03/21/2018 02:02:20 PM - kneaddata.knead_data - INFO: Running kneaddata v0.7.0 03/21/2018 02:02:20 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 02:02:20 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/MSM9VZLT.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/MSM9VZLT_R1.fastq.gz /n/regal/huttenhower_lab/carze/data/hmp2/workflow/deposition/HMP2/2018-03-20/MTX/MSM9VZLT_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 = MSM9VZLT match = 2 03/21/2018 02:02:20 PM - kneaddata.utilities - INFO: Decompressing gzipped file ... 03/21/2018 02:03:06 PM - kneaddata.utilities - INFO: Decompressed file created: /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/decompressed_2Ne5jQ_MSM9VZLT_R1.fastq 03/21/2018 02:03:06 PM - kneaddata.utilities - INFO: Decompressing gzipped file ... 03/21/2018 02:03:49 PM - kneaddata.utilities - INFO: Decompressed file created: /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/decompressed_oCIEGB_MSM9VZLT_R2.fastq 03/21/2018 02:03:49 PM - kneaddata.utilities - INFO: Reformatting file sequence identifiers ... 03/21/2018 02:04:44 PM - kneaddata.utilities - INFO: Reformatting file sequence identifiers ... 03/21/2018 02:11:48 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_identifiersAXF0Iw_decompressed_2Ne5jQ_MSM9VZLT_R1 ): 19237346 03/21/2018 02:14:49 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_identifiersr1sBZu_decompressed_oCIEGB_MSM9VZLT_R2 ): 19237346 03/21/2018 02:14:49 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_identifiersAXF0Iw_decompressed_2Ne5jQ_MSM9VZLT_R1 03/21/2018 02:14:49 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_identifiersr1sBZu_decompressed_oCIEGB_MSM9VZLT_R2 03/21/2018 02:14:49 PM - kneaddata.utilities - INFO: Running Trimmomatic ... 03/21/2018 02:14:49 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_identifiersAXF0Iw_decompressed_2Ne5jQ_MSM9VZLT_R1 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/reformatted_identifiersr1sBZu_decompressed_oCIEGB_MSM9VZLT_R2 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/MSM9VZLT.trimmed.1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/MSM9VZLT.trimmed.single.1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/MSM9VZLT.trimmed.2.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/MSM9VZLT.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 02:20:41 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_identifiersAXF0Iw_decompressed_2Ne5jQ_MSM9VZLT_R1 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/reformatted_identifiersr1sBZu_decompressed_oCIEGB_MSM9VZLT_R2 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/MSM9VZLT.trimmed.1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/MSM9VZLT.trimmed.single.1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/MSM9VZLT.trimmed.2.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/MSM9VZLT.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: 19237346 Both Surviving: 13257214 (68.91%) Forward Only Surviving: 3100650 (16.12%) Reverse Only Surviving: 358181 (1.86%) Dropped: 2521301 (13.11%) TrimmomaticPE: Completed successfully 03/21/2018 02:20:42 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/MSM9VZLT.trimmed.1.fastq 03/21/2018 02:20:42 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/MSM9VZLT.trimmed.single.1.fastq 03/21/2018 02:20:42 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/MSM9VZLT.trimmed.2.fastq 03/21/2018 02:20:42 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/MSM9VZLT.trimmed.single.2.fastq 03/21/2018 02:21:23 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/MSM9VZLT.trimmed.1.fastq ): 13257214 03/21/2018 02:22:44 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/MSM9VZLT.trimmed.2.fastq ): 13257214 03/21/2018 02:22:56 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/MSM9VZLT.trimmed.single.1.fastq ): 3100650 03/21/2018 02:22:57 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/MSM9VZLT.trimmed.single.2.fastq ): 358181 03/21/2018 02:22:57 PM - kneaddata.run - INFO: Decontaminating ... 03/21/2018 02:22:58 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/MSM9VZLT.trimmed.1.fastq 03/21/2018 02:22:58 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/MSM9VZLT.trimmed.2.fastq 03/21/2018 02:22:58 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/MSM9VZLT.trimmed.single.1.fastq 03/21/2018 02:22:58 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/MSM9VZLT.trimmed.single.2.fastq 03/21/2018 02:22:58 PM - kneaddata.utilities - INFO: Running bowtie2 ... 03/21/2018 02:22:58 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/MSM9VZLT.trimmed.1.fastq -2 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/MSM9VZLT.trimmed.2.fastq --un-pair /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/MSM9VZLT_Homo_sapiens_bowtie2_paired_clean_%.fastq --al-pair /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/MSM9VZLT_Homo_sapiens_bowtie2_paired_contam_%.fastq -U /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/MSM9VZLT.trimmed.single.1.fastq,/n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/MSM9VZLT.trimmed.single.2.fastq --un-single /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/MSM9VZLT_Homo_sapiens_bowtie2_unmatched_%_clean.fastq --al-single /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/MSM9VZLT_Homo_sapiens_bowtie2_unmatched_%_contam.fastq -S /dev/null 03/21/2018 03:01:40 PM - kneaddata.utilities - DEBUG: 29973259 reads; of these: 29973259 (100.00%) were unpaired; of these: 29408316 (98.12%) aligned 0 times 36791 (0.12%) aligned exactly 1 time 528152 (1.76%) aligned >1 times 1.88% overall alignment rate pair1_aligned : 157124 pair2_aligned : 157124 orphan1_unaligned : 2878383 orphan2_unaligned : 348583 orphan2_aligned : 19013 pair2_unaligned : 13090675 pair1_unaligned : 13090675 orphan1_aligned : 231682 03/21/2018 03:01:40 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/MSM9VZLT_Homo_sapiens_bowtie2_paired_clean_1.fastq 03/21/2018 03:01:40 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/MSM9VZLT_Homo_sapiens_bowtie2_paired_clean_2.fastq 03/21/2018 03:01:40 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/MSM9VZLT.trimmed.1.fastq 03/21/2018 03:01:40 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/MSM9VZLT.trimmed.2.fastq 03/21/2018 03:01:40 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/MSM9VZLT.trimmed.single.1.fastq 03/21/2018 03:01:40 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/MSM9VZLT.trimmed.single.2.fastq 03/21/2018 03:01:40 PM - kneaddata.utilities - INFO: Running bowtie2 ... 03/21/2018 03:01:40 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/MSM9VZLT_Homo_sapiens_bowtie2_paired_clean_1.fastq -2 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/MSM9VZLT_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/MSM9VZLT_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/MSM9VZLT_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/MSM9VZLT_Homo_sapiens_bowtie2_unmatched_1_clean.fastq,/n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/MSM9VZLT_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/MSM9VZLT_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/MSM9VZLT_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_%_contam.fastq -S /dev/null 03/21/2018 03:28:58 PM - kneaddata.utilities - DEBUG: 29408316 reads; of these: 29408316 (100.00%) were unpaired; of these: 29375942 (99.89%) aligned 0 times 2035 (0.01%) aligned exactly 1 time 30339 (0.10%) aligned >1 times 0.11% overall alignment rate pair1_aligned : 3358 pair2_aligned : 3358 orphan1_unaligned : 2880783 orphan2_unaligned : 353835 orphan2_aligned : 11403 pair2_unaligned : 13070662 pair1_unaligned : 13070662 orphan1_aligned : 14255 03/21/2018 03:28:59 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/MSM9VZLT_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_clean_1.fastq 03/21/2018 03:28:59 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/MSM9VZLT_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_clean_2.fastq 03/21/2018 03:28:59 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/MSM9VZLT.trimmed.1.fastq 03/21/2018 03:28:59 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/MSM9VZLT.trimmed.2.fastq 03/21/2018 03:28:59 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/MSM9VZLT.trimmed.single.1.fastq 03/21/2018 03:28:59 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/MSM9VZLT.trimmed.single.2.fastq 03/21/2018 03:28:59 PM - kneaddata.utilities - INFO: Running bowtie2 ... 03/21/2018 03:28:59 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/MSM9VZLT_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/MSM9VZLT_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/MSM9VZLT_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/MSM9VZLT_human_hg38_refMrna_bowtie2_paired_contam_%.fastq -U /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/MSM9VZLT_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/MSM9VZLT_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/MSM9VZLT_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/MSM9VZLT_human_hg38_refMrna_bowtie2_unmatched_%_contam.fastq -S /dev/null 03/21/2018 03:46:29 PM - kneaddata.utilities - DEBUG: 29375942 reads; of these: 29375942 (100.00%) were unpaired; of these: 29372912 (99.99%) aligned 0 times 1034 (0.00%) aligned exactly 1 time 1996 (0.01%) aligned >1 times 0.01% overall alignment rate pair1_aligned : 481 pair2_aligned : 481 orphan1_unaligned : 2879964 orphan2_unaligned : 352916 orphan2_aligned : 1084 pair2_unaligned : 13070016 pair1_unaligned : 13070016 orphan1_aligned : 984 03/21/2018 03:46:29 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/MSM9VZLT_human_hg38_refMrna_bowtie2_paired_clean_1.fastq 03/21/2018 03:46:29 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/MSM9VZLT_human_hg38_refMrna_bowtie2_paired_clean_2.fastq 03/21/2018 03:46:30 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/MSM9VZLT_Homo_sapiens_bowtie2_paired_contam_1.fastq ) : 157124 03/21/2018 03:46:31 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/MSM9VZLT_Homo_sapiens_bowtie2_paired_contam_2.fastq ) : 157124 03/21/2018 03:46:33 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/MSM9VZLT_Homo_sapiens_bowtie2_unmatched_1_contam.fastq ) : 231682 03/21/2018 03:46:34 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/MSM9VZLT_Homo_sapiens_bowtie2_unmatched_2_contam.fastq ) : 19013 03/21/2018 03:46:34 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/MSM9VZLT_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_contam_1.fastq ) : 3358 03/21/2018 03:46:34 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/MSM9VZLT_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_contam_2.fastq ) : 3358 03/21/2018 03:46:34 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/MSM9VZLT_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_1_contam.fastq ) : 14255 03/21/2018 03:46:35 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/MSM9VZLT_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_2_contam.fastq ) : 11403 03/21/2018 03:46:35 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/MSM9VZLT_human_hg38_refMrna_bowtie2_paired_contam_1.fastq ) : 481 03/21/2018 03:46:35 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/MSM9VZLT_human_hg38_refMrna_bowtie2_paired_contam_2.fastq ) : 481 03/21/2018 03:46:35 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/MSM9VZLT_human_hg38_refMrna_bowtie2_unmatched_1_contam.fastq ) : 984 03/21/2018 03:46:35 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/MSM9VZLT_human_hg38_refMrna_bowtie2_unmatched_2_contam.fastq ) : 1084 03/21/2018 03:47:08 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/MSM9VZLT_Homo_sapiens_bowtie2_paired_clean_1.fastq ): 13090675 03/21/2018 03:47:29 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/MSM9VZLT_Homo_sapiens_bowtie2_paired_clean_2.fastq ): 13090675 03/21/2018 03:50:20 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/MSM9VZLT_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_clean_1.fastq ): 13070662 03/21/2018 03:51:29 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/MSM9VZLT_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_clean_2.fastq ): 13070662 03/21/2018 03:54:07 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/MSM9VZLT_human_hg38_refMrna_bowtie2_paired_clean_1.fastq ): 13070016 03/21/2018 03:55:36 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/MSM9VZLT_human_hg38_refMrna_bowtie2_paired_clean_2.fastq ): 13070016 03/21/2018 04:13:15 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/MSM9VZLT_paired_1.fastq ): 13070016 03/21/2018 04:13:20 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/MSM9VZLT_paired_2.fastq ): 13070016 03/21/2018 04:13:35 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/MSM9VZLT_Homo_sapiens_bowtie2_unmatched_1_clean.fastq ): 2878383 03/21/2018 04:14:13 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/MSM9VZLT_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_1_clean.fastq ): 2880783 03/21/2018 04:14:34 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/MSM9VZLT_human_hg38_refMrna_bowtie2_unmatched_1_clean.fastq ): 2879964 03/21/2018 04:15:33 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/MSM9VZLT_unmatched_1.fastq ): 2870247 03/21/2018 04:15:34 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/MSM9VZLT_Homo_sapiens_bowtie2_unmatched_2_clean.fastq ): 348583 03/21/2018 04:15:36 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/MSM9VZLT_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_2_clean.fastq ): 353835 03/21/2018 04:15:42 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/MSM9VZLT_human_hg38_refMrna_bowtie2_unmatched_2_clean.fastq ): 352916 03/21/2018 04:16:09 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/MSM9VZLT_unmatched_2.fastq ): 345848 03/21/2018 04:16:48 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/MSM9VZLT.fastq