04/23/2018 11:01:08 AM - kneaddata.knead_data - INFO: Running kneaddata v0.7.0 04/23/2018 11:01:08 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 11:01:08 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/HSM67VH1.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/HSM67VH1_R1.fastq.gz /n/regal/huttenhower_lab/carze/data/hmp2/workflow/deposition/HMP2/2018-04-23/MTX/HSM67VH1_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 = HSM67VH1 match = 2 04/23/2018 11:01:08 AM - kneaddata.utilities - INFO: Decompressing gzipped file ... 04/23/2018 11:01:34 AM - kneaddata.utilities - INFO: Decompressed file created: /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/decompressed_1gzrhm_HSM67VH1_R1.fastq 04/23/2018 11:01:34 AM - kneaddata.utilities - INFO: Decompressing gzipped file ... 04/23/2018 11:02:19 AM - kneaddata.utilities - INFO: Decompressed file created: /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/decompressed_MHeUbT_HSM67VH1_R2.fastq 04/23/2018 11:02:19 AM - kneaddata.utilities - INFO: Reformatting file sequence identifiers ... 04/23/2018 11:03:08 AM - kneaddata.utilities - INFO: Reformatting file sequence identifiers ... 04/23/2018 11:04:12 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_identifiers5A_Gns_decompressed_MHeUbT_HSM67VH1_R2 ): 16387865 04/23/2018 11:05:20 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_identifiers6YPY3__decompressed_1gzrhm_HSM67VH1_R1 ): 16387865 04/23/2018 11:05:20 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_identifiers6YPY3__decompressed_1gzrhm_HSM67VH1_R1 04/23/2018 11:05:20 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_identifiers5A_Gns_decompressed_MHeUbT_HSM67VH1_R2 04/23/2018 11:05:20 AM - kneaddata.utilities - INFO: Running Trimmomatic ... 04/23/2018 11:05:20 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_identifiers6YPY3__decompressed_1gzrhm_HSM67VH1_R1 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/reformatted_identifiers5A_Gns_decompressed_MHeUbT_HSM67VH1_R2 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM67VH1.trimmed.1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM67VH1.trimmed.single.1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM67VH1.trimmed.2.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM67VH1.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 11:07:57 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_identifiers6YPY3__decompressed_1gzrhm_HSM67VH1_R1 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/reformatted_identifiers5A_Gns_decompressed_MHeUbT_HSM67VH1_R2 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM67VH1.trimmed.1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM67VH1.trimmed.single.1.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM67VH1.trimmed.2.fastq /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM67VH1.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: 16387865 Both Surviving: 11429214 (69.74%) Forward Only Surviving: 2490254 (15.20%) Reverse Only Surviving: 438292 (2.67%) Dropped: 2030105 (12.39%) TrimmomaticPE: Completed successfully 04/23/2018 11:07:57 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/HSM67VH1.trimmed.1.fastq 04/23/2018 11:07:57 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/HSM67VH1.trimmed.single.1.fastq 04/23/2018 11:07:57 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/HSM67VH1.trimmed.2.fastq 04/23/2018 11:07:57 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/HSM67VH1.trimmed.single.2.fastq 04/23/2018 11:08:07 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/HSM67VH1.trimmed.1.fastq ): 11429214 04/23/2018 11:08:17 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/HSM67VH1.trimmed.2.fastq ): 11429214 04/23/2018 11:08:19 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/HSM67VH1.trimmed.single.1.fastq ): 2490254 04/23/2018 11:08:20 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/HSM67VH1.trimmed.single.2.fastq ): 438292 04/23/2018 11:08:20 AM - kneaddata.run - INFO: Decontaminating ... 04/23/2018 11:08:25 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/HSM67VH1.trimmed.1.fastq 04/23/2018 11:08:25 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/HSM67VH1.trimmed.2.fastq 04/23/2018 11:08:25 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/HSM67VH1.trimmed.single.1.fastq 04/23/2018 11:08:25 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/HSM67VH1.trimmed.single.2.fastq 04/23/2018 11:08:25 AM - kneaddata.utilities - INFO: Running bowtie2 ... 04/23/2018 11:08:25 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/HSM67VH1.trimmed.1.fastq -2 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM67VH1.trimmed.2.fastq --un-pair /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM67VH1_Homo_sapiens_bowtie2_paired_clean_%.fastq --al-pair /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM67VH1_Homo_sapiens_bowtie2_paired_contam_%.fastq -U /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM67VH1.trimmed.single.1.fastq,/n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM67VH1.trimmed.single.2.fastq --un-single /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM67VH1_Homo_sapiens_bowtie2_unmatched_%_clean.fastq --al-single /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM67VH1_Homo_sapiens_bowtie2_unmatched_%_contam.fastq -S /dev/null 04/23/2018 11:18:54 AM - kneaddata.utilities - DEBUG: 25786974 reads; of these: 25786974 (100.00%) were unpaired; of these: 25306643 (98.14%) aligned 0 times 7929 (0.03%) aligned exactly 1 time 472402 (1.83%) aligned >1 times 1.86% overall alignment rate pair1_aligned : 73732 pair2_aligned : 73732 orphan1_unaligned : 2180792 orphan2_unaligned : 420133 orphan2_aligned : 20782 pair2_unaligned : 11352859 pair1_unaligned : 11352859 orphan1_aligned : 312085 04/23/2018 11:18:54 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/HSM67VH1_Homo_sapiens_bowtie2_paired_clean_1.fastq 04/23/2018 11:18:54 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/HSM67VH1_Homo_sapiens_bowtie2_paired_clean_2.fastq 04/23/2018 11:18:54 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/HSM67VH1.trimmed.1.fastq 04/23/2018 11:18:54 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/HSM67VH1.trimmed.2.fastq 04/23/2018 11:18:54 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/HSM67VH1.trimmed.single.1.fastq 04/23/2018 11:18:54 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/HSM67VH1.trimmed.single.2.fastq 04/23/2018 11:18:54 AM - kneaddata.utilities - INFO: Running bowtie2 ... 04/23/2018 11:18:54 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/HSM67VH1_Homo_sapiens_bowtie2_paired_clean_1.fastq -2 /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM67VH1_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/HSM67VH1_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/HSM67VH1_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/HSM67VH1_Homo_sapiens_bowtie2_unmatched_1_clean.fastq,/n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM67VH1_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/HSM67VH1_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/HSM67VH1_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_%_contam.fastq -S /dev/null 04/23/2018 11:28:44 AM - kneaddata.utilities - DEBUG: 25306643 reads; of these: 25306643 (100.00%) were unpaired; of these: 25293827 (99.95%) aligned 0 times 1897 (0.01%) aligned exactly 1 time 10919 (0.04%) aligned >1 times 0.05% overall alignment rate pair1_aligned : 1786 pair2_aligned : 1786 orphan1_unaligned : 2178759 orphan2_unaligned : 419026 orphan2_aligned : 4159 pair2_unaligned : 11348021 pair1_unaligned : 11348021 orphan1_aligned : 5085 04/23/2018 11:28:44 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/HSM67VH1_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_clean_1.fastq 04/23/2018 11:28:44 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/HSM67VH1_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_clean_2.fastq 04/23/2018 11:28:44 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/HSM67VH1.trimmed.1.fastq 04/23/2018 11:28:44 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/HSM67VH1.trimmed.2.fastq 04/23/2018 11:28:44 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/HSM67VH1.trimmed.single.1.fastq 04/23/2018 11:28:44 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/HSM67VH1.trimmed.single.2.fastq 04/23/2018 11:28:44 AM - kneaddata.utilities - INFO: Running bowtie2 ... 04/23/2018 11:28:44 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/HSM67VH1_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/HSM67VH1_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/HSM67VH1_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/HSM67VH1_human_hg38_refMrna_bowtie2_paired_contam_%.fastq -U /n/regal/huttenhower_lab/carze/data/hmp2/workflow/processing/HMP2/2018-04-23/MTX/kneaddata/main/HSM67VH1_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/HSM67VH1_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/HSM67VH1_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/HSM67VH1_human_hg38_refMrna_bowtie2_unmatched_%_contam.fastq -S /dev/null 04/23/2018 11:36:02 AM - kneaddata.utilities - DEBUG: 25293827 reads; of these: 25293827 (100.00%) were unpaired; of these: 25292692 (100.00%) aligned 0 times 159 (0.00%) aligned exactly 1 time 976 (0.00%) aligned >1 times 0.00% overall alignment rate pair1_aligned : 47 pair2_aligned : 47 orphan1_unaligned : 2178590 orphan2_unaligned : 418426 orphan2_aligned : 736 pair2_unaligned : 11347838 pair1_unaligned : 11347838 orphan1_aligned : 305 04/23/2018 11:36:02 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/HSM67VH1_human_hg38_refMrna_bowtie2_paired_clean_1.fastq 04/23/2018 11:36:02 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/HSM67VH1_human_hg38_refMrna_bowtie2_paired_clean_2.fastq 04/23/2018 11:36:03 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/HSM67VH1_Homo_sapiens_bowtie2_paired_contam_1.fastq ) : 73732 04/23/2018 11:36:03 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/HSM67VH1_Homo_sapiens_bowtie2_paired_contam_2.fastq ) : 73732 04/23/2018 11:36:04 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/HSM67VH1_Homo_sapiens_bowtie2_unmatched_1_contam.fastq ) : 312085 04/23/2018 11:36:04 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/HSM67VH1_Homo_sapiens_bowtie2_unmatched_2_contam.fastq ) : 20782 04/23/2018 11:36:05 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/HSM67VH1_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_contam_1.fastq ) : 1786 04/23/2018 11:36:05 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/HSM67VH1_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_contam_2.fastq ) : 1786 04/23/2018 11:36:05 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/HSM67VH1_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_1_contam.fastq ) : 5085 04/23/2018 11:36:05 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/HSM67VH1_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_2_contam.fastq ) : 4159 04/23/2018 11:36:05 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/HSM67VH1_human_hg38_refMrna_bowtie2_paired_contam_1.fastq ) : 47 04/23/2018 11:36:05 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/HSM67VH1_human_hg38_refMrna_bowtie2_paired_contam_2.fastq ) : 47 04/23/2018 11:36:05 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/HSM67VH1_human_hg38_refMrna_bowtie2_unmatched_1_contam.fastq ) : 305 04/23/2018 11:36:05 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/HSM67VH1_human_hg38_refMrna_bowtie2_unmatched_2_contam.fastq ) : 736 04/23/2018 11:36:20 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/HSM67VH1_Homo_sapiens_bowtie2_paired_clean_1.fastq ): 11352859 04/23/2018 11:36:31 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/HSM67VH1_Homo_sapiens_bowtie2_paired_clean_2.fastq ): 11352859 04/23/2018 11:37:22 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/HSM67VH1_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_clean_1.fastq ): 11348021 04/23/2018 11:37:31 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/HSM67VH1_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_paired_clean_2.fastq ): 11348021 04/23/2018 11:37:45 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/HSM67VH1_human_hg38_refMrna_bowtie2_paired_clean_1.fastq ): 11347838 04/23/2018 11:38:00 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/HSM67VH1_human_hg38_refMrna_bowtie2_paired_clean_2.fastq ): 11347838 04/23/2018 11:42:26 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/HSM67VH1_paired_1.fastq ): 11347838 04/23/2018 11:42:31 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/HSM67VH1_paired_2.fastq ): 11347838 04/23/2018 11:42:34 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/HSM67VH1_Homo_sapiens_bowtie2_unmatched_1_clean.fastq ): 2180792 04/23/2018 11:42:37 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/HSM67VH1_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_1_clean.fastq ): 2178759 04/23/2018 11:42:40 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/HSM67VH1_human_hg38_refMrna_bowtie2_unmatched_1_clean.fastq ): 2178590 04/23/2018 11:43:00 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/HSM67VH1_unmatched_1.fastq ): 2176765 04/23/2018 11:43:01 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/HSM67VH1_Homo_sapiens_bowtie2_unmatched_2_clean.fastq ): 420133 04/23/2018 11:43:01 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/HSM67VH1_SILVA_128_LSUParc_SSUParc_ribosomal_RNA_bowtie2_unmatched_2_clean.fastq ): 419026 04/23/2018 11:43:04 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/HSM67VH1_human_hg38_refMrna_bowtie2_unmatched_2_clean.fastq ): 418426 04/23/2018 11:43:08 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/HSM67VH1_unmatched_2.fastq ): 417106 04/23/2018 11:43:45 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/HSM67VH1.fastq