03/21/2018 02:21:48 PM - kneaddata.knead_data - INFO: Running kneaddata v0.7.0 03/21/2018 02:21:48 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 02:21:48 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/MSM79HBB.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/MSM79HBB_R1.fastq.gz /n/regal/huttenhower_lab/carze/data/hmp2/workflow/deposition/HMP2/2018-03-20/MTX/MSM79HBB_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 = MSM79HBB match = 2 03/21/2018 02:21:48 PM - kneaddata.utilities - INFO: Decompressing gzipped file ... 03/21/2018 02:22:31 PM - kneaddata.utilities - INFO: Decompressed file created: /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/decompressed_XiBtfe_MSM79HBB_R1.fastq 03/21/2018 02:22:31 PM - kneaddata.utilities - INFO: Decompressing gzipped file ... 03/21/2018 02:30:33 PM - kneaddata.utilities - INFO: Decompressed file created: /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/decompressed_vRTxm2_MSM79HBB_R2.fastq 03/21/2018 02:30:33 PM - kneaddata.utilities - INFO: Reformatting file sequence identifiers ... 03/21/2018 02:33:39 PM - kneaddata.utilities - INFO: Reformatting file sequence identifiers ... 03/21/2018 02:39:00 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_identifiersGaVCk0_decompressed_vRTxm2_MSM79HBB_R2 ): 19105227 03/21/2018 02:40:26 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_identifiersjOxqUT_decompressed_XiBtfe_MSM79HBB_R1 ): 19105227 03/21/2018 02:40:26 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_identifiersjOxqUT_decompressed_XiBtfe_MSM79HBB_R1 03/21/2018 02:40:26 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_identifiersGaVCk0_decompressed_vRTxm2_MSM79HBB_R2 03/21/2018 02:40:26 PM - kneaddata.utilities - INFO: Running Trimmomatic ... 03/21/2018 02:40:26 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_identifiersjOxqUT_decompressed_XiBtfe_MSM79HBB_R1 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/reformatted_identifiersGaVCk0_decompressed_vRTxm2_MSM79HBB_R2 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/MSM79HBB.trimmed.1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/MSM79HBB.trimmed.single.1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/MSM79HBB.trimmed.2.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/MSM79HBB.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 02:47:09 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_identifiersjOxqUT_decompressed_XiBtfe_MSM79HBB_R1 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/reformatted_identifiersGaVCk0_decompressed_vRTxm2_MSM79HBB_R2 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/MSM79HBB.trimmed.1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/MSM79HBB.trimmed.single.1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/MSM79HBB.trimmed.2.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/MSM79HBB.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: 19105227 Both Surviving: 9465255 (49.54%) Forward Only Surviving: 4556058 (23.85%) Reverse Only Surviving: 1053898 (5.52%) Dropped: 4030016 (21.09%) TrimmomaticPE: Completed successfully 03/21/2018 02:47:09 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/MSM79HBB.trimmed.1.fastq 03/21/2018 02:47:09 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/MSM79HBB.trimmed.single.1.fastq 03/21/2018 02:47:09 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/MSM79HBB.trimmed.2.fastq 03/21/2018 02:47:09 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/MSM79HBB.trimmed.single.2.fastq 03/21/2018 02:47:38 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/MSM79HBB.trimmed.1.fastq ): 9465255 03/21/2018 02:47:54 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/MSM79HBB.trimmed.2.fastq ): 9465255 03/21/2018 02:48:02 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/MSM79HBB.trimmed.single.1.fastq ): 4556058 03/21/2018 02:48:04 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/MSM79HBB.trimmed.single.2.fastq ): 1053898 03/21/2018 02:48:04 PM - kneaddata.run - INFO: Decontaminating ... 03/21/2018 02:48:09 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/MSM79HBB.trimmed.1.fastq 03/21/2018 02:48:09 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/MSM79HBB.trimmed.2.fastq 03/21/2018 02:48:09 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/MSM79HBB.trimmed.single.1.fastq 03/21/2018 02:48:09 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/MSM79HBB.trimmed.single.2.fastq 03/21/2018 02:48:09 PM - kneaddata.utilities - INFO: Running bowtie2 ... 03/21/2018 02:48:09 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/MSM79HBB.trimmed.1.fastq -2 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/MSM79HBB.trimmed.2.fastq --un-pair /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/MSM79HBB_Homo_sapiens_bowtie2_paired_clean_%.fastq --al-pair /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/MSM79HBB_Homo_sapiens_bowtie2_paired_contam_%.fastq -U /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/MSM79HBB.trimmed.single.1.fastq,/n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/MSM79HBB.trimmed.single.2.fastq --un-single /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/MSM79HBB_Homo_sapiens_bowtie2_unmatched_%_clean.fastq --al-single /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/MSM79HBB_Homo_sapiens_bowtie2_unmatched_%_contam.fastq -S /dev/null 03/21/2018 03:03:01 PM - kneaddata.utilities - DEBUG: 24540466 reads; of these: 24540466 (100.00%) were unpaired; of these: 24287205 (98.97%) aligned 0 times 14746 (0.06%) aligned exactly 1 time 238515 (0.97%) aligned >1 times 1.03% overall alignment rate pair1_aligned : 77424 pair2_aligned : 77424 orphan1_unaligned : 4482032 orphan2_unaligned : 1040327 orphan2_aligned : 18979 pair2_unaligned : 9382423 pair1_unaligned : 9382423 orphan1_aligned : 79434 03/21/2018 03:03:01 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/MSM79HBB_Homo_sapiens_bowtie2_paired_clean_1.fastq 03/21/2018 03:03:01 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/MSM79HBB_Homo_sapiens_bowtie2_paired_clean_2.fastq 03/21/2018 03:03:01 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/MSM79HBB.trimmed.1.fastq 03/21/2018 03:03:01 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/MSM79HBB.trimmed.2.fastq 03/21/2018 03:03:01 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/MSM79HBB.trimmed.single.1.fastq 03/21/2018 03:03:01 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/MSM79HBB.trimmed.single.2.fastq 03/21/2018 03:03:01 PM - kneaddata.utilities - INFO: Running bowtie2 ... 03/21/2018 03:03:01 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/MSM79HBB_Homo_sapiens_bowtie2_paired_clean_1.fastq -2 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/MSM79HBB_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/MSM79HBB_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/MSM79HBB_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/MSM79HBB_Homo_sapiens_bowtie2_unmatched_1_clean.fastq,/n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/MSM79HBB_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/MSM79HBB_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/MSM79HBB_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_%_contam.fastq -S /dev/null 03/21/2018 03:17:44 PM - kneaddata.utilities - DEBUG: 24287205 reads; of these: 24287205 (100.00%) were unpaired; of these: 24269551 (99.93%) aligned 0 times 2955 (0.01%) aligned exactly 1 time 14699 (0.06%) aligned >1 times 0.07% overall alignment rate pair1_aligned : 1173 pair2_aligned : 1173 orphan1_unaligned : 4480992 orphan2_unaligned : 1037867 orphan2_aligned : 8364 pair2_unaligned : 9375346 pair1_unaligned : 9375346 orphan1_aligned : 6944 03/21/2018 03:17:44 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/MSM79HBB_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_clean_1.fastq 03/21/2018 03:17:44 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/MSM79HBB_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_clean_2.fastq 03/21/2018 03:17:44 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/MSM79HBB.trimmed.1.fastq 03/21/2018 03:17:44 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/MSM79HBB.trimmed.2.fastq 03/21/2018 03:17:44 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/MSM79HBB.trimmed.single.1.fastq 03/21/2018 03:17:44 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/MSM79HBB.trimmed.single.2.fastq 03/21/2018 03:17:44 PM - kneaddata.utilities - INFO: Running bowtie2 ... 03/21/2018 03:17:44 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/MSM79HBB_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/MSM79HBB_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/MSM79HBB_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/MSM79HBB_human_hg38_refMrna_bowtie2_paired_contam_%.fastq -U /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/MSM79HBB_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/MSM79HBB_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/MSM79HBB_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/MSM79HBB_human_hg38_refMrna_bowtie2_unmatched_%_contam.fastq -S /dev/null 03/21/2018 03:34:11 PM - kneaddata.utilities - DEBUG: 24269551 reads; of these: 24269551 (100.00%) were unpaired; of these: 24267198 (99.99%) aligned 0 times 469 (0.00%) aligned exactly 1 time 1884 (0.01%) aligned >1 times 0.01% overall alignment rate pair1_aligned : 110 pair2_aligned : 110 orphan1_unaligned : 4480878 orphan2_unaligned : 1036212 orphan2_aligned : 1837 pair2_unaligned : 9375054 pair1_unaligned : 9375054 orphan1_aligned : 296 03/21/2018 03:34:11 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/MSM79HBB_human_hg38_refMrna_bowtie2_paired_clean_1.fastq 03/21/2018 03:34:11 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/MSM79HBB_human_hg38_refMrna_bowtie2_paired_clean_2.fastq 03/21/2018 03:34:12 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/MSM79HBB_Homo_sapiens_bowtie2_paired_contam_1.fastq ) : 77424 03/21/2018 03:34:16 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/MSM79HBB_Homo_sapiens_bowtie2_paired_contam_2.fastq ) : 77424 03/21/2018 03:34:18 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/MSM79HBB_Homo_sapiens_bowtie2_unmatched_1_contam.fastq ) : 79434 03/21/2018 03:34:18 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/MSM79HBB_Homo_sapiens_bowtie2_unmatched_2_contam.fastq ) : 18979 03/21/2018 03:34:18 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/MSM79HBB_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_contam_1.fastq ) : 1173 03/21/2018 03:34:19 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/MSM79HBB_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_contam_2.fastq ) : 1173 03/21/2018 03:34:20 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/MSM79HBB_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_1_contam.fastq ) : 6944 03/21/2018 03:34:20 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/MSM79HBB_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_2_contam.fastq ) : 8364 03/21/2018 03:34:20 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/MSM79HBB_human_hg38_refMrna_bowtie2_paired_contam_1.fastq ) : 110 03/21/2018 03:34:20 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/MSM79HBB_human_hg38_refMrna_bowtie2_paired_contam_2.fastq ) : 110 03/21/2018 03:34:20 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/MSM79HBB_human_hg38_refMrna_bowtie2_unmatched_1_contam.fastq ) : 296 03/21/2018 03:34:20 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/MSM79HBB_human_hg38_refMrna_bowtie2_unmatched_2_contam.fastq ) : 1837 03/21/2018 03:34:47 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/MSM79HBB_Homo_sapiens_bowtie2_paired_clean_1.fastq ): 9382423 03/21/2018 03:35:32 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/MSM79HBB_Homo_sapiens_bowtie2_paired_clean_2.fastq ): 9382423 03/21/2018 03:37:53 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/MSM79HBB_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_clean_1.fastq ): 9375346 03/21/2018 03:38:21 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/MSM79HBB_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_clean_2.fastq ): 9375346 03/21/2018 03:38:51 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/MSM79HBB_human_hg38_refMrna_bowtie2_paired_clean_1.fastq ): 9375054 03/21/2018 03:39:03 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/MSM79HBB_human_hg38_refMrna_bowtie2_paired_clean_2.fastq ): 9375054 03/21/2018 03:47:22 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/MSM79HBB_paired_1.fastq ): 9375054 03/21/2018 03:47:26 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/MSM79HBB_paired_2.fastq ): 9375054 03/21/2018 03:48:33 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/MSM79HBB_Homo_sapiens_bowtie2_unmatched_1_clean.fastq ): 4482032 03/21/2018 03:48:41 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/MSM79HBB_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_1_clean.fastq ): 4480992 03/21/2018 03:49:35 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/MSM79HBB_human_hg38_refMrna_bowtie2_unmatched_1_clean.fastq ): 4480878 03/21/2018 03:50:15 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/MSM79HBB_unmatched_1.fastq ): 4477522 03/21/2018 03:50:17 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/MSM79HBB_Homo_sapiens_bowtie2_unmatched_2_clean.fastq ): 1040327 03/21/2018 03:50:19 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/MSM79HBB_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_2_clean.fastq ): 1037867 03/21/2018 03:50:23 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/MSM79HBB_human_hg38_refMrna_bowtie2_unmatched_2_clean.fastq ): 1036212 03/21/2018 03:50:50 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/MSM79HBB_unmatched_2.fastq ): 1033605 03/21/2018 03:52:23 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/MSM79HBB.fastq