03/02/2018 05:42:33 PM - kneaddata.knead_data - INFO: Running kneaddata v0.7.0 03/02/2018 05:42:33 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 03/02/2018 05:42:33 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/MSM6J2JB.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/MSM6J2JB_R1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/fastq/MSM6J2JB_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 = 4 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 = MSM6J2JB match = 2 03/02/2018 05:42:49 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/MSM6J2JB_R1.fastq ): 7788459 03/02/2018 05:43:47 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/MSM6J2JB_R2.fastq ): 7788459 03/02/2018 05:43:47 PM - kneaddata.utilities - DEBUG: Checking input file to Trimmomatic : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/fastq/MSM6J2JB_R1.fastq 03/02/2018 05:43:47 PM - kneaddata.utilities - DEBUG: Checking input file to Trimmomatic : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/fastq/MSM6J2JB_R2.fastq 03/02/2018 05:43:47 PM - kneaddata.utilities - INFO: Running Trimmomatic ... 03/02/2018 05:43:47 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 4 -phred33 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/fastq/MSM6J2JB_R1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/fastq/MSM6J2JB_R2.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSM6J2JB.trimmed.1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSM6J2JB.trimmed.single.1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSM6J2JB.trimmed.2.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSM6J2JB.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 03/02/2018 05:45:53 PM - kneaddata.utilities - DEBUG: TrimmomaticPE: Started with arguments: -threads 4 -phred33 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/fastq/MSM6J2JB_R1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/fastq/MSM6J2JB_R2.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSM6J2JB.trimmed.1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSM6J2JB.trimmed.single.1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSM6J2JB.trimmed.2.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSM6J2JB.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: 7788459 Both Surviving: 6166650 (79.18%) Forward Only Surviving: 367501 (4.72%) Reverse Only Surviving: 255412 (3.28%) Dropped: 998896 (12.83%) TrimmomaticPE: Completed successfully 03/02/2018 05:45:53 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/MSM6J2JB.trimmed.1.fastq 03/02/2018 05:45:53 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/MSM6J2JB.trimmed.single.1.fastq 03/02/2018 05:45:53 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/MSM6J2JB.trimmed.2.fastq 03/02/2018 05:45:53 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/MSM6J2JB.trimmed.single.2.fastq 03/02/2018 05:45:55 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/MSM6J2JB.trimmed.1.fastq ): 6166650 03/02/2018 05:45:58 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/MSM6J2JB.trimmed.2.fastq ): 6166650 03/02/2018 05:45:58 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/MSM6J2JB.trimmed.single.1.fastq ): 367501 03/02/2018 05:45:58 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/MSM6J2JB.trimmed.single.2.fastq ): 255412 03/02/2018 05:45:58 PM - kneaddata.run - INFO: Decontaminating ... 03/02/2018 05:46:03 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/MSM6J2JB.trimmed.1.fastq 03/02/2018 05:46:03 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/MSM6J2JB.trimmed.2.fastq 03/02/2018 05:46:03 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/MSM6J2JB.trimmed.single.1.fastq 03/02/2018 05:46:03 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/MSM6J2JB.trimmed.single.2.fastq 03/02/2018 05:46:03 PM - kneaddata.utilities - INFO: Running bowtie2 ... 03/02/2018 05:46:03 PM - kneaddata.utilities - INFO: Execute command: kneaddata_bowtie2_discordant_pairs --bowtie2 /n/sw/centos6/bowtie2-2.2.1/bowtie2 --threads 4 -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/MSM6J2JB.trimmed.1.fastq -2 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSM6J2JB.trimmed.2.fastq --un-pair /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSM6J2JB_Homo_sapiens_bowtie2_paired_clean_%.fastq --al-pair /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSM6J2JB_Homo_sapiens_bowtie2_paired_contam_%.fastq -U /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSM6J2JB.trimmed.single.1.fastq,/n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSM6J2JB.trimmed.single.2.fastq --un-single /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSM6J2JB_Homo_sapiens_bowtie2_unmatched_%_clean.fastq --al-single /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSM6J2JB_Homo_sapiens_bowtie2_unmatched_%_contam.fastq -S /dev/null 03/02/2018 05:53:15 PM - kneaddata.utilities - DEBUG: 12956213 reads; of these: 12956213 (100.00%) were unpaired; of these: 12940646 (99.88%) aligned 0 times 11412 (0.09%) aligned exactly 1 time 4155 (0.03%) aligned >1 times 0.12% overall alignment rate pair1_aligned : 7064 pair2_aligned : 7064 orphan1_unaligned : 366665 orphan2_unaligned : 254971 orphan2_aligned : 522 pair2_unaligned : 6159505 pair1_unaligned : 6159505 orphan1_aligned : 917 03/02/2018 05:53:15 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/MSM6J2JB_Homo_sapiens_bowtie2_paired_clean_1.fastq 03/02/2018 05:53:15 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/MSM6J2JB_Homo_sapiens_bowtie2_paired_clean_2.fastq 03/02/2018 05:53:15 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/MSM6J2JB_Homo_sapiens_bowtie2_paired_contam_1.fastq ) : 7064 03/02/2018 05:53:15 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/MSM6J2JB_Homo_sapiens_bowtie2_paired_contam_2.fastq ) : 7064 03/02/2018 05:53:15 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/MSM6J2JB_Homo_sapiens_bowtie2_unmatched_1_contam.fastq ) : 917 03/02/2018 05:53:15 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/MSM6J2JB_Homo_sapiens_bowtie2_unmatched_2_contam.fastq ) : 522 03/02/2018 05:53:28 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/MSM6J2JB_Homo_sapiens_bowtie2_paired_clean_1.fastq ): 6159505 03/02/2018 05:53:31 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/MSM6J2JB_Homo_sapiens_bowtie2_paired_clean_2.fastq ): 6159505 03/02/2018 05:53:34 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/MSM6J2JB_paired_1.fastq ): 6159505 03/02/2018 05:53:36 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/MSM6J2JB_paired_2.fastq ): 6159505 03/02/2018 05:53:36 PM - kneaddata.utilities - WARNING: Unable to remove file: /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSM6J2JB_Homo_sapiens_bowtie2_paired_clean_1.fastq 03/02/2018 05:53:36 PM - kneaddata.utilities - WARNING: Unable to remove file: /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSM6J2JB_Homo_sapiens_bowtie2_paired_clean_2.fastq 03/02/2018 05:53:36 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/MSM6J2JB_Homo_sapiens_bowtie2_unmatched_1_clean.fastq ): 366665 03/02/2018 05:53:37 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/MSM6J2JB_unmatched_1.fastq ): 366665 03/02/2018 05:53:37 PM - kneaddata.utilities - WARNING: Unable to remove file: /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSM6J2JB_Homo_sapiens_bowtie2_unmatched_1_clean.fastq 03/02/2018 05:53:37 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/MSM6J2JB_Homo_sapiens_bowtie2_unmatched_2_clean.fastq ): 254971 03/02/2018 05:53:37 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/MSM6J2JB_unmatched_2.fastq ): 254971 03/02/2018 05:53:37 PM - kneaddata.utilities - WARNING: Unable to remove file: /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/hmp2/2018-02-14/WGS/kneaddata/main/MSM6J2JB_Homo_sapiens_bowtie2_unmatched_2_clean.fastq 03/02/2018 05:53:58 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/MSM6J2JB.fastq