03/21/2018 03:32:13 PM - kneaddata.knead_data - INFO: Running kneaddata v0.7.0 03/21/2018 03:32:13 PM - kneaddata.knead_data - INFO: Output files will be written to: /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main 03/21/2018 03:32:13 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/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3.log max_memory = 500m remove_intermediate_output = True fastqc_path = None output_dir = /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main trf_path = None remove_temp_output = True reference_db = /n/huttenhower_lab/data/kneaddata_databases/Homo_sapiens /n/huttenhower_lab/data/kneaddata_databases/ribosomal_RNA/SILVA_128_LSUParc_SSUParc_ribosomal_RNA /n/huttenhower_lab/data/kneaddata_databases/transcriptome/human_hg38_refMrna input = /n/regal/huttenhower_lab/carze/data/hmp2/workflow/deposition/HMP2/2018-03-20/MTX/HSM7J4O3_R1.fastq.gz /n/regal/huttenhower_lab/carze/data/hmp2/workflow/deposition/HMP2/2018-03-20/MTX/HSM7J4O3_R2.fastq.gz 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 = ILLUMINACLIP:/n/home07/carze/.local/bin/Trimmomatic-0.36/adapters/TruSeq3-PE-2.fa:2:30:10:8:TRUE SLIDINGWINDOW:4:20 MINLEN:50 output_prefix = HSM7J4O3 match = 2 03/21/2018 03:32:13 PM - kneaddata.utilities - INFO: Decompressing gzipped file ... 03/21/2018 03:32:39 PM - kneaddata.utilities - INFO: Decompressed file created: /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/decompressed_vfLo0D_HSM7J4O3_R1.fastq 03/21/2018 03:32:39 PM - kneaddata.utilities - INFO: Decompressing gzipped file ... 03/21/2018 03:33:55 PM - kneaddata.utilities - INFO: Decompressed file created: /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/decompressed_8HfHCx_HSM7J4O3_R2.fastq 03/21/2018 03:33:55 PM - kneaddata.utilities - INFO: Reformatting file sequence identifiers ... 03/21/2018 03:34:35 PM - kneaddata.utilities - INFO: Reformatting file sequence identifiers ... 03/21/2018 03:35:07 PM - kneaddata.utilities - INFO: READ COUNT: raw pair1 : Initial number of reads ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/reformatted_identifiers5TWNc9_decompressed_vfLo0D_HSM7J4O3_R1 ): 8440604 03/21/2018 03:35:10 PM - kneaddata.utilities - INFO: READ COUNT: raw pair2 : Initial number of reads ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/reformatted_identifiersiFek47_decompressed_8HfHCx_HSM7J4O3_R2 ): 8440604 03/21/2018 03:35:10 PM - kneaddata.utilities - DEBUG: Checking input file to Trimmomatic : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/reformatted_identifiers5TWNc9_decompressed_vfLo0D_HSM7J4O3_R1 03/21/2018 03:35:10 PM - kneaddata.utilities - DEBUG: Checking input file to Trimmomatic : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/reformatted_identifiersiFek47_decompressed_8HfHCx_HSM7J4O3_R2 03/21/2018 03:35:10 PM - kneaddata.utilities - INFO: Running Trimmomatic ... 03/21/2018 03:35:10 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/HMP2/2018-03-20/MTX/kneaddata/main/reformatted_identifiers5TWNc9_decompressed_vfLo0D_HSM7J4O3_R1 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/reformatted_identifiersiFek47_decompressed_8HfHCx_HSM7J4O3_R2 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3.trimmed.1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3.trimmed.single.1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3.trimmed.2.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3.trimmed.single.2.fastq ILLUMINACLIP:/n/home07/carze/.local/bin/Trimmomatic-0.36/adapters/TruSeq3-PE-2.fa:2:30:10:8:TRUE SLIDINGWINDOW:4:20 MINLEN:50 03/21/2018 03:37:41 PM - kneaddata.utilities - DEBUG: TrimmomaticPE: Started with arguments: -threads 4 -phred33 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/reformatted_identifiers5TWNc9_decompressed_vfLo0D_HSM7J4O3_R1 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/reformatted_identifiersiFek47_decompressed_8HfHCx_HSM7J4O3_R2 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3.trimmed.1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3.trimmed.single.1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3.trimmed.2.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3.trimmed.single.2.fastq ILLUMINACLIP:/n/home07/carze/.local/bin/Trimmomatic-0.36/adapters/TruSeq3-PE-2.fa:2:30:10:8:TRUE SLIDINGWINDOW:4:20 MINLEN:50 Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT' Using Long Clipping Sequence: 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC' Using Long Clipping Sequence: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' Using Long Clipping Sequence: 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT' Using Long Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA' ILLUMINACLIP: Using 1 prefix pairs, 4 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences Input Read Pairs: 8440604 Both Surviving: 3812875 (45.17%) Forward Only Surviving: 2092051 (24.79%) Reverse Only Surviving: 628568 (7.45%) Dropped: 1907110 (22.59%) TrimmomaticPE: Completed successfully 03/21/2018 03:37:42 PM - kneaddata.utilities - DEBUG: Checking output file from Trimmomatic : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3.trimmed.1.fastq 03/21/2018 03:37:42 PM - kneaddata.utilities - DEBUG: Checking output file from Trimmomatic : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3.trimmed.single.1.fastq 03/21/2018 03:37:42 PM - kneaddata.utilities - DEBUG: Checking output file from Trimmomatic : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3.trimmed.2.fastq 03/21/2018 03:37:42 PM - kneaddata.utilities - DEBUG: Checking output file from Trimmomatic : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3.trimmed.single.2.fastq 03/21/2018 03:37:44 PM - kneaddata.utilities - INFO: READ COUNT: trimmed pair1 : Total reads after trimming ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3.trimmed.1.fastq ): 3812875 03/21/2018 03:37:45 PM - kneaddata.utilities - INFO: READ COUNT: trimmed pair2 : Total reads after trimming ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3.trimmed.2.fastq ): 3812875 03/21/2018 03:37:46 PM - kneaddata.utilities - INFO: READ COUNT: trimmed orphan1 : Total reads after trimming ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3.trimmed.single.1.fastq ): 2092051 03/21/2018 03:37:46 PM - kneaddata.utilities - INFO: READ COUNT: trimmed orphan2 : Total reads after trimming ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3.trimmed.single.2.fastq ): 628568 03/21/2018 03:37:46 PM - kneaddata.run - INFO: Decontaminating ... 03/21/2018 03:37:47 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3.trimmed.1.fastq 03/21/2018 03:37:47 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3.trimmed.2.fastq 03/21/2018 03:37:47 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3.trimmed.single.1.fastq 03/21/2018 03:37:47 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3.trimmed.single.2.fastq 03/21/2018 03:37:47 PM - kneaddata.utilities - INFO: Running bowtie2 ... 03/21/2018 03:37:47 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/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3.trimmed.1.fastq -2 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3.trimmed.2.fastq --un-pair /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3_Homo_sapiens_bowtie2_paired_clean_%.fastq --al-pair /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3_Homo_sapiens_bowtie2_paired_contam_%.fastq -U /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3.trimmed.single.1.fastq,/n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3.trimmed.single.2.fastq --un-single /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3_Homo_sapiens_bowtie2_unmatched_%_clean.fastq --al-single /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3_Homo_sapiens_bowtie2_unmatched_%_contam.fastq -S /dev/null 03/21/2018 03:50:41 PM - kneaddata.utilities - DEBUG: 10346369 reads; of these: 10346369 (100.00%) were unpaired; of these: 10030167 (96.94%) aligned 0 times 22145 (0.21%) aligned exactly 1 time 294057 (2.84%) aligned >1 times 3.06% overall alignment rate pair1_aligned : 77474 pair2_aligned : 77474 orphan1_unaligned : 1963138 orphan2_unaligned : 608229 orphan2_aligned : 26340 pair2_unaligned : 3729400 pair1_unaligned : 3729400 orphan1_aligned : 134914 03/21/2018 03:50:41 PM - kneaddata.utilities - DEBUG: Checking output file from bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3_Homo_sapiens_bowtie2_paired_clean_1.fastq 03/21/2018 03:50:41 PM - kneaddata.utilities - DEBUG: Checking output file from bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3_Homo_sapiens_bowtie2_paired_clean_2.fastq 03/21/2018 03:50:41 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3.trimmed.1.fastq 03/21/2018 03:50:41 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3.trimmed.2.fastq 03/21/2018 03:50:41 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3.trimmed.single.1.fastq 03/21/2018 03:50:41 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3.trimmed.single.2.fastq 03/21/2018 03:50:41 PM - kneaddata.utilities - INFO: Running bowtie2 ... 03/21/2018 03:50:41 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/ribosomal_RNA/SILVA_128_LSUParc_SSUParc_ribosomal_RNA --bowtie2-options "--very-sensitive --phred33" -1 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3_Homo_sapiens_bowtie2_paired_clean_1.fastq -2 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3_Homo_sapiens_bowtie2_paired_clean_2.fastq --un-pair /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_clean_%.fastq --al-pair /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_contam_%.fastq -U /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3_Homo_sapiens_bowtie2_unmatched_1_clean.fastq,/n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3_Homo_sapiens_bowtie2_unmatched_2_clean.fastq --un-single /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_%_clean.fastq --al-single /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_%_contam.fastq -S /dev/null 03/21/2018 03:57:21 PM - kneaddata.utilities - DEBUG: 10030167 reads; of these: 10030167 (100.00%) were unpaired; of these: 9923023 (98.93%) aligned 0 times 18117 (0.18%) aligned exactly 1 time 89027 (0.89%) aligned >1 times 1.07% overall alignment rate pair1_aligned : 16895 pair2_aligned : 16895 orphan1_unaligned : 1977363 orphan2_unaligned : 613666 orphan2_aligned : 41071 pair2_unaligned : 3665997 pair1_unaligned : 3665997 orphan1_aligned : 32283 03/21/2018 03:57:22 PM - kneaddata.utilities - DEBUG: Checking output file from bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_clean_1.fastq 03/21/2018 03:57:22 PM - kneaddata.utilities - DEBUG: Checking output file from bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_clean_2.fastq 03/21/2018 03:57:22 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3.trimmed.1.fastq 03/21/2018 03:57:22 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3.trimmed.2.fastq 03/21/2018 03:57:22 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3.trimmed.single.1.fastq 03/21/2018 03:57:22 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3.trimmed.single.2.fastq 03/21/2018 03:57:22 PM - kneaddata.utilities - INFO: Running bowtie2 ... 03/21/2018 03:57:22 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/transcriptome/human_hg38_refMrna --bowtie2-options "--very-sensitive --phred33" -1 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_clean_1.fastq -2 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_clean_2.fastq --un-pair /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3_human_hg38_refMrna_bowtie2_paired_clean_%.fastq --al-pair /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3_human_hg38_refMrna_bowtie2_paired_contam_%.fastq -U /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_1_clean.fastq,/n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_2_clean.fastq --un-single /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3_human_hg38_refMrna_bowtie2_unmatched_%_clean.fastq --al-single /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3_human_hg38_refMrna_bowtie2_unmatched_%_contam.fastq -S /dev/null 03/21/2018 04:03:09 PM - kneaddata.utilities - DEBUG: 9923023 reads; of these: 9923023 (100.00%) were unpaired; of these: 9919620 (99.97%) aligned 0 times 636 (0.01%) aligned exactly 1 time 2767 (0.03%) aligned >1 times 0.03% overall alignment rate pair1_aligned : 134 pair2_aligned : 134 orphan1_unaligned : 1976766 orphan2_unaligned : 611368 orphan2_aligned : 2418 pair2_unaligned : 3665743 pair1_unaligned : 3665743 orphan1_aligned : 717 03/21/2018 04:03:09 PM - kneaddata.utilities - DEBUG: Checking output file from bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3_human_hg38_refMrna_bowtie2_paired_clean_1.fastq 03/21/2018 04:03:09 PM - kneaddata.utilities - DEBUG: Checking output file from bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3_human_hg38_refMrna_bowtie2_paired_clean_2.fastq 03/21/2018 04:03:13 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3_Homo_sapiens_bowtie2_paired_contam_1.fastq ) : 77474 03/21/2018 04:03:15 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3_Homo_sapiens_bowtie2_paired_contam_2.fastq ) : 77474 03/21/2018 04:03:16 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3_Homo_sapiens_bowtie2_unmatched_1_contam.fastq ) : 134914 03/21/2018 04:03:16 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3_Homo_sapiens_bowtie2_unmatched_2_contam.fastq ) : 26340 03/21/2018 04:03:16 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_contam_1.fastq ) : 16895 03/21/2018 04:03:16 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_contam_2.fastq ) : 16895 03/21/2018 04:03:16 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_1_contam.fastq ) : 32283 03/21/2018 04:03:16 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_2_contam.fastq ) : 41071 03/21/2018 04:03:16 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3_human_hg38_refMrna_bowtie2_paired_contam_1.fastq ) : 134 03/21/2018 04:03:16 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3_human_hg38_refMrna_bowtie2_paired_contam_2.fastq ) : 134 03/21/2018 04:03:16 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3_human_hg38_refMrna_bowtie2_unmatched_1_contam.fastq ) : 717 03/21/2018 04:03:16 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3_human_hg38_refMrna_bowtie2_unmatched_2_contam.fastq ) : 2418 03/21/2018 04:04:28 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/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3_Homo_sapiens_bowtie2_paired_clean_1.fastq ): 3729400 03/21/2018 04:04:43 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/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3_Homo_sapiens_bowtie2_paired_clean_2.fastq ): 3729400 03/21/2018 04:04:44 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated SILVA_128_LSUParc_SSUParc_ribosomal_RNA pair1 : Total reads after removing those found in reference database ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_clean_1.fastq ): 3665997 03/21/2018 04:04:46 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated SILVA_128_LSUParc_SSUParc_ribosomal_RNA pair2 : Total reads after removing those found in reference database ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_clean_2.fastq ): 3665997 03/21/2018 04:04:48 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated human_hg38_refMrna pair1 : Total reads after removing those found in reference database ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3_human_hg38_refMrna_bowtie2_paired_clean_1.fastq ): 3665743 03/21/2018 04:04:49 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated human_hg38_refMrna pair2 : Total reads after removing those found in reference database ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3_human_hg38_refMrna_bowtie2_paired_clean_2.fastq ): 3665743 03/21/2018 04:08:33 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/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3_paired_1.fastq ): 3665743 03/21/2018 04:08:47 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/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3_paired_2.fastq ): 3665743 03/21/2018 04:09:15 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/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3_Homo_sapiens_bowtie2_unmatched_1_clean.fastq ): 1963138 03/21/2018 04:09:30 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated SILVA_128_LSUParc_SSUParc_ribosomal_RNA orphan1 : Total reads after removing those found in reference database ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_1_clean.fastq ): 1977363 03/21/2018 04:09:43 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated human_hg38_refMrna orphan1 : Total reads after removing those found in reference database ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3_human_hg38_refMrna_bowtie2_unmatched_1_clean.fastq ): 1976766 03/21/2018 04:10:06 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/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3_unmatched_1.fastq ): 1948872 03/21/2018 04:10:10 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/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3_Homo_sapiens_bowtie2_unmatched_2_clean.fastq ): 608229 03/21/2018 04:10:11 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated SILVA_128_LSUParc_SSUParc_ribosomal_RNA orphan2 : Total reads after removing those found in reference database ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_2_clean.fastq ): 613666 03/21/2018 04:10:14 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated human_hg38_refMrna orphan2 : Total reads after removing those found in reference database ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3_human_hg38_refMrna_bowtie2_unmatched_2_clean.fastq ): 611368 03/21/2018 04:10:22 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/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3_unmatched_2.fastq ): 592702 03/21/2018 04:13:12 PM - kneaddata.knead_data - INFO: Final output file created: /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/HSM7J4O3.fastq