08/17/2020 12:15:07 PM - kneaddata.knead_data - INFO: Running kneaddata v0.7.4 08/17/2020 12:15:07 PM - kneaddata.knead_data - INFO: Output files will be written to: /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1 08/17/2020 12:15:07 PM - kneaddata.knead_data - DEBUG: Running with the following arguments: verbose = False bmtagger_path = None minscore = 50 bowtie2_path = /home/plicht/anaconda3/envs/kneaddata_env/bin/bowtie2 maxperiod = 500 no_discordant = False serial = False fastqc_start = True bmtagger = False cat_final_output = False log_level = DEBUG log = /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata.log max_memory = 500m remove_intermediate_output = False fastqc_path = /home/plicht/anaconda3/envs/kneaddata_env/bin/fastqc output_dir = /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1 trf_path = None remove_temp_output = True reference_db = /home/plicht/KneadData_db/hg37/hg37dec_v0.1 /home/plicht/KneadData_db/phi-x174/phi-x174 input = /home/plicht/Microbiome_Data/Novogene/Validation_samples_PL018/Raw_Data/X204SC20041115-Z01-F001/raw_data/a1_1/Novogene_1_PL0182303_1_R1.fq.gz /home/plicht/Microbiome_Data/Novogene/Validation_samples_PL018/Raw_Data/X204SC20041115-Z01-F001/raw_data/a1_1/Novogene_1_PL0182303_1_R2.fq.gz pi = 10 reorder = False pm = 80 trimmomatic_path = /home/plicht/anaconda3/envs/kneaddata_env/share/trimmomatic-0.39-1/trimmomatic.jar store_temp_output = False mismatch = 7 threads = 12 delta = 7 bowtie2_options = --very-sensitive --phred33 bypass_trim = False processes = 12 trimmomatic_quality_scores = -phred33 fastqc_end = True trf = False trimmomatic_options = None output_prefix = Novogene_1_PL0182303_1_R1_kneaddata match = 2 08/17/2020 12:15:07 PM - kneaddata.utilities - INFO: Decompressing gzipped file ... 08/17/2020 12:15:32 PM - kneaddata.utilities - INFO: Decompressed file created: /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/decompressed_FkL2uI_Novogene_1_PL0182303_1_R1.fq 08/17/2020 12:15:32 PM - kneaddata.utilities - INFO: Decompressing gzipped file ... 08/17/2020 12:15:58 PM - kneaddata.utilities - INFO: Decompressed file created: /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/decompressed_ew2hSJ_Novogene_1_PL0182303_1_R2.fq 08/17/2020 12:15:58 PM - kneaddata.utilities - INFO: Reformatting file sequence identifiers ... 08/17/2020 12:16:24 PM - kneaddata.utilities - INFO: Reformatting file sequence identifiers ... 08/17/2020 12:17:53 PM - kneaddata.utilities - INFO: READ COUNT: raw pair1 : Initial number of reads ( /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/reformatted_identifiersjZn_rX_decompressed_ew2hSJ_Novogene_1_PL0182303_1_R2 ): 16164148 08/17/2020 12:17:58 PM - kneaddata.utilities - INFO: READ COUNT: raw pair2 : Initial number of reads ( /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/reformatted_identifiersxCzp0i_decompressed_FkL2uI_Novogene_1_PL0182303_1_R1 ): 16164148 08/17/2020 12:17:58 PM - kneaddata.utilities - DEBUG: Creating output directory: /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/fastqc 08/17/2020 12:17:58 PM - kneaddata.utilities - DEBUG: Checking input file to fastqc : /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/reformatted_identifiersxCzp0i_decompressed_FkL2uI_Novogene_1_PL0182303_1_R1 08/17/2020 12:17:58 PM - kneaddata.utilities - DEBUG: Checking input file to fastqc : /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/reformatted_identifiersjZn_rX_decompressed_ew2hSJ_Novogene_1_PL0182303_1_R2 08/17/2020 12:17:58 PM - kneaddata.utilities - INFO: Running fastqc ... 08/17/2020 12:17:58 PM - kneaddata.utilities - INFO: Execute command: /home/plicht/anaconda3/envs/kneaddata_env/bin/fastqc /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/reformatted_identifiersxCzp0i_decompressed_FkL2uI_Novogene_1_PL0182303_1_R1 /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/reformatted_identifiersjZn_rX_decompressed_ew2hSJ_Novogene_1_PL0182303_1_R2 --threads 12 --outdir /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/fastqc 08/17/2020 12:19:25 PM - kneaddata.utilities - DEBUG: Started analysis of reformatted_identifiersxCzp0i_decompressed_FkL2uI_Novogene_1_PL0182303_1_R1 Started analysis of reformatted_identifiersjZn_rX_decompressed_ew2hSJ_Novogene_1_PL0182303_1_R2 Approx 5% complete for reformatted_identifiersxCzp0i_decompressed_FkL2uI_Novogene_1_PL0182303_1_R1 Approx 5% complete for reformatted_identifiersjZn_rX_decompressed_ew2hSJ_Novogene_1_PL0182303_1_R2 Approx 10% complete for reformatted_identifiersxCzp0i_decompressed_FkL2uI_Novogene_1_PL0182303_1_R1 Approx 10% complete for reformatted_identifiersjZn_rX_decompressed_ew2hSJ_Novogene_1_PL0182303_1_R2 Approx 15% complete for reformatted_identifiersxCzp0i_decompressed_FkL2uI_Novogene_1_PL0182303_1_R1 Approx 15% complete for reformatted_identifiersjZn_rX_decompressed_ew2hSJ_Novogene_1_PL0182303_1_R2 Approx 20% complete for reformatted_identifiersxCzp0i_decompressed_FkL2uI_Novogene_1_PL0182303_1_R1 Approx 20% complete for reformatted_identifiersjZn_rX_decompressed_ew2hSJ_Novogene_1_PL0182303_1_R2 Approx 25% complete for reformatted_identifiersxCzp0i_decompressed_FkL2uI_Novogene_1_PL0182303_1_R1 Approx 25% complete for reformatted_identifiersjZn_rX_decompressed_ew2hSJ_Novogene_1_PL0182303_1_R2 Approx 30% complete for reformatted_identifiersxCzp0i_decompressed_FkL2uI_Novogene_1_PL0182303_1_R1 Approx 30% complete for reformatted_identifiersjZn_rX_decompressed_ew2hSJ_Novogene_1_PL0182303_1_R2 Approx 35% complete for reformatted_identifiersxCzp0i_decompressed_FkL2uI_Novogene_1_PL0182303_1_R1 Approx 35% complete for reformatted_identifiersjZn_rX_decompressed_ew2hSJ_Novogene_1_PL0182303_1_R2 Approx 40% complete for reformatted_identifiersxCzp0i_decompressed_FkL2uI_Novogene_1_PL0182303_1_R1 Approx 40% complete for reformatted_identifiersjZn_rX_decompressed_ew2hSJ_Novogene_1_PL0182303_1_R2 Approx 45% complete for reformatted_identifiersxCzp0i_decompressed_FkL2uI_Novogene_1_PL0182303_1_R1 Approx 45% complete for reformatted_identifiersjZn_rX_decompressed_ew2hSJ_Novogene_1_PL0182303_1_R2 Approx 50% complete for reformatted_identifiersxCzp0i_decompressed_FkL2uI_Novogene_1_PL0182303_1_R1 Approx 50% complete for reformatted_identifiersjZn_rX_decompressed_ew2hSJ_Novogene_1_PL0182303_1_R2 Approx 55% complete for reformatted_identifiersxCzp0i_decompressed_FkL2uI_Novogene_1_PL0182303_1_R1 Approx 55% complete for reformatted_identifiersjZn_rX_decompressed_ew2hSJ_Novogene_1_PL0182303_1_R2 Approx 60% complete for reformatted_identifiersxCzp0i_decompressed_FkL2uI_Novogene_1_PL0182303_1_R1 Approx 60% complete for reformatted_identifiersjZn_rX_decompressed_ew2hSJ_Novogene_1_PL0182303_1_R2 Approx 65% complete for reformatted_identifiersxCzp0i_decompressed_FkL2uI_Novogene_1_PL0182303_1_R1 Approx 65% complete for reformatted_identifiersjZn_rX_decompressed_ew2hSJ_Novogene_1_PL0182303_1_R2 Approx 70% complete for reformatted_identifiersxCzp0i_decompressed_FkL2uI_Novogene_1_PL0182303_1_R1 Approx 70% complete for reformatted_identifiersjZn_rX_decompressed_ew2hSJ_Novogene_1_PL0182303_1_R2 Approx 75% complete for reformatted_identifiersxCzp0i_decompressed_FkL2uI_Novogene_1_PL0182303_1_R1 Approx 75% complete for reformatted_identifiersjZn_rX_decompressed_ew2hSJ_Novogene_1_PL0182303_1_R2 Approx 80% complete for reformatted_identifiersxCzp0i_decompressed_FkL2uI_Novogene_1_PL0182303_1_R1 Approx 80% complete for reformatted_identifiersjZn_rX_decompressed_ew2hSJ_Novogene_1_PL0182303_1_R2 Approx 85% complete for reformatted_identifiersxCzp0i_decompressed_FkL2uI_Novogene_1_PL0182303_1_R1 Approx 85% complete for reformatted_identifiersjZn_rX_decompressed_ew2hSJ_Novogene_1_PL0182303_1_R2 Approx 90% complete for reformatted_identifiersxCzp0i_decompressed_FkL2uI_Novogene_1_PL0182303_1_R1 Approx 90% complete for reformatted_identifiersjZn_rX_decompressed_ew2hSJ_Novogene_1_PL0182303_1_R2 Approx 95% complete for reformatted_identifiersxCzp0i_decompressed_FkL2uI_Novogene_1_PL0182303_1_R1 Approx 95% complete for reformatted_identifiersjZn_rX_decompressed_ew2hSJ_Novogene_1_PL0182303_1_R2 Analysis complete for reformatted_identifiersxCzp0i_decompressed_FkL2uI_Novogene_1_PL0182303_1_R1 Analysis complete for reformatted_identifiersjZn_rX_decompressed_ew2hSJ_Novogene_1_PL0182303_1_R2 08/17/2020 12:19:25 PM - kneaddata.utilities - DEBUG: Checking input file to Trimmomatic : /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/reformatted_identifiersxCzp0i_decompressed_FkL2uI_Novogene_1_PL0182303_1_R1 08/17/2020 12:19:25 PM - kneaddata.utilities - DEBUG: Checking input file to Trimmomatic : /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/reformatted_identifiersjZn_rX_decompressed_ew2hSJ_Novogene_1_PL0182303_1_R2 08/17/2020 12:19:25 PM - kneaddata.utilities - INFO: Running Trimmomatic ... 08/17/2020 12:19:25 PM - kneaddata.utilities - INFO: Execute command: java -Xmx500m -jar /home/plicht/anaconda3/envs/kneaddata_env/share/trimmomatic-0.39-1/trimmomatic.jar PE -threads 12 -phred33 /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/reformatted_identifiersxCzp0i_decompressed_FkL2uI_Novogene_1_PL0182303_1_R1 /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/reformatted_identifiersjZn_rX_decompressed_ew2hSJ_Novogene_1_PL0182303_1_R2 /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata.trimmed.1.fastq /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata.trimmed.single.1.fastq /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata.trimmed.2.fastq /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata.trimmed.single.2.fastq ILLUMINACLIP:/home/plicht/anaconda3/envs/kneaddata_env/lib/python2.7/site-packages/kneaddata/adapters/NexteraPE-PE.fa:2:30:10:8:TRUE SLIDINGWINDOW:4:20 MINLEN:75 08/17/2020 12:20:18 PM - kneaddata.utilities - DEBUG: TrimmomaticPE: Started with arguments: -threads 12 -phred33 /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/reformatted_identifiersxCzp0i_decompressed_FkL2uI_Novogene_1_PL0182303_1_R1 /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/reformatted_identifiersjZn_rX_decompressed_ew2hSJ_Novogene_1_PL0182303_1_R2 /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata.trimmed.1.fastq /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata.trimmed.single.1.fastq /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata.trimmed.2.fastq /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata.trimmed.single.2.fastq ILLUMINACLIP:/home/plicht/anaconda3/envs/kneaddata_env/lib/python2.7/site-packages/kneaddata/adapters/NexteraPE-PE.fa:2:30:10:8:TRUE SLIDINGWINDOW:4:20 MINLEN:75 Using PrefixPair: 'AGATGTGTATAAGAGACAG' and 'AGATGTGTATAAGAGACAG' Using Long Clipping Sequence: 'GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG' Using Long Clipping Sequence: 'TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG' Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTCCGAGCCCACGAGAC' Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTGACGCTGCCGACGA' ILLUMINACLIP: Using 1 prefix pairs, 4 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences Input Read Pairs: 16164148 Both Surviving: 14909372 (92.24%) Forward Only Surviving: 533445 (3.30%) Reverse Only Surviving: 500586 (3.10%) Dropped: 220745 (1.37%) TrimmomaticPE: Completed successfully 08/17/2020 12:20:18 PM - kneaddata.utilities - DEBUG: Checking output file from Trimmomatic : /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata.trimmed.1.fastq 08/17/2020 12:20:18 PM - kneaddata.utilities - DEBUG: Checking output file from Trimmomatic : /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata.trimmed.single.1.fastq 08/17/2020 12:20:18 PM - kneaddata.utilities - DEBUG: Checking output file from Trimmomatic : /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata.trimmed.2.fastq 08/17/2020 12:20:18 PM - kneaddata.utilities - DEBUG: Checking output file from Trimmomatic : /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata.trimmed.single.2.fastq 08/17/2020 12:20:22 PM - kneaddata.utilities - INFO: READ COUNT: trimmed pair1 : Total reads after trimming ( /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata.trimmed.1.fastq ): 14909372 08/17/2020 12:20:26 PM - kneaddata.utilities - INFO: READ COUNT: trimmed pair2 : Total reads after trimming ( /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata.trimmed.2.fastq ): 14909372 08/17/2020 12:20:26 PM - kneaddata.utilities - INFO: READ COUNT: trimmed orphan1 : Total reads after trimming ( /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata.trimmed.single.1.fastq ): 533445 08/17/2020 12:20:26 PM - kneaddata.utilities - INFO: READ COUNT: trimmed orphan2 : Total reads after trimming ( /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata.trimmed.single.2.fastq ): 500586 08/17/2020 12:20:26 PM - kneaddata.run - INFO: Decontaminating ... 08/17/2020 12:20:26 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata.trimmed.1.fastq 08/17/2020 12:20:26 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata.trimmed.1.fastq 08/17/2020 12:20:26 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata.trimmed.2.fastq 08/17/2020 12:20:26 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata.trimmed.2.fastq 08/17/2020 12:20:26 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata.trimmed.single.1.fastq 08/17/2020 12:20:26 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata.trimmed.single.1.fastq 08/17/2020 12:20:26 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata.trimmed.single.2.fastq 08/17/2020 12:20:26 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata.trimmed.single.2.fastq 08/17/2020 12:20:26 PM - kneaddata.utilities - INFO: Running bowtie2 ... 08/17/2020 12:20:26 PM - kneaddata.utilities - INFO: Running bowtie2 ... 08/17/2020 12:20:26 PM - kneaddata.utilities - INFO: Execute command: kneaddata_bowtie2_discordant_pairs --bowtie2 /home/plicht/anaconda3/envs/kneaddata_env/bin/bowtie2 --threads 12 -x /home/plicht/KneadData_db/hg37/hg37dec_v0.1 --bowtie2-options "--very-sensitive --phred33" -1 /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata.trimmed.1.fastq -2 /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata.trimmed.2.fastq --un-pair /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata_hg37dec_v0.1_bowtie2_paired_clean_%.fastq --al-pair /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata_hg37dec_v0.1_bowtie2_paired_contam_%.fastq -U /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata.trimmed.single.1.fastq,/home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata.trimmed.single.2.fastq --un-single /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata_hg37dec_v0.1_bowtie2_unmatched_%_clean.fastq --al-single /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata_hg37dec_v0.1_bowtie2_unmatched_%_contam.fastq -S /dev/null 08/17/2020 12:20:26 PM - kneaddata.utilities - INFO: Execute command: kneaddata_bowtie2_discordant_pairs --bowtie2 /home/plicht/anaconda3/envs/kneaddata_env/bin/bowtie2 --threads 12 -x /home/plicht/KneadData_db/phi-x174/phi-x174 --bowtie2-options "--very-sensitive --phred33" -1 /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata.trimmed.1.fastq -2 /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata.trimmed.2.fastq --un-pair /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata_phi-x174_bowtie2_paired_clean_%.fastq --al-pair /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata_phi-x174_bowtie2_paired_contam_%.fastq -U /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata.trimmed.single.1.fastq,/home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata.trimmed.single.2.fastq --un-single /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata_phi-x174_bowtie2_unmatched_%_clean.fastq --al-single /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata_phi-x174_bowtie2_unmatched_%_contam.fastq -S /dev/null 08/17/2020 12:48:01 PM - kneaddata.utilities - DEBUG: 30852775 reads; of these: 30852775 (100.00%) were unpaired; of these: 30852773 (100.00%) aligned 0 times 2 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate pair1_aligned : 0 pair2_aligned : 0 orphan1_unaligned : 533443 orphan2_unaligned : 500586 orphan2_aligned : 0 pair2_unaligned : 14909372 pair1_unaligned : 14909372 orphan1_aligned : 2 08/17/2020 12:48:01 PM - kneaddata.utilities - DEBUG: Checking output file from bowtie2 : /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata_phi-x174_bowtie2_paired_clean_1.fastq 08/17/2020 12:48:01 PM - kneaddata.utilities - DEBUG: Checking output file from bowtie2 : /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata_phi-x174_bowtie2_paired_clean_2.fastq 08/17/2020 01:19:28 PM - kneaddata.utilities - DEBUG: 30852775 reads; of these: 30852775 (100.00%) were unpaired; of these: 10593388 (34.34%) aligned 0 times 16494531 (53.46%) aligned exactly 1 time 3764856 (12.20%) aligned >1 times 65.66% overall alignment rate pair1_aligned : 9396772 pair2_aligned : 9396772 orphan1_unaligned : 924593 orphan2_unaligned : 264899 orphan2_aligned : 1046339 pair2_unaligned : 4701948 pair1_unaligned : 4701948 orphan1_aligned : 419504 08/17/2020 01:19:28 PM - kneaddata.utilities - DEBUG: Checking output file from bowtie2 : /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata_hg37dec_v0.1_bowtie2_paired_clean_1.fastq 08/17/2020 01:19:28 PM - kneaddata.utilities - DEBUG: Checking output file from bowtie2 : /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata_hg37dec_v0.1_bowtie2_paired_clean_2.fastq 08/17/2020 01:19:31 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata_hg37dec_v0.1_bowtie2_paired_contam_1.fastq ) : 9396772 08/17/2020 01:19:33 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata_hg37dec_v0.1_bowtie2_paired_contam_2.fastq ) : 9396772 08/17/2020 01:19:33 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata_hg37dec_v0.1_bowtie2_unmatched_1_contam.fastq ) : 419504 08/17/2020 01:19:34 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata_hg37dec_v0.1_bowtie2_unmatched_2_contam.fastq ) : 1046339 08/17/2020 01:19:34 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata_phi-x174_bowtie2_paired_contam_1.fastq ) : 0 08/17/2020 01:19:34 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata_phi-x174_bowtie2_paired_contam_2.fastq ) : 0 08/17/2020 01:19:34 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata_phi-x174_bowtie2_unmatched_1_contam.fastq ) : 2 08/17/2020 01:19:34 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata_phi-x174_bowtie2_unmatched_2_contam.fastq ) : 0 08/17/2020 01:19:35 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated hg37dec_v0.1 pair1 : Total reads after removing those found in reference database ( /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata_hg37dec_v0.1_bowtie2_paired_clean_1.fastq ): 4701948 08/17/2020 01:19:36 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated hg37dec_v0.1 pair2 : Total reads after removing those found in reference database ( /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata_hg37dec_v0.1_bowtie2_paired_clean_2.fastq ): 4701948 08/17/2020 01:19:42 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated phi-x174 pair1 : Total reads after removing those found in reference database ( /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata_phi-x174_bowtie2_paired_clean_1.fastq ): 14909372 08/17/2020 01:19:46 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated phi-x174 pair2 : Total reads after removing those found in reference database ( /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata_phi-x174_bowtie2_paired_clean_2.fastq ): 14909372 08/17/2020 01:20:50 PM - kneaddata.utilities - INFO: READ COUNT: final pair1 : Total reads after merging results from multiple databases ( /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata_paired_1.fastq ): 4701948 08/17/2020 01:20:51 PM - kneaddata.utilities - INFO: READ COUNT: final pair2 : Total reads after merging results from multiple databases ( /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata_paired_2.fastq ): 4701948 08/17/2020 01:20:52 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated hg37dec_v0.1 orphan1 : Total reads after removing those found in reference database ( /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata_hg37dec_v0.1_bowtie2_unmatched_1_clean.fastq ): 924593 08/17/2020 01:20:52 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated phi-x174 orphan1 : Total reads after removing those found in reference database ( /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata_phi-x174_bowtie2_unmatched_1_clean.fastq ): 533443 08/17/2020 01:20:55 PM - kneaddata.utilities - INFO: READ COUNT: final orphan1 : Total reads after merging results from multiple databases ( /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata_unmatched_1.fastq ): 225958 08/17/2020 01:20:55 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated hg37dec_v0.1 orphan2 : Total reads after removing those found in reference database ( /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata_hg37dec_v0.1_bowtie2_unmatched_2_clean.fastq ): 264899 08/17/2020 01:20:55 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated phi-x174 orphan2 : Total reads after removing those found in reference database ( /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata_phi-x174_bowtie2_unmatched_2_clean.fastq ): 500586 08/17/2020 01:20:56 PM - kneaddata.utilities - INFO: READ COUNT: final orphan2 : Total reads after merging results from multiple databases ( /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata_unmatched_2.fastq ): 152880 08/17/2020 01:20:57 PM - kneaddata.utilities - DEBUG: Checking input file to fastqc : /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata_paired_1.fastq 08/17/2020 01:20:57 PM - kneaddata.utilities - DEBUG: Checking input file to fastqc : /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata_paired_2.fastq 08/17/2020 01:20:57 PM - kneaddata.utilities - DEBUG: Checking input file to fastqc : /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata_unmatched_1.fastq 08/17/2020 01:20:57 PM - kneaddata.utilities - DEBUG: Checking input file to fastqc : /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata_unmatched_2.fastq 08/17/2020 01:20:57 PM - kneaddata.utilities - INFO: Running fastqc ... 08/17/2020 01:20:57 PM - kneaddata.utilities - INFO: Execute command: /home/plicht/anaconda3/envs/kneaddata_env/bin/fastqc /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata_paired_1.fastq /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata_paired_2.fastq /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata_unmatched_1.fastq /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata_unmatched_2.fastq --threads 12 --outdir /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/fastqc 08/17/2020 01:21:24 PM - kneaddata.utilities - DEBUG: Started analysis of Novogene_1_PL0182303_1_R1_kneaddata_paired_1.fastq Started analysis of Novogene_1_PL0182303_1_R1_kneaddata_paired_2.fastq Started analysis of Novogene_1_PL0182303_1_R1_kneaddata_unmatched_1.fastq Approx 5% complete for Novogene_1_PL0182303_1_R1_kneaddata_unmatched_1.fastq Approx 10% complete for Novogene_1_PL0182303_1_R1_kneaddata_unmatched_1.fastq Approx 15% complete for Novogene_1_PL0182303_1_R1_kneaddata_unmatched_1.fastq Approx 20% complete for Novogene_1_PL0182303_1_R1_kneaddata_unmatched_1.fastq Approx 25% complete for Novogene_1_PL0182303_1_R1_kneaddata_unmatched_1.fastq Started analysis of Novogene_1_PL0182303_1_R1_kneaddata_unmatched_2.fastq Approx 5% complete for Novogene_1_PL0182303_1_R1_kneaddata_unmatched_2.fastq Approx 30% complete for Novogene_1_PL0182303_1_R1_kneaddata_unmatched_1.fastq Approx 10% complete for Novogene_1_PL0182303_1_R1_kneaddata_unmatched_2.fastq Approx 35% complete for Novogene_1_PL0182303_1_R1_kneaddata_unmatched_1.fastq Approx 15% complete for Novogene_1_PL0182303_1_R1_kneaddata_unmatched_2.fastq Approx 40% complete for Novogene_1_PL0182303_1_R1_kneaddata_unmatched_1.fastq Approx 20% complete for Novogene_1_PL0182303_1_R1_kneaddata_unmatched_2.fastq Approx 5% complete for Novogene_1_PL0182303_1_R1_kneaddata_paired_1.fastq Approx 25% complete for Novogene_1_PL0182303_1_R1_kneaddata_unmatched_2.fastq Approx 45% complete for Novogene_1_PL0182303_1_R1_kneaddata_unmatched_1.fastq Approx 30% complete for Novogene_1_PL0182303_1_R1_kneaddata_unmatched_2.fastq Approx 50% complete for Novogene_1_PL0182303_1_R1_kneaddata_unmatched_1.fastq Approx 35% complete for Novogene_1_PL0182303_1_R1_kneaddata_unmatched_2.fastq Approx 55% complete for Novogene_1_PL0182303_1_R1_kneaddata_unmatched_1.fastq Approx 40% complete for Novogene_1_PL0182303_1_R1_kneaddata_unmatched_2.fastq Approx 45% complete for Novogene_1_PL0182303_1_R1_kneaddata_unmatched_2.fastq Approx 60% complete for Novogene_1_PL0182303_1_R1_kneaddata_unmatched_1.fastq Approx 50% complete for Novogene_1_PL0182303_1_R1_kneaddata_unmatched_2.fastq Approx 65% complete for Novogene_1_PL0182303_1_R1_kneaddata_unmatched_1.fastq Approx 55% complete for Novogene_1_PL0182303_1_R1_kneaddata_unmatched_2.fastq Approx 5% complete for Novogene_1_PL0182303_1_R1_kneaddata_paired_2.fastq Approx 70% complete for Novogene_1_PL0182303_1_R1_kneaddata_unmatched_1.fastq Approx 60% complete for Novogene_1_PL0182303_1_R1_kneaddata_unmatched_2.fastq Approx 65% complete for Novogene_1_PL0182303_1_R1_kneaddata_unmatched_2.fastq Approx 75% complete for Novogene_1_PL0182303_1_R1_kneaddata_unmatched_1.fastq Approx 70% complete for Novogene_1_PL0182303_1_R1_kneaddata_unmatched_2.fastq Approx 80% complete for Novogene_1_PL0182303_1_R1_kneaddata_unmatched_1.fastq Approx 75% complete for Novogene_1_PL0182303_1_R1_kneaddata_unmatched_2.fastq Approx 85% complete for Novogene_1_PL0182303_1_R1_kneaddata_unmatched_1.fastq Approx 80% complete for Novogene_1_PL0182303_1_R1_kneaddata_unmatched_2.fastq Approx 90% complete for Novogene_1_PL0182303_1_R1_kneaddata_unmatched_1.fastq Approx 85% complete for Novogene_1_PL0182303_1_R1_kneaddata_unmatched_2.fastq Approx 90% complete for Novogene_1_PL0182303_1_R1_kneaddata_unmatched_2.fastq Approx 95% complete for Novogene_1_PL0182303_1_R1_kneaddata_unmatched_1.fastq Approx 95% complete for Novogene_1_PL0182303_1_R1_kneaddata_unmatched_2.fastq Analysis complete for Novogene_1_PL0182303_1_R1_kneaddata_unmatched_1.fastq Analysis complete for Novogene_1_PL0182303_1_R1_kneaddata_unmatched_2.fastq Approx 10% complete for Novogene_1_PL0182303_1_R1_kneaddata_paired_1.fastq Approx 10% complete for Novogene_1_PL0182303_1_R1_kneaddata_paired_2.fastq Approx 15% complete for Novogene_1_PL0182303_1_R1_kneaddata_paired_1.fastq Approx 15% complete for Novogene_1_PL0182303_1_R1_kneaddata_paired_2.fastq Approx 20% complete for Novogene_1_PL0182303_1_R1_kneaddata_paired_1.fastq Approx 20% complete for Novogene_1_PL0182303_1_R1_kneaddata_paired_2.fastq Approx 25% complete for Novogene_1_PL0182303_1_R1_kneaddata_paired_1.fastq Approx 25% complete for Novogene_1_PL0182303_1_R1_kneaddata_paired_2.fastq Approx 30% complete for Novogene_1_PL0182303_1_R1_kneaddata_paired_1.fastq Approx 30% complete for Novogene_1_PL0182303_1_R1_kneaddata_paired_2.fastq Approx 35% complete for Novogene_1_PL0182303_1_R1_kneaddata_paired_1.fastq Approx 35% complete for Novogene_1_PL0182303_1_R1_kneaddata_paired_2.fastq Approx 40% complete for Novogene_1_PL0182303_1_R1_kneaddata_paired_1.fastq Approx 40% complete for Novogene_1_PL0182303_1_R1_kneaddata_paired_2.fastq Approx 45% complete for Novogene_1_PL0182303_1_R1_kneaddata_paired_1.fastq Approx 45% complete for Novogene_1_PL0182303_1_R1_kneaddata_paired_2.fastq Approx 50% complete for Novogene_1_PL0182303_1_R1_kneaddata_paired_1.fastq Approx 50% complete for Novogene_1_PL0182303_1_R1_kneaddata_paired_2.fastq Approx 55% complete for Novogene_1_PL0182303_1_R1_kneaddata_paired_1.fastq Approx 55% complete for Novogene_1_PL0182303_1_R1_kneaddata_paired_2.fastq Approx 60% complete for Novogene_1_PL0182303_1_R1_kneaddata_paired_1.fastq Approx 60% complete for Novogene_1_PL0182303_1_R1_kneaddata_paired_2.fastq Approx 65% complete for Novogene_1_PL0182303_1_R1_kneaddata_paired_1.fastq Approx 65% complete for Novogene_1_PL0182303_1_R1_kneaddata_paired_2.fastq Approx 70% complete for Novogene_1_PL0182303_1_R1_kneaddata_paired_1.fastq Approx 70% complete for Novogene_1_PL0182303_1_R1_kneaddata_paired_2.fastq Approx 75% complete for Novogene_1_PL0182303_1_R1_kneaddata_paired_1.fastq Approx 75% complete for Novogene_1_PL0182303_1_R1_kneaddata_paired_2.fastq Approx 80% complete for Novogene_1_PL0182303_1_R1_kneaddata_paired_1.fastq Approx 80% complete for Novogene_1_PL0182303_1_R1_kneaddata_paired_2.fastq Approx 85% complete for Novogene_1_PL0182303_1_R1_kneaddata_paired_1.fastq Approx 85% complete for Novogene_1_PL0182303_1_R1_kneaddata_paired_2.fastq Approx 90% complete for Novogene_1_PL0182303_1_R1_kneaddata_paired_1.fastq Approx 90% complete for Novogene_1_PL0182303_1_R1_kneaddata_paired_2.fastq Approx 95% complete for Novogene_1_PL0182303_1_R1_kneaddata_paired_1.fastq Approx 95% complete for Novogene_1_PL0182303_1_R1_kneaddata_paired_2.fastq Analysis complete for Novogene_1_PL0182303_1_R1_kneaddata_paired_1.fastq Analysis complete for Novogene_1_PL0182303_1_R1_kneaddata_paired_2.fastq 08/17/2020 01:21:24 PM - kneaddata.knead_data - INFO: Final output files created: /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata_paired_1.fastq /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata_paired_2.fastq /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata_unmatched_1.fastq /home/plicht/Microbiome_Data/Analysis/Validation_samples/KneadData/sample1/Novogene_1_PL0182303_1_R1_kneaddata_unmatched_2.fastq