02/16/2018 02:00:26 PM - kneaddata.knead_data - INFO: Running kneaddata v0.7.0 02/16/2018 02:00:26 PM - kneaddata.knead_data - INFO: Output files will be written to: /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main 02/16/2018 02:00:26 PM - kneaddata.knead_data - DEBUG: Running with the following arguments: verbose = False bmtagger_path = None minscore = 50 bowtie2_path = /n/sw/centos6/bowtie2-2.2.1/bowtie2 maxperiod = 500 no_discordant = False serial = True fastqc_start = False bmtagger = False cat_final_output = True log_level = DEBUG log = /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/PSM7J1BF.log max_memory = 500m remove_intermediate_output = True fastqc_path = None output_dir = /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main trf_path = None remove_temp_output = True reference_db = /n/huttenhower_lab/data/kneaddata_databases/Homo_sapiens input = /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/fastq/PSM7J1BF_R1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/fastq/PSM7J1BF_R2.fastq pi = 10 reorder = False pm = 80 trimmomatic_path = /n/huttenhower_lab/tools/kneaddata/bin_v0.7.0_devel/trimmomatic-0.33.jar store_temp_output = False mismatch = 7 threads = 6 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 = PSM7J1BF match = 2 02/16/2018 02:00:48 PM - kneaddata.utilities - INFO: READ COUNT: raw pair1 : Initial number of reads ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/fastq/PSM7J1BF_R1.fastq ): 18801808 02/16/2018 02:01:08 PM - kneaddata.utilities - INFO: READ COUNT: raw pair2 : Initial number of reads ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/fastq/PSM7J1BF_R2.fastq ): 18801808 02/16/2018 02:01:08 PM - kneaddata.utilities - DEBUG: Checking input file to Trimmomatic : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/fastq/PSM7J1BF_R1.fastq 02/16/2018 02:01:08 PM - kneaddata.utilities - DEBUG: Checking input file to Trimmomatic : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/fastq/PSM7J1BF_R2.fastq 02/16/2018 02:01:08 PM - kneaddata.utilities - INFO: Running Trimmomatic ... 02/16/2018 02:01:08 PM - kneaddata.utilities - INFO: Execute command: java -Xmx500m -d64 -jar /n/huttenhower_lab/tools/kneaddata/bin_v0.7.0_devel/trimmomatic-0.33.jar PE -threads 6 -phred33 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/fastq/PSM7J1BF_R1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/fastq/PSM7J1BF_R2.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/PSM7J1BF.trimmed.1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/PSM7J1BF.trimmed.single.1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/PSM7J1BF.trimmed.2.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/PSM7J1BF.trimmed.single.2.fastq ILLUMINACLIP:/n/huttenhower_lab/tools/kneaddata/lib_v0.7.0_devel/kneaddata/adapters/NexteraPE-PE.fa:2:30:10:8:TRUE SLIDINGWINDOW:4:20 MINLEN:50 02/16/2018 02:04:38 PM - kneaddata.utilities - DEBUG: TrimmomaticPE: Started with arguments: -threads 6 -phred33 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/fastq/PSM7J1BF_R1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/fastq/PSM7J1BF_R2.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/PSM7J1BF.trimmed.1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/PSM7J1BF.trimmed.single.1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/PSM7J1BF.trimmed.2.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/PSM7J1BF.trimmed.single.2.fastq ILLUMINACLIP:/n/huttenhower_lab/tools/kneaddata/lib_v0.7.0_devel/kneaddata/adapters/NexteraPE-PE.fa:2:30:10:8:TRUE SLIDINGWINDOW:4:20 MINLEN:50 Using PrefixPair: 'AGATGTGTATAAGAGACAG' and 'AGATGTGTATAAGAGACAG' Using Long Clipping Sequence: 'GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG' Using Long Clipping Sequence: 'TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG' Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTGACGCTGCCGACGA' Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTCCGAGCCCACGAGAC' ILLUMINACLIP: Using 1 prefix pairs, 4 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences Input Read Pairs: 18801808 Both Surviving: 14529703 (77.28%) Forward Only Surviving: 821320 (4.37%) Reverse Only Surviving: 659629 (3.51%) Dropped: 2791156 (14.85%) TrimmomaticPE: Completed successfully 02/16/2018 02:04:38 PM - kneaddata.utilities - DEBUG: Checking output file from Trimmomatic : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/PSM7J1BF.trimmed.1.fastq 02/16/2018 02:04:38 PM - kneaddata.utilities - DEBUG: Checking output file from Trimmomatic : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/PSM7J1BF.trimmed.single.1.fastq 02/16/2018 02:04:38 PM - kneaddata.utilities - DEBUG: Checking output file from Trimmomatic : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/PSM7J1BF.trimmed.2.fastq 02/16/2018 02:04:38 PM - kneaddata.utilities - DEBUG: Checking output file from Trimmomatic : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/PSM7J1BF.trimmed.single.2.fastq 02/16/2018 02:04:45 PM - kneaddata.utilities - INFO: READ COUNT: trimmed pair1 : Total reads after trimming ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/PSM7J1BF.trimmed.1.fastq ): 14529703 02/16/2018 02:04:54 PM - kneaddata.utilities - INFO: READ COUNT: trimmed pair2 : Total reads after trimming ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/PSM7J1BF.trimmed.2.fastq ): 14529703 02/16/2018 02:04:54 PM - kneaddata.utilities - INFO: READ COUNT: trimmed orphan1 : Total reads after trimming ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/PSM7J1BF.trimmed.single.1.fastq ): 821320 02/16/2018 02:04:54 PM - kneaddata.utilities - INFO: READ COUNT: trimmed orphan2 : Total reads after trimming ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/PSM7J1BF.trimmed.single.2.fastq ): 659629 02/16/2018 02:04:54 PM - kneaddata.run - INFO: Decontaminating ... 02/16/2018 02:04:57 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/PSM7J1BF.trimmed.1.fastq 02/16/2018 02:04:57 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/PSM7J1BF.trimmed.2.fastq 02/16/2018 02:04:57 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/PSM7J1BF.trimmed.single.1.fastq 02/16/2018 02:04:57 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/PSM7J1BF.trimmed.single.2.fastq 02/16/2018 02:04:57 PM - kneaddata.utilities - INFO: Running bowtie2 ... 02/16/2018 02:04:57 PM - kneaddata.utilities - INFO: Execute command: kneaddata_bowtie2_discordant_pairs --bowtie2 /n/sw/centos6/bowtie2-2.2.1/bowtie2 --threads 6 -x /n/huttenhower_lab/data/kneaddata_databases/Homo_sapiens --bowtie2-options "--very-sensitive --phred33" -1 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/PSM7J1BF.trimmed.1.fastq -2 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/PSM7J1BF.trimmed.2.fastq --un-pair /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/PSM7J1BF_Homo_sapiens_bowtie2_paired_clean_%.fastq --al-pair /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/PSM7J1BF_Homo_sapiens_bowtie2_paired_contam_%.fastq -U /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/PSM7J1BF.trimmed.single.1.fastq,/n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/PSM7J1BF.trimmed.single.2.fastq --un-single /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/PSM7J1BF_Homo_sapiens_bowtie2_unmatched_%_clean.fastq --al-single /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/PSM7J1BF_Homo_sapiens_bowtie2_unmatched_%_contam.fastq -S /dev/null 02/16/2018 02:22:57 PM - kneaddata.utilities - DEBUG: 30540355 reads; of these: 30540355 (100.00%) were unpaired; of these: 27441961 (89.85%) aligned 0 times 2367286 (7.75%) aligned exactly 1 time 731108 (2.39%) aligned >1 times 10.15% overall alignment rate pair1_aligned : 1463510 pair2_aligned : 1463510 orphan1_unaligned : 748023 orphan2_unaligned : 593226 orphan2_aligned : 82240 pair2_unaligned : 13050356 pair1_unaligned : 13050356 orphan1_aligned : 89134 02/16/2018 02:22:57 PM - kneaddata.utilities - DEBUG: Checking output file from bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/PSM7J1BF_Homo_sapiens_bowtie2_paired_clean_1.fastq 02/16/2018 02:22:57 PM - kneaddata.utilities - DEBUG: Checking output file from bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/PSM7J1BF_Homo_sapiens_bowtie2_paired_clean_2.fastq 02/16/2018 02:22:58 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/PSM7J1BF_Homo_sapiens_bowtie2_paired_contam_1.fastq ) : 1463510 02/16/2018 02:22:59 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/PSM7J1BF_Homo_sapiens_bowtie2_paired_contam_2.fastq ) : 1463510 02/16/2018 02:22:59 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/PSM7J1BF_Homo_sapiens_bowtie2_unmatched_1_contam.fastq ) : 89134 02/16/2018 02:22:59 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/PSM7J1BF_Homo_sapiens_bowtie2_unmatched_2_contam.fastq ) : 82240 02/16/2018 02:23:07 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated Homo_sapiens pair1 : Total reads after removing those found in reference database ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/PSM7J1BF_Homo_sapiens_bowtie2_paired_clean_1.fastq ): 13050356 02/16/2018 02:23:14 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated Homo_sapiens pair2 : Total reads after removing those found in reference database ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/PSM7J1BF_Homo_sapiens_bowtie2_paired_clean_2.fastq ): 13050356 02/16/2018 02:23:20 PM - kneaddata.utilities - INFO: READ COUNT: final pair1 : Total reads after merging results from multiple databases ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/PSM7J1BF_paired_1.fastq ): 13050356 02/16/2018 02:23:26 PM - kneaddata.utilities - INFO: READ COUNT: final pair2 : Total reads after merging results from multiple databases ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/PSM7J1BF_paired_2.fastq ): 13050356 02/16/2018 02:23:26 PM - kneaddata.utilities - WARNING: Unable to remove file: /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/PSM7J1BF_Homo_sapiens_bowtie2_paired_clean_1.fastq 02/16/2018 02:23:26 PM - kneaddata.utilities - WARNING: Unable to remove file: /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/PSM7J1BF_Homo_sapiens_bowtie2_paired_clean_2.fastq 02/16/2018 02:23:26 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated Homo_sapiens orphan1 : Total reads after removing those found in reference database ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/PSM7J1BF_Homo_sapiens_bowtie2_unmatched_1_clean.fastq ): 748023 02/16/2018 02:23:27 PM - kneaddata.utilities - INFO: READ COUNT: final orphan1 : Total reads after merging results from multiple databases ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/PSM7J1BF_unmatched_1.fastq ): 748023 02/16/2018 02:23:27 PM - kneaddata.utilities - WARNING: Unable to remove file: /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/PSM7J1BF_Homo_sapiens_bowtie2_unmatched_1_clean.fastq 02/16/2018 02:23:27 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated Homo_sapiens orphan2 : Total reads after removing those found in reference database ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/PSM7J1BF_Homo_sapiens_bowtie2_unmatched_2_clean.fastq ): 593226 02/16/2018 02:23:27 PM - kneaddata.utilities - INFO: READ COUNT: final orphan2 : Total reads after merging results from multiple databases ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/PSM7J1BF_unmatched_2.fastq ): 593226 02/16/2018 02:23:27 PM - kneaddata.utilities - WARNING: Unable to remove file: /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/PSM7J1BF_Homo_sapiens_bowtie2_unmatched_2_clean.fastq 02/16/2018 02:23:49 PM - kneaddata.knead_data - INFO: Final output file created: /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/PSM7J1BF.fastq