04/23/2018 11:01:43 AM - kneaddata.knead_data - INFO: Running kneaddata v0.7.0 04/23/2018 11:01:43 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 11:01:43 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/PSMA265J.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/PSMA265J_R1.fastq.gz /n/regal/huttenhower_lab/carze/data/hmp2/workflow/deposition/HMP2/2018-04-23/MTX/PSMA265J_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 = PSMA265J match = 2 04/23/2018 11:01:43 AM - kneaddata.utilities - INFO: Decompressing gzipped file ... 04/23/2018 11:02:11 AM - kneaddata.utilities - INFO: Decompressed file created: /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/decompressed_9vjXor_PSMA265J_R1.fastq 04/23/2018 11:02:11 AM - kneaddata.utilities - INFO: Decompressing gzipped file ... 04/23/2018 11:02:44 AM - kneaddata.utilities - INFO: Decompressed file created: /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/decompressed_5obGG9_PSMA265J_R2.fastq 04/23/2018 11:02:44 AM - kneaddata.utilities - INFO: Reformatting file sequence identifiers ... 04/23/2018 11:03:34 AM - kneaddata.utilities - INFO: Reformatting file sequence identifiers ... 04/23/2018 11:05:29 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_identifiersgByKxb_decompressed_5obGG9_PSMA265J_R2 ): 16502654 04/23/2018 11:07:00 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_identifiersiNl2UT_decompressed_9vjXor_PSMA265J_R1 ): 16502654 04/23/2018 11:07:00 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_identifiersiNl2UT_decompressed_9vjXor_PSMA265J_R1 04/23/2018 11:07:00 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_identifiersgByKxb_decompressed_5obGG9_PSMA265J_R2 04/23/2018 11:07:00 AM - kneaddata.utilities - INFO: Running Trimmomatic ... 04/23/2018 11:07:00 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_identifiersiNl2UT_decompressed_9vjXor_PSMA265J_R1 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/reformatted_identifiersgByKxb_decompressed_5obGG9_PSMA265J_R2 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/PSMA265J.trimmed.1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/PSMA265J.trimmed.single.1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/PSMA265J.trimmed.2.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/PSMA265J.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 11:10:14 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_identifiersiNl2UT_decompressed_9vjXor_PSMA265J_R1 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/reformatted_identifiersgByKxb_decompressed_5obGG9_PSMA265J_R2 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/PSMA265J.trimmed.1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/PSMA265J.trimmed.single.1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/PSMA265J.trimmed.2.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/PSMA265J.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: 16502654 Both Surviving: 10412189 (63.09%) Forward Only Surviving: 3333818 (20.20%) Reverse Only Surviving: 431958 (2.62%) Dropped: 2324689 (14.09%) TrimmomaticPE: Completed successfully 04/23/2018 11:10:14 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/PSMA265J.trimmed.1.fastq 04/23/2018 11:10:14 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/PSMA265J.trimmed.single.1.fastq 04/23/2018 11:10:14 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/PSMA265J.trimmed.2.fastq 04/23/2018 11:10:14 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/PSMA265J.trimmed.single.2.fastq 04/23/2018 11:10:23 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/PSMA265J.trimmed.1.fastq ): 10412189 04/23/2018 11:10:33 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/PSMA265J.trimmed.2.fastq ): 10412189 04/23/2018 11:10:38 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/PSMA265J.trimmed.single.1.fastq ): 3333818 04/23/2018 11:10:38 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/PSMA265J.trimmed.single.2.fastq ): 431958 04/23/2018 11:10:38 AM - kneaddata.run - INFO: Decontaminating ... 04/23/2018 11:10:43 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/PSMA265J.trimmed.1.fastq 04/23/2018 11:10:43 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/PSMA265J.trimmed.2.fastq 04/23/2018 11:10:43 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/PSMA265J.trimmed.single.1.fastq 04/23/2018 11:10:43 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/PSMA265J.trimmed.single.2.fastq 04/23/2018 11:10:43 AM - kneaddata.utilities - INFO: Running bowtie2 ... 04/23/2018 11:10:43 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/PSMA265J.trimmed.1.fastq -2 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/PSMA265J.trimmed.2.fastq --un-pair /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/PSMA265J_Homo_sapiens_bowtie2_paired_clean_%.fastq --al-pair /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/PSMA265J_Homo_sapiens_bowtie2_paired_contam_%.fastq -U /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/PSMA265J.trimmed.single.1.fastq,/n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/PSMA265J.trimmed.single.2.fastq --un-single /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/PSMA265J_Homo_sapiens_bowtie2_unmatched_%_clean.fastq --al-single /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/PSMA265J_Homo_sapiens_bowtie2_unmatched_%_contam.fastq -S /dev/null 04/23/2018 11:22:02 AM - kneaddata.utilities - DEBUG: 24590154 reads; of these: 24590154 (100.00%) were unpaired; of these: 22522425 (91.59%) aligned 0 times 26468 (0.11%) aligned exactly 1 time 2041261 (8.30%) aligned >1 times 8.41% overall alignment rate pair1_aligned : 293374 pair2_aligned : 293374 orphan1_unaligned : 1932380 orphan2_unaligned : 371063 orphan2_aligned : 70219 pair2_unaligned : 10109491 pair1_unaligned : 10109491 orphan1_aligned : 1410762 04/23/2018 11:22:02 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/PSMA265J_Homo_sapiens_bowtie2_paired_clean_1.fastq 04/23/2018 11:22:02 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/PSMA265J_Homo_sapiens_bowtie2_paired_clean_2.fastq 04/23/2018 11:22:02 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/PSMA265J.trimmed.1.fastq 04/23/2018 11:22:02 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/PSMA265J.trimmed.2.fastq 04/23/2018 11:22:02 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/PSMA265J.trimmed.single.1.fastq 04/23/2018 11:22:02 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/PSMA265J.trimmed.single.2.fastq 04/23/2018 11:22:02 AM - kneaddata.utilities - INFO: Running bowtie2 ... 04/23/2018 11:22:02 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/PSMA265J_Homo_sapiens_bowtie2_paired_clean_1.fastq -2 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/PSMA265J_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/PSMA265J_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/PSMA265J_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/PSMA265J_Homo_sapiens_bowtie2_unmatched_1_clean.fastq,/n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/PSMA265J_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/PSMA265J_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/PSMA265J_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_%_contam.fastq -S /dev/null 04/23/2018 11:31:10 AM - kneaddata.utilities - DEBUG: 22522425 reads; of these: 22522425 (100.00%) were unpaired; of these: 22501288 (99.91%) aligned 0 times 2825 (0.01%) aligned exactly 1 time 18312 (0.08%) aligned >1 times 0.09% overall alignment rate pair1_aligned : 554 pair2_aligned : 554 orphan1_unaligned : 1924953 orphan2_unaligned : 368549 orphan2_aligned : 7558 pair2_unaligned : 10103893 pair1_unaligned : 10103893 orphan1_aligned : 12471 04/23/2018 11:31:10 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/PSMA265J_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_clean_1.fastq 04/23/2018 11:31:10 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/PSMA265J_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_clean_2.fastq 04/23/2018 11:31:10 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/PSMA265J.trimmed.1.fastq 04/23/2018 11:31:10 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/PSMA265J.trimmed.2.fastq 04/23/2018 11:31:10 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/PSMA265J.trimmed.single.1.fastq 04/23/2018 11:31:10 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/PSMA265J.trimmed.single.2.fastq 04/23/2018 11:31:10 AM - kneaddata.utilities - INFO: Running bowtie2 ... 04/23/2018 11:31:10 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/PSMA265J_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/PSMA265J_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/PSMA265J_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/PSMA265J_human_hg38_refMrna_bowtie2_paired_contam_%.fastq -U /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/PSMA265J_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/PSMA265J_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/PSMA265J_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/PSMA265J_human_hg38_refMrna_bowtie2_unmatched_%_contam.fastq -S /dev/null 04/23/2018 11:38:29 AM - kneaddata.utilities - DEBUG: 22501288 reads; of these: 22501288 (100.00%) were unpaired; of these: 22498625 (99.99%) aligned 0 times 499 (0.00%) aligned exactly 1 time 2164 (0.01%) aligned >1 times 0.01% overall alignment rate pair1_aligned : 189 pair2_aligned : 189 orphan1_unaligned : 1923995 orphan2_unaligned : 367420 orphan2_aligned : 1228 pair2_unaligned : 10103605 pair1_unaligned : 10103605 orphan1_aligned : 1057 04/23/2018 11:38:29 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/PSMA265J_human_hg38_refMrna_bowtie2_paired_clean_1.fastq 04/23/2018 11:38:29 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/PSMA265J_human_hg38_refMrna_bowtie2_paired_clean_2.fastq 04/23/2018 11:38:30 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/PSMA265J_Homo_sapiens_bowtie2_paired_contam_1.fastq ) : 293374 04/23/2018 11:38:31 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/PSMA265J_Homo_sapiens_bowtie2_paired_contam_2.fastq ) : 293374 04/23/2018 11:38:34 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/PSMA265J_Homo_sapiens_bowtie2_unmatched_1_contam.fastq ) : 1410762 04/23/2018 11:38:34 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/PSMA265J_Homo_sapiens_bowtie2_unmatched_2_contam.fastq ) : 70219 04/23/2018 11:38:34 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/PSMA265J_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_contam_1.fastq ) : 554 04/23/2018 11:38:34 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/PSMA265J_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_contam_2.fastq ) : 554 04/23/2018 11:38:35 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/PSMA265J_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_1_contam.fastq ) : 12471 04/23/2018 11:38:35 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/PSMA265J_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_2_contam.fastq ) : 7558 04/23/2018 11:38:35 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/PSMA265J_human_hg38_refMrna_bowtie2_paired_contam_1.fastq ) : 189 04/23/2018 11:38:35 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/PSMA265J_human_hg38_refMrna_bowtie2_paired_contam_2.fastq ) : 189 04/23/2018 11:38:35 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/PSMA265J_human_hg38_refMrna_bowtie2_unmatched_1_contam.fastq ) : 1057 04/23/2018 11:38:35 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/PSMA265J_human_hg38_refMrna_bowtie2_unmatched_2_contam.fastq ) : 1228 04/23/2018 11:39:04 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/PSMA265J_Homo_sapiens_bowtie2_paired_clean_1.fastq ): 10109491 04/23/2018 11:39:20 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/PSMA265J_Homo_sapiens_bowtie2_paired_clean_2.fastq ): 10109491 04/23/2018 11:39:34 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/PSMA265J_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_clean_1.fastq ): 10103893 04/23/2018 11:39:41 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/PSMA265J_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_clean_2.fastq ): 10103893 04/23/2018 11:39:57 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/PSMA265J_human_hg38_refMrna_bowtie2_paired_clean_1.fastq ): 10103605 04/23/2018 11:40:16 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/PSMA265J_human_hg38_refMrna_bowtie2_paired_clean_2.fastq ): 10103605 04/23/2018 11:45:58 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/PSMA265J_paired_1.fastq ): 10103605 04/23/2018 11:46:03 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/PSMA265J_paired_2.fastq ): 10103605 04/23/2018 11:46:12 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/PSMA265J_Homo_sapiens_bowtie2_unmatched_1_clean.fastq ): 1932380 04/23/2018 11:46:17 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/PSMA265J_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_1_clean.fastq ): 1924953 04/23/2018 11:46:20 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/PSMA265J_human_hg38_refMrna_bowtie2_unmatched_1_clean.fastq ): 1923995 04/23/2018 11:46:38 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/PSMA265J_unmatched_1.fastq ): 1921158 04/23/2018 11:46:39 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/PSMA265J_Homo_sapiens_bowtie2_unmatched_2_clean.fastq ): 371063 04/23/2018 11:46:39 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/PSMA265J_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_2_clean.fastq ): 368549 04/23/2018 11:46:42 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/PSMA265J_human_hg38_refMrna_bowtie2_unmatched_2_clean.fastq ): 367420 04/23/2018 11:46:45 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/PSMA265J_unmatched_2.fastq ): 365180 04/23/2018 11:47:05 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/PSMA265J.fastq