneaddata_trf_parallel --input /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata.trimmed.2.fasta --output /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata.trimmed.2.fasta.trf.parameters.2.7.7.80.10.50.500.dat --trf-path /home/lliu/software/miniconda3/envs/biobakery/bin/trf --trf-options '2 7 7 80 10 50 500 -h -ngs' --nproc 1
10/05/2022 04:31:21 PM - kneaddata.utilities - DEBUG: 0
10/05/2022 04:31:21 PM - kneaddata.utilities - DEBUG: Checking output file from trf : /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata.trimmed.2.fasta.trf.parameters.2.7.7.80.10.50.500.dat
10/05/2022 04:31:21 PM - kneaddata.run - INFO: Total number of sequences with repeats removed from file ( /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata.trimmed.1.fastq ): 0
10/05/2022 04:31:21 PM - kneaddata.run - INFO: Total number of sequences with repeats removed from file ( /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata.trimmed.2.fastq ): 0
10/05/2022 04:31:21 PM - kneaddata.utilities - DEBUG: Checking input file to trf : /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata.trimmed.single.1.fasta
10/05/2022 04:31:21 PM - kneaddata.utilities - INFO: Running trf ... 
10/05/2022 04:31:21 PM - kneaddata.utilities - INFO: Execute command: kneaddata_trf_parallel --input /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata.trimmed.single.1.fasta --output /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata.trimmed.single.1.fasta.trf.parameters.2.7.7.80.10.50.500.dat --trf-path /home/lliu/software/miniconda3/envs/biobakery/bin/trf --trf-options '2 7 7 80 10 50 500 -h -ngs' --nproc 1
10/05/2022 04:31:22 PM - kneaddata.utilities - DEBUG: 0
10/05/2022 04:31:22 PM - kneaddata.utilities - DEBUG: Checking output file from trf : /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata.trimmed.single.1.fasta.trf.parameters.2.7.7.80.10.50.500.dat
10/05/2022 04:31:22 PM - kneaddata.run - INFO: Total number of sequences with repeats removed from file ( /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata.trimmed.single.1.fastq ): 0
10/05/2022 04:31:22 PM - kneaddata.utilities - DEBUG: Checking input file to trf : /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata.trimmed.single.2.fasta
10/05/2022 04:31:22 PM - kneaddata.utilities - INFO: Running trf ... 
10/05/2022 04:31:22 PM - kneaddata.utilities - INFO: Execute command: kneaddata_trf_parallel --input /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata.trimmed.single.2.fasta --output /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata.trimmed.single.2.fasta.trf.parameters.2.7.7.80.10.50.500.dat --trf-path /home/lliu/software/miniconda3/envs/biobakery/bin/trf --trf-options '2 7 7 80 10 50 500 -h -ngs' --nproc 1
10/05/2022 04:31:22 PM - kneaddata.utilities - DEBUG: 0
10/05/2022 04:31:22 PM - kneaddata.utilities - DEBUG: Checking output file from trf : /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata.trimmed.single.2.fasta.trf.parameters.2.7.7.80.10.50.500.dat
10/05/2022 04:31:22 PM - kneaddata.run - INFO: Total number of sequences with repeats removed from file ( /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata.trimmed.single.2.fastq ): 0
10/05/2022 04:31:22 PM - kneaddata.run - INFO: Decontaminating ...
10/05/2022 04:31:22 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata.repeats.removed.1.fastq
10/05/2022 04:31:22 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata.repeats.removed.2.fastq
10/05/2022 04:31:22 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata.repeats.removed.unmatched.1.fastq
10/05/2022 04:31:22 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata.repeats.removed.unmatched.2.fastq
10/05/2022 04:31:22 PM - kneaddata.utilities - INFO: Running bowtie2 ... 
10/05/2022 04:31:22 PM - kneaddata.utilities - INFO: Execute command: kneaddata_bowtie2_discordant_pairs --bowtie2 /home/lliu/software/miniconda3/envs/biobakery/bin/bowtie2 --threads 1 -x /data1/projects/liullab/metagenome/kneaddata_database/human_genome/hg37dec_v0.1 --mode strict --bowtie2-options "--very-sensitive-local --phred33" -1 /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata.repeats.removed.1.fastq -2 /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata.repeats.removed.2.fastq --un-pair /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_hg37dec_v0.1_bowtie2_paired_clean_%.fastq --al-pair /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_hg37dec_v0.1_bowtie2_paired_contam_%.fastq -U /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata.repeats.removed.unmatched.1.fastq,/home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata.repeats.removed.unmatched.2.fastq --un-single /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_hg37dec_v0.1_bowtie2_unmatched_%_clean.fastq --al-single /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_hg37dec_v0.1_bowtie2_unmatched_%_contam.fastq -S /dev/null
10/05/2022 04:31:27 PM - kneaddata.utilities - DEBUG: b'786 reads; of these:\n  786 (100.00%) were unpaired; of these:\n    786 (100.00%) aligned 0 times\n    0 (0.00%) aligned exactly 1 time\n    0 (0.00%) aligned >1 times\n0.00% overall alignment rate\npair1_aligned : 0\npair2_aligned : 0\npair1_unaligned : 387\npair2_unaligned : 387\norphan1_aligned : 0\norphan2_aligned : 0\norphan1_unaligned : 1\norphan2_unaligned : 11\n'
10/05/2022 04:31:27 PM - kneaddata.utilities - DEBUG: Checking output file from bowtie2 : /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_hg37dec_v0.1_bowtie2_paired_clean_1.fastq
10/05/2022 04:31:27 PM - kneaddata.utilities - DEBUG: Checking output file from bowtie2 : /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_hg37dec_v0.1_bowtie2_paired_clean_2.fastq
10/05/2022 04:31:27 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata.repeats.removed.1.fastq
10/05/2022 04:31:27 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata.repeats.removed.2.fastq
10/05/2022 04:31:27 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata.repeats.removed.unmatched.1.fastq
10/05/2022 04:31:27 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata.repeats.removed.unmatched.2.fastq
10/05/2022 04:31:27 PM - kneaddata.utilities - INFO: Running bowtie2 ... 
10/05/2022 04:31:27 PM - kneaddata.utilities - INFO: Execute command: kneaddata_bowtie2_discordant_pairs --bowtie2 /home/lliu/software/miniconda3/envs/biobakery/bin/bowtie2 --threads 1 -x /data1/projects/liullab/metagenome/kneaddata_database/human_transcriptome/human_hg38_refMrna --mode strict --bowtie2-options "--very-sensitive-local --phred33" -1 /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_hg37dec_v0.1_bowtie2_paired_clean_1.fastq -2 /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_hg37dec_v0.1_bowtie2_paired_clean_2.fastq --un-pair /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_human_hg38_refMrna_bowtie2_paired_clean_%.fastq --al-pair /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_human_hg38_refMrna_bowtie2_paired_contam_%.fastq -U /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_hg37dec_v0.1_bowtie2_unmatched_1_clean.fastq,/home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_hg37dec_v0.1_bowtie2_unmatched_2_clean.fastq --un-single /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_human_hg38_refMrna_bowtie2_unmatched_%_clean.fastq --al-single /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_human_hg38_refMrna_bowtie2_unmatched_%_contam.fastq -S /dev/null
10/05/2022 04:31:29 PM - kneaddata.utilities - DEBUG: b'786 reads; of these:\n  786 (100.00%) were unpaired; of these:\n    786 (100.00%) aligned 0 times\n    0 (0.00%) aligned exactly 1 time\n    0 (0.00%) aligned >1 times\n0.00% overall alignment rate\npair1_aligned : 0\npair2_aligned : 0\npair1_unaligned : 387\npair2_unaligned : 387\norphan1_aligned : 0\norphan2_aligned : 0\norphan1_unaligned : 1\norphan2_unaligned : 11\n'
10/05/2022 04:31:29 PM - kneaddata.utilities - DEBUG: Checking output file from bowtie2 : /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_human_hg38_refMrna_bowtie2_paired_clean_1.fastq
10/05/2022 04:31:29 PM - kneaddata.utilities - DEBUG: Checking output file from bowtie2 : /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_human_hg38_refMrna_bowtie2_paired_clean_2.fastq
10/05/2022 04:31:29 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata.repeats.removed.1.fastq
10/05/2022 04:31:29 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata.repeats.removed.2.fastq
10/05/2022 04:31:29 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata.repeats.removed.unmatched.1.fastq
10/05/2022 04:31:29 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata.repeats.removed.unmatched.2.fastq
10/05/2022 04:31:29 PM - kneaddata.utilities - INFO: Running bowtie2 ... 
10/05/2022 04:31:29 PM - kneaddata.utilities - INFO: Execute command: kneaddata_bowtie2_discordant_pairs --bowtie2 /home/lliu/software/miniconda3/envs/biobakery/bin/bowtie2 --threads 1 -x /data1/projects/liullab/metagenome/kneaddata_database/mouse_C57BL/mouse_C57BL_6NJ --mode strict --bowtie2-options "--very-sensitive-local --phred33" -1 /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_human_hg38_refMrna_bowtie2_paired_clean_1.fastq -2 /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_human_hg38_refMrna_bowtie2_paired_clean_2.fastq --un-pair /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_mouse_C57BL_6NJ_bowtie2_paired_clean_%.fastq --al-pair /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_mouse_C57BL_6NJ_bowtie2_paired_contam_%.fastq -U /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_human_hg38_refMrna_bowtie2_unmatched_1_clean.fastq,/home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_human_hg38_refMrna_bowtie2_unmatched_2_clean.fastq --un-single /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_mouse_C57BL_6NJ_bowtie2_unmatched_%_clean.fastq --al-single /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_mouse_C57BL_6NJ_bowtie2_unmatched_%_contam.fastq -S /dev/null
10/05/2022 04:31:31 PM - kneaddata.utilities - DEBUG: b'786 reads; of these:\n  786 (100.00%) were unpaired; of these:\n    786 (100.00%) aligned 0 times\n    0 (0.00%) aligned exactly 1 time\n    0 (0.00%) aligned >1 times\n0.00% overall alignment rate\npair1_aligned : 0\npair2_aligned : 0\npair1_unaligned : 387\npair2_unaligned : 387\norphan1_aligned : 0\norphan2_aligned : 0\norphan1_unaligned : 1\norphan2_unaligned : 11\n'
10/05/2022 04:31:31 PM - kneaddata.utilities - DEBUG: Checking output file from bowtie2 : /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_mouse_C57BL_6NJ_bowtie2_paired_clean_1.fastq
10/05/2022 04:31:31 PM - kneaddata.utilities - DEBUG: Checking output file from bowtie2 : /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_mouse_C57BL_6NJ_bowtie2_paired_clean_2.fastq
10/05/2022 04:31:31 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_hg37dec_v0.1_bowtie2_paired_contam_1.fastq ) : 0.0
10/05/2022 04:31:31 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_hg37dec_v0.1_bowtie2_paired_contam_2.fastq ) : 0.0
10/05/2022 04:31:31 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_hg37dec_v0.1_bowtie2_unmatched_1_contam.fastq ) : 0.0
10/05/2022 04:31:31 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_hg37dec_v0.1_bowtie2_unmatched_2_contam.fastq ) : 0.0
10/05/2022 04:31:31 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_human_hg38_refMrna_bowtie2_paired_contam_1.fastq ) : 0.0
10/05/2022 04:31:31 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_human_hg38_refMrna_bowtie2_paired_contam_2.fastq ) : 0.0
10/05/2022 04:31:31 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_human_hg38_refMrna_bowtie2_unmatched_1_contam.fastq ) : 0.0
10/05/2022 04:31:31 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_human_hg38_refMrna_bowtie2_unmatched_2_contam.fastq ) : 0.0
10/05/2022 04:31:31 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_mouse_C57BL_6NJ_bowtie2_paired_contam_1.fastq ) : 0.0
10/05/2022 04:31:31 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_mouse_C57BL_6NJ_bowtie2_paired_contam_2.fastq ) : 0.0
10/05/2022 04:31:31 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_mouse_C57BL_6NJ_bowtie2_unmatched_1_contam.fastq ) : 0.0
10/05/2022 04:31:31 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_mouse_C57BL_6NJ_bowtie2_unmatched_2_contam.fastq ) : 0.0
10/05/2022 04:31:31 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated hg37dec_v0.1 pair1 : Total reads after removing those found in reference database ( /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_hg37dec_v0.1_bowtie2_paired_clean_1.fastq ): 387.0
10/05/2022 04:31:31 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated hg37dec_v0.1 pair2 : Total reads after removing those found in reference database ( /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_hg37dec_v0.1_bowtie2_paired_clean_2.fastq ): 387.0
10/05/2022 04:31:31 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated human_hg38_refMrna pair1 : Total reads after removing those found in reference database ( /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_human_hg38_refMrna_bowtie2_paired_clean_1.fastq ): 387.0
10/05/2022 04:31:31 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated human_hg38_refMrna pair2 : Total reads after removing those found in reference database ( /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_human_hg38_refMrna_bowtie2_paired_clean_2.fastq ): 387.0
10/05/2022 04:31:31 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated mouse_C57BL_6NJ pair1 : Total reads after removing those found in reference database ( /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_mouse_C57BL_6NJ_bowtie2_paired_clean_1.fastq ): 387.0
10/05/2022 04:31:31 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated mouse_C57BL_6NJ pair2 : Total reads after removing those found in reference database ( /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_mouse_C57BL_6NJ_bowtie2_paired_clean_2.fastq ): 387.0
10/05/2022 04:31:31 PM - kneaddata.utilities - INFO: READ COUNT: final pair1 : Total reads after merging results from multiple databases ( /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_paired_1.fastq ): 387.0
10/05/2022 04:31:31 PM - kneaddata.utilities - INFO: READ COUNT: final pair2 : Total reads after merging results from multiple databases ( /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_paired_2.fastq ): 387.0
10/05/2022 04:31:31 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated hg37dec_v0.1 orphan1 : Total reads after removing those found in reference database ( /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_hg37dec_v0.1_bowtie2_unmatched_1_clean.fastq ): 1.0
10/05/2022 04:31:31 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated human_hg38_refMrna orphan1 : Total reads after removing those found in reference database ( /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_human_hg38_refMrna_bowtie2_unmatched_1_clean.fastq ): 1.0
10/05/2022 04:31:31 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated mouse_C57BL_6NJ orphan1 : Total reads after removing those found in reference database ( /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_mouse_C57BL_6NJ_bowtie2_unmatched_1_clean.fastq ): 1.0
10/05/2022 04:31:31 PM - kneaddata.utilities - INFO: READ COUNT: final orphan1 : Total reads after merging results from multiple databases ( /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_unmatched_1.fastq ): 1.0
10/05/2022 04:31:31 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated hg37dec_v0.1 orphan2 : Total reads after removing those found in reference database ( /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_hg37dec_v0.1_bowtie2_unmatched_2_clean.fastq ): 11.0
10/05/2022 04:31:31 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated human_hg38_refMrna orphan2 : Total reads after removing those found in reference database ( /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_human_hg38_refMrna_bowtie2_unmatched_2_clean.fastq ): 11.0
10/05/2022 04:31:31 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated mouse_C57BL_6NJ orphan2 : Total reads after removing those found in reference database ( /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_mouse_C57BL_6NJ_bowtie2_unmatched_2_clean.fastq ): 11.0
10/05/2022 04:31:31 PM - kneaddata.utilities - INFO: READ COUNT: final orphan2 : Total reads after merging results from multiple databases ( /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_unmatched_2.fastq ): 11.0
10/05/2022 04:31:31 PM - kneaddata.utilities - DEBUG: Checking input file to fastqc : /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_paired_1.fastq
10/05/2022 04:31:31 PM - kneaddata.utilities - DEBUG: Checking input file to fastqc : /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_paired_2.fastq
10/05/2022 04:31:31 PM - kneaddata.utilities - DEBUG: Checking input file to fastqc : /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_unmatched_1.fastq
10/05/2022 04:31:31 PM - kneaddata.utilities - DEBUG: Checking input file to fastqc : /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_unmatched_2.fastq
10/05/2022 04:31:31 PM - kneaddata.utilities - DEBUG: Checking input file to fastqc : /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata.fastq
10/05/2022 04:31:31 PM - kneaddata.utilities - INFO: Running fastqc ... 
10/05/2022 04:31:31 PM - kneaddata.utilities - INFO: Execute command: /home/lliu/software/miniconda3/envs/biobakery/bin/fastqc /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_paired_1.fastq /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_paired_2.fastq /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_unmatched_1.fastq /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_unmatched_2.fastq /home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata.fastq --threads 1 --outdir /home/lliu/ZhangJ/try/demoo9/fastqc --extract
10/05/2022 04:31:49 PM - kneaddata.utilities - DEBUG: b'Started analysis of demoR_1_kneaddata_paired_1.fastq\nAnalysis complete for demoR_1_kneaddata_paired_1.fastq\nStarted analysis of demoR_1_kneaddata_paired_2.fastq\nAnalysis complete for demoR_1_kneaddata_paired_2.fastq\nStarted analysis of demoR_1_kneaddata_unmatched_1.fastq\nAnalysis complete for demoR_1_kneaddata_unmatched_1.fastq\nStarted analysis of demoR_1_kneaddata_unmatched_2.fastq\nAnalysis complete for demoR_1_kneaddata_unmatched_2.fastq\nStarted analysis of demoR_1_kneaddata.fastq\nAnalysis complete for demoR_1_kneaddata.fastq\n'
10/05/2022 04:31:49 PM - kneaddata.knead_data - INFO: 
Final output files created: 
/home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_paired_1.fastq
/home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_paired_2.fastq
/home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_unmatched_1.fastq
/home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata_unmatched_2.fastq
/home/lliu/ZhangJ/try/demoo9/demoR_1_kneaddata.fastq