03/21/2018 01:49:40 PM - kneaddata.knead_data - INFO: Running kneaddata v0.7.0 03/21/2018 01:49:40 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 01:49:40 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/MSMB4LZR.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/MSMB4LZR_R1.fastq.gz /n/regal/huttenhower_lab/carze/data/hmp2/workflow/deposition/HMP2/2018-03-20/MTX/MSMB4LZR_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 = MSMB4LZR match = 2 03/21/2018 01:49:40 PM - kneaddata.utilities - INFO: Decompressing gzipped file ... 03/21/2018 01:49:50 PM - kneaddata.utilities - INFO: Decompressed file created: /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/decompressed_hMccLB_MSMB4LZR_R1.fastq 03/21/2018 01:49:50 PM - kneaddata.utilities - INFO: Decompressing gzipped file ... 03/21/2018 01:50:06 PM - kneaddata.utilities - INFO: Decompressed file created: /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/decompressed_IBDvHp_MSMB4LZR_R2.fastq 03/21/2018 01:50:06 PM - kneaddata.utilities - INFO: Reformatting file sequence identifiers ... 03/21/2018 01:50:23 PM - kneaddata.utilities - INFO: Reformatting file sequence identifiers ... 03/21/2018 01:50:45 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_identifiers0hnfAq_decompressed_IBDvHp_MSMB4LZR_R2 ): 6741909 03/21/2018 01:50:48 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_identifiersbfHyGi_decompressed_hMccLB_MSMB4LZR_R1 ): 6741909 03/21/2018 01:50:48 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_identifiersbfHyGi_decompressed_hMccLB_MSMB4LZR_R1 03/21/2018 01:50:48 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_identifiers0hnfAq_decompressed_IBDvHp_MSMB4LZR_R2 03/21/2018 01:50:48 PM - kneaddata.utilities - INFO: Running Trimmomatic ... 03/21/2018 01:50:48 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_identifiersbfHyGi_decompressed_hMccLB_MSMB4LZR_R1 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/reformatted_identifiers0hnfAq_decompressed_IBDvHp_MSMB4LZR_R2 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/MSMB4LZR.trimmed.1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/MSMB4LZR.trimmed.single.1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/MSMB4LZR.trimmed.2.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/MSMB4LZR.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 01:52:49 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_identifiersbfHyGi_decompressed_hMccLB_MSMB4LZR_R1 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/reformatted_identifiers0hnfAq_decompressed_IBDvHp_MSMB4LZR_R2 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/MSMB4LZR.trimmed.1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/MSMB4LZR.trimmed.single.1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/MSMB4LZR.trimmed.2.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/MSMB4LZR.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: 6741909 Both Surviving: 4357545 (64.63%) Forward Only Surviving: 1292401 (19.17%) Reverse Only Surviving: 166002 (2.46%) Dropped: 925961 (13.73%) TrimmomaticPE: Completed successfully 03/21/2018 01:52:49 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/MSMB4LZR.trimmed.1.fastq 03/21/2018 01:52:49 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/MSMB4LZR.trimmed.single.1.fastq 03/21/2018 01:52:49 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/MSMB4LZR.trimmed.2.fastq 03/21/2018 01:52:49 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/MSMB4LZR.trimmed.single.2.fastq 03/21/2018 01:52:51 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/MSMB4LZR.trimmed.1.fastq ): 4357545 03/21/2018 01:52:52 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/MSMB4LZR.trimmed.2.fastq ): 4357545 03/21/2018 01:52:53 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/MSMB4LZR.trimmed.single.1.fastq ): 1292401 03/21/2018 01:52:53 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/MSMB4LZR.trimmed.single.2.fastq ): 166002 03/21/2018 01:52:53 PM - kneaddata.run - INFO: Decontaminating ... 03/21/2018 01:52:58 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/MSMB4LZR.trimmed.1.fastq 03/21/2018 01:52:58 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/MSMB4LZR.trimmed.2.fastq 03/21/2018 01:52:58 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/MSMB4LZR.trimmed.single.1.fastq 03/21/2018 01:52:58 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/MSMB4LZR.trimmed.single.2.fastq 03/21/2018 01:52:58 PM - kneaddata.utilities - INFO: Running bowtie2 ... 03/21/2018 01:52:58 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/MSMB4LZR.trimmed.1.fastq -2 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/MSMB4LZR.trimmed.2.fastq --un-pair /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/MSMB4LZR_Homo_sapiens_bowtie2_paired_clean_%.fastq --al-pair /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/MSMB4LZR_Homo_sapiens_bowtie2_paired_contam_%.fastq -U /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/MSMB4LZR.trimmed.single.1.fastq,/n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/MSMB4LZR.trimmed.single.2.fastq --un-single /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/MSMB4LZR_Homo_sapiens_bowtie2_unmatched_%_clean.fastq --al-single /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/MSMB4LZR_Homo_sapiens_bowtie2_unmatched_%_contam.fastq -S /dev/null 03/21/2018 01:59:27 PM - kneaddata.utilities - DEBUG: 10173493 reads; of these: 10173493 (100.00%) were unpaired; of these: 9346833 (91.87%) aligned 0 times 43623 (0.43%) aligned exactly 1 time 783037 (7.70%) aligned >1 times 8.13% overall alignment rate pair1_aligned : 191262 pair2_aligned : 191262 orphan1_unaligned : 893674 orphan2_unaligned : 143965 orphan2_aligned : 33723 pair2_unaligned : 4154597 pair1_unaligned : 4154597 orphan1_aligned : 410413 03/21/2018 01:59:27 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/MSMB4LZR_Homo_sapiens_bowtie2_paired_clean_1.fastq 03/21/2018 01:59:27 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/MSMB4LZR_Homo_sapiens_bowtie2_paired_clean_2.fastq 03/21/2018 01:59:27 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/MSMB4LZR.trimmed.1.fastq 03/21/2018 01:59:27 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/MSMB4LZR.trimmed.2.fastq 03/21/2018 01:59:27 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/MSMB4LZR.trimmed.single.1.fastq 03/21/2018 01:59:27 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/MSMB4LZR.trimmed.single.2.fastq 03/21/2018 01:59:27 PM - kneaddata.utilities - INFO: Running bowtie2 ... 03/21/2018 01:59:27 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/MSMB4LZR_Homo_sapiens_bowtie2_paired_clean_1.fastq -2 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/MSMB4LZR_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/MSMB4LZR_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/MSMB4LZR_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/MSMB4LZR_Homo_sapiens_bowtie2_unmatched_1_clean.fastq,/n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/MSMB4LZR_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/MSMB4LZR_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/MSMB4LZR_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_%_contam.fastq -S /dev/null 03/21/2018 02:04:30 PM - kneaddata.utilities - DEBUG: 9346833 reads; of these: 9346833 (100.00%) were unpaired; of these: 9338349 (99.91%) aligned 0 times 773 (0.01%) aligned exactly 1 time 7711 (0.08%) aligned >1 times 0.09% overall alignment rate pair1_aligned : 223 pair2_aligned : 223 orphan1_unaligned : 890579 orphan2_unaligned : 142278 orphan2_aligned : 3315 pair2_unaligned : 4152746 pair1_unaligned : 4152746 orphan1_aligned : 4723 03/21/2018 02:04:30 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/MSMB4LZR_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_clean_1.fastq 03/21/2018 02:04:30 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/MSMB4LZR_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_clean_2.fastq 03/21/2018 02:04:30 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/MSMB4LZR.trimmed.1.fastq 03/21/2018 02:04:30 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/MSMB4LZR.trimmed.2.fastq 03/21/2018 02:04:30 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/MSMB4LZR.trimmed.single.1.fastq 03/21/2018 02:04:30 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/MSMB4LZR.trimmed.single.2.fastq 03/21/2018 02:04:30 PM - kneaddata.utilities - INFO: Running bowtie2 ... 03/21/2018 02:04:30 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/MSMB4LZR_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/MSMB4LZR_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/MSMB4LZR_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/MSMB4LZR_human_hg38_refMrna_bowtie2_paired_contam_%.fastq -U /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-03-20/MTX/kneaddata/main/MSMB4LZR_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/MSMB4LZR_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/MSMB4LZR_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/MSMB4LZR_human_hg38_refMrna_bowtie2_unmatched_%_contam.fastq -S /dev/null 03/21/2018 02:07:59 PM - kneaddata.utilities - DEBUG: 9338349 reads; of these: 9338349 (100.00%) were unpaired; of these: 9335058 (99.96%) aligned 0 times 1030 (0.01%) aligned exactly 1 time 2261 (0.02%) aligned >1 times 0.04% overall alignment rate pair1_aligned : 364 pair2_aligned : 364 orphan1_unaligned : 889461 orphan2_unaligned : 140977 orphan2_aligned : 1373 pair2_unaligned : 4152310 pair1_unaligned : 4152310 orphan1_aligned : 1190 03/21/2018 02:07:59 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/MSMB4LZR_human_hg38_refMrna_bowtie2_paired_clean_1.fastq 03/21/2018 02:07:59 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/MSMB4LZR_human_hg38_refMrna_bowtie2_paired_clean_2.fastq 03/21/2018 02:08:00 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/MSMB4LZR_Homo_sapiens_bowtie2_paired_contam_1.fastq ) : 191262 03/21/2018 02:08:01 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/MSMB4LZR_Homo_sapiens_bowtie2_paired_contam_2.fastq ) : 191262 03/21/2018 02:08:02 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/MSMB4LZR_Homo_sapiens_bowtie2_unmatched_1_contam.fastq ) : 410413 03/21/2018 02:08:02 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/MSMB4LZR_Homo_sapiens_bowtie2_unmatched_2_contam.fastq ) : 33723 03/21/2018 02:08:02 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/MSMB4LZR_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_contam_1.fastq ) : 223 03/21/2018 02:08:02 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/MSMB4LZR_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_contam_2.fastq ) : 223 03/21/2018 02:08:02 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/MSMB4LZR_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_1_contam.fastq ) : 4723 03/21/2018 02:08:02 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/MSMB4LZR_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_2_contam.fastq ) : 3315 03/21/2018 02:08:02 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/MSMB4LZR_human_hg38_refMrna_bowtie2_paired_contam_1.fastq ) : 364 03/21/2018 02:08:02 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/MSMB4LZR_human_hg38_refMrna_bowtie2_paired_contam_2.fastq ) : 364 03/21/2018 02:08:02 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/MSMB4LZR_human_hg38_refMrna_bowtie2_unmatched_1_contam.fastq ) : 1190 03/21/2018 02:08:02 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/MSMB4LZR_human_hg38_refMrna_bowtie2_unmatched_2_contam.fastq ) : 1373 03/21/2018 02:08:21 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/MSMB4LZR_Homo_sapiens_bowtie2_paired_clean_1.fastq ): 4154597 03/21/2018 02:08:28 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/MSMB4LZR_Homo_sapiens_bowtie2_paired_clean_2.fastq ): 4154597 03/21/2018 02:08:29 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/MSMB4LZR_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_clean_1.fastq ): 4152746 03/21/2018 02:08:31 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/MSMB4LZR_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_clean_2.fastq ): 4152746 03/21/2018 02:08:33 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/MSMB4LZR_human_hg38_refMrna_bowtie2_paired_clean_1.fastq ): 4152310 03/21/2018 02:08:35 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/MSMB4LZR_human_hg38_refMrna_bowtie2_paired_clean_2.fastq ): 4152310 03/21/2018 02:10:14 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/MSMB4LZR_paired_1.fastq ): 4152310 03/21/2018 02:10:15 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/MSMB4LZR_paired_2.fastq ): 4152310 03/21/2018 02:10:16 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/MSMB4LZR_Homo_sapiens_bowtie2_unmatched_1_clean.fastq ): 893674 03/21/2018 02:10:16 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/MSMB4LZR_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_1_clean.fastq ): 890579 03/21/2018 02:10:17 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/MSMB4LZR_human_hg38_refMrna_bowtie2_unmatched_1_clean.fastq ): 889461 03/21/2018 02:10:24 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/MSMB4LZR_unmatched_1.fastq ): 888434 03/21/2018 02:10:24 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/MSMB4LZR_Homo_sapiens_bowtie2_unmatched_2_clean.fastq ): 143965 03/21/2018 02:10:24 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/MSMB4LZR_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_2_clean.fastq ): 142278 03/21/2018 02:10:24 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/MSMB4LZR_human_hg38_refMrna_bowtie2_unmatched_2_clean.fastq ): 140977 03/21/2018 02:10:25 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/MSMB4LZR_unmatched_2.fastq ): 140358 03/21/2018 02:10:45 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/MSMB4LZR.fastq