10/05/2022 04:35:09 PM - kneaddata.knead_data - INFO: Running kneaddata v0.12.0 10/05/2022 04:35:09 PM - kneaddata.knead_data - INFO: Output files will be written to: /home/lliu/ZhangJ/try/demoo12 10/05/2022 04:35:09 PM - kneaddata.knead_data - DEBUG: Running with the following arguments: verbose = True input1 = examples/demoR_1.fastq input2 = examples/demoR_2.fastq unpaired = None output_dir = /home/lliu/ZhangJ/try/demoo12 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 = 6 processes = 1 trimmomatic_quality_scores = -phred33 bmtagger = False bypass_trf = False run_trf = True 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/demoo12/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 04:35:09 PM - kneaddata.utilities - INFO: Reformatting file sequence identifiers ... 10/05/2022 04:35:09 PM - kneaddata.utilities - INFO: Reformatting file sequence identifiers ... 10/05/2022 04:35:09 PM - kneaddata.utilities - INFO: READ COUNT: raw pair1 : Initial number of reads ( /home/lliu/ZhangJ/try/demoo12/reformatted_identifiersg4x1o8b9_demoR_1 ): 400.0 10/05/2022 04:35:09 PM - kneaddata.utilities - INFO: READ COUNT: raw pair2 : Initial number of reads ( /home/lliu/ZhangJ/try/demoo12/reformatted_identifiersn8rzxuyk_demoR_2 ): 400.0 10/05/2022 04:35:09 PM - kneaddata.utilities - DEBUG: Creating output directory: /home/lliu/ZhangJ/try/demoo12/fastqc 10/05/2022 04:35:09 PM - kneaddata.utilities - DEBUG: Checking input file to fastqc : /home/lliu/ZhangJ/try/examples/demoR_1.fastq 10/05/2022 04:35:09 PM - kneaddata.utilities - DEBUG: Checking input file to fastqc : /home/lliu/ZhangJ/try/examples/demoR_2.fastq 10/05/2022 04:35:09 PM - kneaddata.utilities - INFO: Running fastqc ... 10/05/2022 04:35:09 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 6 --outdir /home/lliu/ZhangJ/try/demoo12/fastqc --extract 10/05/2022 04:35:13 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 04:35:13 PM - kneaddata.utilities - DEBUG: Checking input file to Trimmomatic : /home/lliu/ZhangJ/try/demoo12/reformatted_identifiersg4x1o8b9_demoR_1 10/05/2022 04:35:13 PM - kneaddata.utilities - DEBUG: Checking input file to Trimmomatic : /home/lliu/ZhangJ/try/demoo12/reformatted_identifiersn8rzxuyk_demoR_2 10/05/2022 04:35:13 PM - kneaddata.utilities - INFO: Running Trimmomatic ... 10/05/2022 04:35:13 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 6 -phred33 /home/lliu/ZhangJ/try/demoo12/reformatted_identifiersg4x1o8b9_demoR_1 /home/lliu/ZhangJ/try/demoo12/reformatted_identifiersn8rzxuyk_demoR_2 /home/lliu/ZhangJ/try/demoo12/demoR_1_kneaddata.trimmed.1.fastq /home/lliu/ZhangJ/try/demoo12/demoR_1_kneaddata.trimmed.single.1.fastq /home/lliu/ZhangJ/try/demoo12/demoR_1_kneaddata.trimmed.2.fastq /home/lliu/ZhangJ/try/demoo12/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 04:35:13 PM - kneaddata.utilities - DEBUG: b"TrimmomaticPE: Started with arguments: -threads 6 -phred33 /home/lliu/ZhangJ/try/demoo12/reformatted_identifiersg4x1o8b9_demoR_1 /home/lliu/ZhangJ/try/demoo12/reformatted_identifiersn8rzxuyk_demoR_2 /home/lliu/ZhangJ/try/demoo12/demoR_1_kneaddata.trimmed.1.fastq /home/lliu/ZhangJ/try/demoo12/demoR_1_kneaddata.trimmed.single.1.fastq /home/lliu/ZhangJ/try/demoo12/demoR_1_kneaddata.trimmed.2.fastq /home/lliu/ZhangJ/try/demoo12/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 04:35:13 PM - kneaddata.utilities - DEBUG: Checking output file from Trimmomatic : /home/lliu/ZhangJ/try/demoo12/demoR_1_kneaddata.trimmed.1.fastq 10/05/2022 04:35:13 PM - kneaddata.utilities - DEBUG: Checking output file from Trimmomatic : /home/lliu/ZhangJ/try/demoo12/demoR_1_kneaddata.trimmed.single.1.fastq 10/05/2022 04:35:13 PM - kneaddata.utilities - DEBUG: Checking output file from Trimmomatic : /home/lliu/ZhangJ/try/demoo12/demoR_1_kneaddata.trimmed.2.fastq 10/05/2022 04:35:13 PM - kneaddata.utilities - DEBUG: Checking output file from Trimmomatic : /home/lliu/ZhangJ/try/demoo12/demoR_1_kneaddata.trimmed.single.2.fastq 10/05/2022 04:35:13 PM - kneaddata.utilities - INFO: READ COUNT: trimmed pair1 : Total reads after trimming ( /home/lliu/ZhangJ/try/demoo12/demoR_1_kneaddata.trimmed.1.fastq ): 387.0 10/05/2022 04:35:13 PM - kneaddata.utilities - INFO: READ COUNT: trimmed pair2 : Total reads after trimming ( /home/lliu/ZhangJ/try/demoo12/demoR_1_kneaddata.trimmed.2.fastq ): 387.0 10/05/2022 04:35:13 PM - kneaddata.utilities - INFO: READ COUNT: trimmed orphan1 : Total reads after trimming ( /home/lliu/ZhangJ/try/demoo12/demoR_1_kneaddata.trimmed.single.1.fastq ): 1.0 10/05/2022 04:35:13 PM - kneaddata.utilities - INFO: READ COUNT: trimmed orphan2 : Total reads after trimming ( /home/lliu/ZhangJ/try/demoo12/demoR_1_kneaddata.trimmed.single.2.fastq ): 11.0 10/05/2022 04:35:13 PM - kneaddata.utilities - DEBUG: Checking input file to trf : /home/lliu/ZhangJ/try/demoo12/demoR_1_kneaddata.trimmed.1.fasta 10/05/2022 04:35:13 PM - kneaddata.utilities - INFO: Running trf ... 10/05/2022 04:35:13 PM - kneaddata.utilities - INFO: Execute command: kneaddata_trf_parallel --input /home/lliu/ZhangJ/try/demoo12/demoR_1_kneaddata.trimmed.1.fasta --output /home/lliu/ZhangJ/try/demoo12/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 6 10/05/2022 04:35:14 PM - kneaddata.utilities - DEBUG: 0 10/05/2022 04:35:14 PM - kneaddata.utilities - DEBUG: Checking output file from trf : /home/lliu/ZhangJ/try/demoo12/demoR_1_kneaddata.trimmed.1.fasta.trf.parameters.2.7.7.80.10.50.500.dat 10/05/2022 04:35:14 PM - kneaddata.utilities - DEBUG: Checking input file to trf : /home/lliu/ZhangJ/try/demoo12/demoR_1_kneaddata.trimmed.2.fasta 10/05/2022 04:35:14 PM - kneaddata.utilities - INFO: Running trf ... 10/05/2022 04:35:14 PM - kneaddata.utilities - INFO: Execute command: kneaddata_trf_parallel --input /home/lliu/ZhangJ/try/demoo12/demoR_1_kneaddata.trimmed.2.fasta --output /home/lliu/ZhangJ/try/demoo12/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 6 10/05/2022 04:35:14 PM - kneaddata.utilities - DEBUG: 0 10/05/2022 04:35:14 PM - kneaddata.utilities - DEBUG: Checking output file from trf : /home/lliu/ZhangJ/try/demoo12/demoR_1_kneaddata.trimmed.2.fasta.trf.parameters.2.7.7.80.10.50.500.dat 10/05/2022 04:35:14 PM - kneaddata.run - INFO: Total number of sequences with repeats removed from file ( /home/lliu/ZhangJ/try/demoo12/demoR_1_kneaddata.trimmed.1.fastq ): 1 10/05/2022 04:35:14 PM - kneaddata.run - INFO: Total number of sequences with repeats removed from file ( /home/lliu/ZhangJ/try/demoo12/demoR_1_kneaddata.trimmed.2.fastq ): 1 10/05/2022 04:35:14 PM - kneaddata.utilities - DEBUG: Checking input file to trf : /home/lliu/ZhangJ/try/demoo12/demoR_1_kneaddata.trimmed.single.1.fasta 10/05/2022 04:35:14 PM - kneaddata.utilities - INFO: Running trf ... 10/05/2022 04:35:14 PM - kneaddata.utilities - INFO: Execute command: kneaddata_trf_parallel --input /home/lliu/ZhangJ/try/demoo12/demoR_1_kneaddata.trimmed.single.1.fasta --output /home/lliu/ZhangJ/try/demoo12/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 6 10/05/2022 04:35:14 PM - kneaddata.utilities - CRITICAL: Error executing: kneaddata_trf_parallel --input /home/lliu/ZhangJ/try/demoo12/demoR_1_kneaddata.trimmed.single.1.fasta --output /home/lliu/ZhangJ/try/demoo12/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 6