04/23/2018 11:01:07 AM - kneaddata.knead_data - INFO: Running kneaddata v0.7.0 04/23/2018 11:01:07 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 11:01:07 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/PSMA266U.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/PSMA266U_R1.fastq.gz /n/regal/huttenhower_lab/carze/data/hmp2/workflow/deposition/HMP2/2018-04-23/MTX/PSMA266U_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 = PSMA266U match = 2 04/23/2018 11:01:07 AM - kneaddata.utilities - INFO: Decompressing gzipped file ... 04/23/2018 11:01:46 AM - kneaddata.utilities - INFO: Decompressed file created: /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/decompressed_Ua6Tjv_PSMA266U_R1.fastq 04/23/2018 11:01:46 AM - kneaddata.utilities - INFO: Decompressing gzipped file ... 04/23/2018 11:02:38 AM - kneaddata.utilities - INFO: Decompressed file created: /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/decompressed_JJmbzz_PSMA266U_R2.fastq 04/23/2018 11:02:38 AM - kneaddata.utilities - INFO: Reformatting file sequence identifiers ... 04/23/2018 11:04:35 AM - kneaddata.utilities - INFO: Reformatting file sequence identifiers ... 04/23/2018 11:06:25 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_identifiersP6_aAE_decompressed_Ua6Tjv_PSMA266U_R1 ): 18516951 04/23/2018 11:06:36 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_identifiersTUhAfD_decompressed_JJmbzz_PSMA266U_R2 ): 18516951 04/23/2018 11:06:36 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_identifiersP6_aAE_decompressed_Ua6Tjv_PSMA266U_R1 04/23/2018 11:06:36 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_identifiersTUhAfD_decompressed_JJmbzz_PSMA266U_R2 04/23/2018 11:06:36 AM - kneaddata.utilities - INFO: Running Trimmomatic ... 04/23/2018 11:06:36 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_identifiersP6_aAE_decompressed_Ua6Tjv_PSMA266U_R1 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/reformatted_identifiersTUhAfD_decompressed_JJmbzz_PSMA266U_R2 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/PSMA266U.trimmed.1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/PSMA266U.trimmed.single.1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/PSMA266U.trimmed.2.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/PSMA266U.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 11:10:04 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_identifiersP6_aAE_decompressed_Ua6Tjv_PSMA266U_R1 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/reformatted_identifiersTUhAfD_decompressed_JJmbzz_PSMA266U_R2 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/PSMA266U.trimmed.1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/PSMA266U.trimmed.single.1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/PSMA266U.trimmed.2.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/PSMA266U.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: 18516951 Both Surviving: 9864145 (53.27%) Forward Only Surviving: 6279590 (33.91%) Reverse Only Surviving: 350399 (1.89%) Dropped: 2022817 (10.92%) TrimmomaticPE: Completed successfully 04/23/2018 11:10:04 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/PSMA266U.trimmed.1.fastq 04/23/2018 11:10:04 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/PSMA266U.trimmed.single.1.fastq 04/23/2018 11:10:04 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/PSMA266U.trimmed.2.fastq 04/23/2018 11:10:04 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/PSMA266U.trimmed.single.2.fastq 04/23/2018 11:10:15 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/PSMA266U.trimmed.1.fastq ): 9864145 04/23/2018 11:10:27 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/PSMA266U.trimmed.2.fastq ): 9864145 04/23/2018 11:10:35 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/PSMA266U.trimmed.single.1.fastq ): 6279590 04/23/2018 11:10:35 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/PSMA266U.trimmed.single.2.fastq ): 350399 04/23/2018 11:10:35 AM - kneaddata.run - INFO: Decontaminating ... 04/23/2018 11:10:40 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/PSMA266U.trimmed.1.fastq 04/23/2018 11:10:40 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/PSMA266U.trimmed.2.fastq 04/23/2018 11:10:40 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/PSMA266U.trimmed.single.1.fastq 04/23/2018 11:10:40 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/PSMA266U.trimmed.single.2.fastq 04/23/2018 11:10:40 AM - kneaddata.utilities - INFO: Running bowtie2 ... 04/23/2018 11:10:40 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/PSMA266U.trimmed.1.fastq -2 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/PSMA266U.trimmed.2.fastq --un-pair /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/PSMA266U_Homo_sapiens_bowtie2_paired_clean_%.fastq --al-pair /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/PSMA266U_Homo_sapiens_bowtie2_paired_contam_%.fastq -U /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/PSMA266U.trimmed.single.1.fastq,/n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/PSMA266U.trimmed.single.2.fastq --un-single /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/PSMA266U_Homo_sapiens_bowtie2_unmatched_%_clean.fastq --al-single /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/PSMA266U_Homo_sapiens_bowtie2_unmatched_%_contam.fastq -S /dev/null 04/23/2018 11:23:42 AM - kneaddata.utilities - DEBUG: 26358279 reads; of these: 26358279 (100.00%) were unpaired; of these: 22741395 (86.28%) aligned 0 times 48904 (0.19%) aligned exactly 1 time 3567980 (13.54%) aligned >1 times 13.72% overall alignment rate pair1_aligned : 1197493 pair2_aligned : 1197493 orphan1_unaligned : 5292316 orphan2_unaligned : 150371 orphan2_aligned : 217326 pair2_unaligned : 8649354 pair1_unaligned : 8649354 orphan1_aligned : 1004572 04/23/2018 11:23:42 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/PSMA266U_Homo_sapiens_bowtie2_paired_clean_1.fastq 04/23/2018 11:23:42 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/PSMA266U_Homo_sapiens_bowtie2_paired_clean_2.fastq 04/23/2018 11:23:42 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/PSMA266U.trimmed.1.fastq 04/23/2018 11:23:42 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/PSMA266U.trimmed.2.fastq 04/23/2018 11:23:42 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/PSMA266U.trimmed.single.1.fastq 04/23/2018 11:23:42 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/PSMA266U.trimmed.single.2.fastq 04/23/2018 11:23:42 AM - kneaddata.utilities - INFO: Running bowtie2 ... 04/23/2018 11:23:42 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/PSMA266U_Homo_sapiens_bowtie2_paired_clean_1.fastq -2 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/PSMA266U_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/PSMA266U_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/PSMA266U_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/PSMA266U_Homo_sapiens_bowtie2_unmatched_1_clean.fastq,/n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/PSMA266U_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/PSMA266U_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/PSMA266U_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_%_contam.fastq -S /dev/null 04/23/2018 11:31:40 AM - kneaddata.utilities - DEBUG: 22741395 reads; of these: 22741395 (100.00%) were unpaired; of these: 22707533 (99.85%) aligned 0 times 2518 (0.01%) aligned exactly 1 time 31344 (0.14%) aligned >1 times 0.15% overall alignment rate pair1_aligned : 1542 pair2_aligned : 1542 orphan1_unaligned : 5287044 orphan2_unaligned : 138577 orphan2_aligned : 18650 pair2_unaligned : 8640956 pair1_unaligned : 8640956 orphan1_aligned : 12128 04/23/2018 11:31:40 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/PSMA266U_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_clean_1.fastq 04/23/2018 11:31:40 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/PSMA266U_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_clean_2.fastq 04/23/2018 11:31:40 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/PSMA266U.trimmed.1.fastq 04/23/2018 11:31:40 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/PSMA266U.trimmed.2.fastq 04/23/2018 11:31:40 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/PSMA266U.trimmed.single.1.fastq 04/23/2018 11:31:40 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/PSMA266U.trimmed.single.2.fastq 04/23/2018 11:31:40 AM - kneaddata.utilities - INFO: Running bowtie2 ... 04/23/2018 11:31:40 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/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/PSMA266U_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/PSMA266U_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/PSMA266U_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/PSMA266U_human_hg38_refMrna_bowtie2_paired_contam_%.fastq -U /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/PSMA266U_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/PSMA266U_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/PSMA266U_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/PSMA266U_human_hg38_refMrna_bowtie2_unmatched_%_contam.fastq -S /dev/null 04/23/2018 11:37:52 AM - kneaddata.utilities - DEBUG: 22707533 reads; of these: 22707533 (100.00%) were unpaired; of these: 22701799 (99.97%) aligned 0 times 1094 (0.00%) aligned exactly 1 time 4640 (0.02%) aligned >1 times 0.03% overall alignment rate pair1_aligned : 359 pair2_aligned : 359 orphan1_unaligned : 5285767 orphan2_unaligned : 136218 orphan2_aligned : 3049 pair2_unaligned : 8639907 pair1_unaligned : 8639907 orphan1_aligned : 1967 04/23/2018 11:37:52 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/PSMA266U_human_hg38_refMrna_bowtie2_paired_clean_1.fastq 04/23/2018 11:37:52 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/PSMA266U_human_hg38_refMrna_bowtie2_paired_clean_2.fastq 04/23/2018 11:37:55 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/PSMA266U_Homo_sapiens_bowtie2_paired_contam_1.fastq ) : 1197493 04/23/2018 11:37:57 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/PSMA266U_Homo_sapiens_bowtie2_paired_contam_2.fastq ) : 1197493 04/23/2018 11:37:59 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/PSMA266U_Homo_sapiens_bowtie2_unmatched_1_contam.fastq ) : 1004572 04/23/2018 11:38:00 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/PSMA266U_Homo_sapiens_bowtie2_unmatched_2_contam.fastq ) : 217326 04/23/2018 11:38:00 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/PSMA266U_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_contam_1.fastq ) : 1542 04/23/2018 11:38:00 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/PSMA266U_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_contam_2.fastq ) : 1542 04/23/2018 11:38:00 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/PSMA266U_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_1_contam.fastq ) : 12128 04/23/2018 11:38:01 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/PSMA266U_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_2_contam.fastq ) : 18650 04/23/2018 11:38:01 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/PSMA266U_human_hg38_refMrna_bowtie2_paired_contam_1.fastq ) : 359 04/23/2018 11:38:01 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/PSMA266U_human_hg38_refMrna_bowtie2_paired_contam_2.fastq ) : 359 04/23/2018 11:38:01 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/PSMA266U_human_hg38_refMrna_bowtie2_unmatched_1_contam.fastq ) : 1967 04/23/2018 11:38:01 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/PSMA266U_human_hg38_refMrna_bowtie2_unmatched_2_contam.fastq ) : 3049 04/23/2018 11:38:13 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/PSMA266U_Homo_sapiens_bowtie2_paired_clean_1.fastq ): 8649354 04/23/2018 11:38:31 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/PSMA266U_Homo_sapiens_bowtie2_paired_clean_2.fastq ): 8649354 04/23/2018 11:38:47 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/PSMA266U_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_clean_1.fastq ): 8640956 04/23/2018 11:38:55 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/PSMA266U_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_clean_2.fastq ): 8640956 04/23/2018 11:39:20 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/PSMA266U_human_hg38_refMrna_bowtie2_paired_clean_1.fastq ): 8639907 04/23/2018 11:39:36 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/PSMA266U_human_hg38_refMrna_bowtie2_paired_clean_2.fastq ): 8639907 04/23/2018 11:42:56 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/PSMA266U_paired_1.fastq ): 8639907 04/23/2018 11:43:00 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/PSMA266U_paired_2.fastq ): 8639907 04/23/2018 11:43:18 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/PSMA266U_Homo_sapiens_bowtie2_unmatched_1_clean.fastq ): 5292316 04/23/2018 11:43:32 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/PSMA266U_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_1_clean.fastq ): 5287044 04/23/2018 11:43:41 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/PSMA266U_human_hg38_refMrna_bowtie2_unmatched_1_clean.fastq ): 5285767 04/23/2018 11:44:24 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/PSMA266U_unmatched_1.fastq ): 5279840 04/23/2018 11:44:24 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/PSMA266U_Homo_sapiens_bowtie2_unmatched_2_clean.fastq ): 150371 04/23/2018 11:44:24 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/PSMA266U_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_2_clean.fastq ): 138577 04/23/2018 11:44:26 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/PSMA266U_human_hg38_refMrna_bowtie2_unmatched_2_clean.fastq ): 136218 04/23/2018 11:44:27 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/PSMA266U_unmatched_2.fastq ): 134931 04/23/2018 11:44:43 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/PSMA266U.fastq