04/23/2018 11:01:06 AM - kneaddata.knead_data - INFO: Running kneaddata v0.7.0 04/23/2018 11:01:06 AM - kneaddata.knead_data - INFO: Output files will be written to: /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main 04/23/2018 11:01:06 AM - 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/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E.log max_memory = 500m remove_intermediate_output = True fastqc_path = None output_dir = /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/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/HMP2/2018-04-23/MTX/MSM79H5E_R1.fastq.gz /n/regal/huttenhower_lab/carze/data/hmp2/workflow/deposition/HMP2/2018-04-23/MTX/MSM79H5E_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 = 8 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 = MSM79H5E match = 2 04/23/2018 11:01:06 AM - kneaddata.utilities - INFO: Decompressing gzipped file ... 04/23/2018 11:01:09 AM - kneaddata.utilities - INFO: Decompressed file created: /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/decompressed_PnaYqk_MSM79H5E_R1.fastq 04/23/2018 11:01:09 AM - kneaddata.utilities - INFO: Decompressing gzipped file ... 04/23/2018 11:01:12 AM - kneaddata.utilities - INFO: Decompressed file created: /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/decompressed_i70NY__MSM79H5E_R2.fastq 04/23/2018 11:01:12 AM - kneaddata.utilities - INFO: Reformatting file sequence identifiers ... 04/23/2018 11:01:16 AM - kneaddata.utilities - INFO: Reformatting file sequence identifiers ... 04/23/2018 11:01:21 AM - kneaddata.utilities - INFO: READ COUNT: raw pair1 : Initial number of reads ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/reformatted_identifiersHrh_8H_decompressed_i70NY__MSM79H5E_R2 ): 1587404 04/23/2018 11:01:21 AM - kneaddata.utilities - INFO: READ COUNT: raw pair2 : Initial number of reads ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/reformatted_identifiersQJGtKB_decompressed_PnaYqk_MSM79H5E_R1 ): 1587404 04/23/2018 11:01:21 AM - kneaddata.utilities - DEBUG: Checking input file to Trimmomatic : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/reformatted_identifiersQJGtKB_decompressed_PnaYqk_MSM79H5E_R1 04/23/2018 11:01:21 AM - kneaddata.utilities - DEBUG: Checking input file to Trimmomatic : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/reformatted_identifiersHrh_8H_decompressed_i70NY__MSM79H5E_R2 04/23/2018 11:01:21 AM - kneaddata.utilities - INFO: Running Trimmomatic ... 04/23/2018 11:01:21 AM - 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 8 -phred33 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/reformatted_identifiersQJGtKB_decompressed_PnaYqk_MSM79H5E_R1 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/reformatted_identifiersHrh_8H_decompressed_i70NY__MSM79H5E_R2 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E.trimmed.1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E.trimmed.single.1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E.trimmed.2.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E.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 04/23/2018 11:01:35 AM - kneaddata.utilities - DEBUG: TrimmomaticPE: Started with arguments: -threads 8 -phred33 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/reformatted_identifiersQJGtKB_decompressed_PnaYqk_MSM79H5E_R1 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/reformatted_identifiersHrh_8H_decompressed_i70NY__MSM79H5E_R2 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E.trimmed.1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E.trimmed.single.1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E.trimmed.2.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E.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: 1587404 Both Surviving: 207822 (13.09%) Forward Only Surviving: 113846 (7.17%) Reverse Only Surviving: 10822 (0.68%) Dropped: 1254914 (79.05%) TrimmomaticPE: Completed successfully 04/23/2018 11:01:35 AM - kneaddata.utilities - DEBUG: Checking output file from Trimmomatic : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E.trimmed.1.fastq 04/23/2018 11:01:35 AM - kneaddata.utilities - DEBUG: Checking output file from Trimmomatic : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E.trimmed.single.1.fastq 04/23/2018 11:01:35 AM - kneaddata.utilities - DEBUG: Checking output file from Trimmomatic : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E.trimmed.2.fastq 04/23/2018 11:01:35 AM - kneaddata.utilities - DEBUG: Checking output file from Trimmomatic : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E.trimmed.single.2.fastq 04/23/2018 11:01:35 AM - kneaddata.utilities - INFO: READ COUNT: trimmed pair1 : Total reads after trimming ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E.trimmed.1.fastq ): 207822 04/23/2018 11:01:35 AM - kneaddata.utilities - INFO: READ COUNT: trimmed pair2 : Total reads after trimming ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E.trimmed.2.fastq ): 207822 04/23/2018 11:01:36 AM - kneaddata.utilities - INFO: READ COUNT: trimmed orphan1 : Total reads after trimming ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E.trimmed.single.1.fastq ): 113846 04/23/2018 11:01:36 AM - kneaddata.utilities - INFO: READ COUNT: trimmed orphan2 : Total reads after trimming ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E.trimmed.single.2.fastq ): 10822 04/23/2018 11:01:36 AM - kneaddata.run - INFO: Decontaminating ... 04/23/2018 11:01:40 AM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E.trimmed.1.fastq 04/23/2018 11:01:40 AM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E.trimmed.2.fastq 04/23/2018 11:01:40 AM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E.trimmed.single.1.fastq 04/23/2018 11:01:40 AM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E.trimmed.single.2.fastq 04/23/2018 11:01:40 AM - kneaddata.utilities - INFO: Running bowtie2 ... 04/23/2018 11:01:40 AM - kneaddata.utilities - INFO: Execute command: kneaddata_bowtie2_discordant_pairs --bowtie2 /n/sw/centos6/bowtie2-2.2.1/bowtie2 --threads 8 -x /n/huttenhower_lab/data/kneaddata_databases/Homo_sapiens --bowtie2-options "--very-sensitive --phred33" -1 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E.trimmed.1.fastq -2 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E.trimmed.2.fastq --un-pair /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E_Homo_sapiens_bowtie2_paired_clean_%.fastq --al-pair /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E_Homo_sapiens_bowtie2_paired_contam_%.fastq -U /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E.trimmed.single.1.fastq,/n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E.trimmed.single.2.fastq --un-single /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E_Homo_sapiens_bowtie2_unmatched_%_clean.fastq --al-single /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E_Homo_sapiens_bowtie2_unmatched_%_contam.fastq -S /dev/null 04/23/2018 11:02:22 AM - kneaddata.utilities - DEBUG: 540312 reads; of these: 540312 (100.00%) were unpaired; of these: 502009 (92.91%) aligned 0 times 3395 (0.63%) aligned exactly 1 time 34908 (6.46%) aligned >1 times 7.09% overall alignment rate pair1_aligned : 12538 pair2_aligned : 12538 orphan1_unaligned : 103815 orphan2_unaligned : 9036 orphan2_aligned : 2491 pair2_unaligned : 194579 pair1_unaligned : 194579 orphan1_aligned : 10736 04/23/2018 11:02:22 AM - kneaddata.utilities - DEBUG: Checking output file from bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E_Homo_sapiens_bowtie2_paired_clean_1.fastq 04/23/2018 11:02:22 AM - kneaddata.utilities - DEBUG: Checking output file from bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E_Homo_sapiens_bowtie2_paired_clean_2.fastq 04/23/2018 11:02:22 AM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E.trimmed.1.fastq 04/23/2018 11:02:22 AM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E.trimmed.2.fastq 04/23/2018 11:02:22 AM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E.trimmed.single.1.fastq 04/23/2018 11:02:22 AM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E.trimmed.single.2.fastq 04/23/2018 11:02:22 AM - kneaddata.utilities - INFO: Running bowtie2 ... 04/23/2018 11:02:22 AM - kneaddata.utilities - INFO: Execute command: kneaddata_bowtie2_discordant_pairs --bowtie2 /n/sw/centos6/bowtie2-2.2.1/bowtie2 --threads 8 -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/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E_Homo_sapiens_bowtie2_paired_clean_1.fastq -2 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E_Homo_sapiens_bowtie2_paired_clean_2.fastq --un-pair /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_clean_%.fastq --al-pair /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_contam_%.fastq -U /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E_Homo_sapiens_bowtie2_unmatched_1_clean.fastq,/n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E_Homo_sapiens_bowtie2_unmatched_2_clean.fastq --un-single /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_%_clean.fastq --al-single /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_%_contam.fastq -S /dev/null 04/23/2018 11:04:25 AM - kneaddata.utilities - DEBUG: 502009 reads; of these: 502009 (100.00%) were unpaired; of these: 500797 (99.76%) aligned 0 times 167 (0.03%) aligned exactly 1 time 1045 (0.21%) aligned >1 times 0.24% overall alignment rate pair1_aligned : 84 pair2_aligned : 84 orphan1_unaligned : 103797 orphan2_unaligned : 8954 orphan2_aligned : 554 pair2_unaligned : 194023 pair1_unaligned : 194023 orphan1_aligned : 490 04/23/2018 11:04:26 AM - kneaddata.utilities - DEBUG: Checking output file from bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_clean_1.fastq 04/23/2018 11:04:26 AM - kneaddata.utilities - DEBUG: Checking output file from bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_clean_2.fastq 04/23/2018 11:04:26 AM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E.trimmed.1.fastq 04/23/2018 11:04:26 AM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E.trimmed.2.fastq 04/23/2018 11:04:26 AM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E.trimmed.single.1.fastq 04/23/2018 11:04:26 AM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E.trimmed.single.2.fastq 04/23/2018 11:04:26 AM - kneaddata.utilities - INFO: Running bowtie2 ... 04/23/2018 11:04:26 AM - kneaddata.utilities - INFO: Execute command: kneaddata_bowtie2_discordant_pairs --bowtie2 /n/sw/centos6/bowtie2-2.2.1/bowtie2 --threads 8 -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/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_clean_1.fastq -2 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_clean_2.fastq --un-pair /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E_human_hg38_refMrna_bowtie2_paired_clean_%.fastq --al-pair /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E_human_hg38_refMrna_bowtie2_paired_contam_%.fastq -U /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_1_clean.fastq,/n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_2_clean.fastq --un-single /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E_human_hg38_refMrna_bowtie2_unmatched_%_clean.fastq --al-single /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E_human_hg38_refMrna_bowtie2_unmatched_%_contam.fastq -S /dev/null 04/23/2018 11:04:38 AM - kneaddata.utilities - DEBUG: 500797 reads; of these: 500797 (100.00%) were unpaired; of these: 500552 (99.95%) aligned 0 times 94 (0.02%) aligned exactly 1 time 151 (0.03%) aligned >1 times 0.05% overall alignment rate pair1_aligned : 13 pair2_aligned : 13 orphan1_unaligned : 103717 orphan2_unaligned : 8837 orphan2_aligned : 128 pair2_unaligned : 193999 pair1_unaligned : 193999 orphan1_aligned : 91 04/23/2018 11:04:38 AM - kneaddata.utilities - DEBUG: Checking output file from bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E_human_hg38_refMrna_bowtie2_paired_clean_1.fastq 04/23/2018 11:04:38 AM - kneaddata.utilities - DEBUG: Checking output file from bowtie2 : /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E_human_hg38_refMrna_bowtie2_paired_clean_2.fastq 04/23/2018 11:04:38 AM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E_Homo_sapiens_bowtie2_paired_contam_1.fastq ) : 12538 04/23/2018 11:04:38 AM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E_Homo_sapiens_bowtie2_paired_contam_2.fastq ) : 12538 04/23/2018 11:04:38 AM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E_Homo_sapiens_bowtie2_unmatched_1_contam.fastq ) : 10736 04/23/2018 11:04:38 AM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E_Homo_sapiens_bowtie2_unmatched_2_contam.fastq ) : 2491 04/23/2018 11:04:38 AM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_contam_1.fastq ) : 84 04/23/2018 11:04:38 AM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_contam_2.fastq ) : 84 04/23/2018 11:04:38 AM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_1_contam.fastq ) : 490 04/23/2018 11:04:38 AM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_2_contam.fastq ) : 554 04/23/2018 11:04:38 AM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E_human_hg38_refMrna_bowtie2_paired_contam_1.fastq ) : 13 04/23/2018 11:04:38 AM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E_human_hg38_refMrna_bowtie2_paired_contam_2.fastq ) : 13 04/23/2018 11:04:38 AM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E_human_hg38_refMrna_bowtie2_unmatched_1_contam.fastq ) : 91 04/23/2018 11:04:38 AM - kneaddata.run - INFO: Total contaminate sequences in file ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E_human_hg38_refMrna_bowtie2_unmatched_2_contam.fastq ) : 128 04/23/2018 11:04:38 AM - 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/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E_Homo_sapiens_bowtie2_paired_clean_1.fastq ): 194579 04/23/2018 11:04:39 AM - 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/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E_Homo_sapiens_bowtie2_paired_clean_2.fastq ): 194579 04/23/2018 11:04:39 AM - 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/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_clean_1.fastq ): 194023 04/23/2018 11:04:39 AM - 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/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_clean_2.fastq ): 194023 04/23/2018 11:04:39 AM - 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/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E_human_hg38_refMrna_bowtie2_paired_clean_1.fastq ): 193999 04/23/2018 11:04:39 AM - 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/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E_human_hg38_refMrna_bowtie2_paired_clean_2.fastq ): 193999 04/23/2018 11:04:42 AM - kneaddata.utilities - INFO: READ COUNT: final pair1 : Total reads after merging results from multiple databases ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E_paired_1.fastq ): 193999 04/23/2018 11:04:42 AM - kneaddata.utilities - INFO: READ COUNT: final pair2 : Total reads after merging results from multiple databases ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E_paired_2.fastq ): 193999 04/23/2018 11:04:42 AM - 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/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E_Homo_sapiens_bowtie2_unmatched_1_clean.fastq ): 103815 04/23/2018 11:04:42 AM - 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/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_1_clean.fastq ): 103797 04/23/2018 11:04:42 AM - 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/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E_human_hg38_refMrna_bowtie2_unmatched_1_clean.fastq ): 103717 04/23/2018 11:04:43 AM - kneaddata.utilities - INFO: READ COUNT: final orphan1 : Total reads after merging results from multiple databases ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E_unmatched_1.fastq ): 103440 04/23/2018 11:04:43 AM - 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/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E_Homo_sapiens_bowtie2_unmatched_2_clean.fastq ): 9036 04/23/2018 11:04:43 AM - 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/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_2_clean.fastq ): 8954 04/23/2018 11:04:43 AM - 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/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E_human_hg38_refMrna_bowtie2_unmatched_2_clean.fastq ): 8837 04/23/2018 11:04:43 AM - kneaddata.utilities - INFO: READ COUNT: final orphan2 : Total reads after merging results from multiple databases ( /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E_unmatched_2.fastq ): 8636 04/23/2018 11:04:43 AM - kneaddata.knead_data - INFO: Final output file created: /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/MSM79H5E.fastq