03/02/2023 09:49:52 PM - kneaddata.knead_data - INFO: Running kneaddata v0.10.0 03/02/2023 09:49:52 PM - kneaddata.knead_data - INFO: Output files will be written to: /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A 03/02/2023 09:49:52 PM - kneaddata.knead_data - DEBUG: Running with the following arguments: verbose = False input = /home/jsadeghi/project/Javad/Ch4-trans/Chapter4_Transcriptomics/67A_R1.fastq.gz /home/jsadeghi/project/Javad/Ch4-trans/Chapter4_Transcriptomics/67A_R2.fastq.gz output_dir = /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A reference_db = /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/Ref/Chinook_Trinity bypass_trim = False output_prefix = 67A_R1_kneaddata threads = 32 processes = 32 trimmomatic_quality_scores = -phred33 bmtagger = False bypass_trf = False run_trf = False fastqc_start = True fastqc_end = True store_temp_output = False remove_intermediate_output = False cat_final_output = False log_level = DEBUG log = /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata.log trimmomatic_path = /scratch/st-spakpour-1/envs/kneaddata/Trimmomatic-0.39/trimmomatic-0.39.jar run_trim_repetitive = False max_memory = 500m trimmomatic_options = None sequencer_source = NexteraPE bowtie2_path = /home/jsadeghi/scratch/envs/kneaddata/bin/bowtie2 bowtie2_options = --very-sensitive-local --phred33 decontaminate_pairs = strict reorder = False serial = False bmtagger_path = None trf_path = /home/jsadeghi/scratch/envs/kneaddata/bin/trf match = 2 mismatch = 7 delta = 7 pm = 80 pi = 10 minscore = 50 maxperiod = 500 fastqc_path = /home/jsadeghi/scratch/envs/kneaddata/bin/fastqc remove_temp_output = True discordant = True 03/02/2023 09:49:52 PM - kneaddata.utilities - INFO: Decompressing gzipped file ... 03/02/2023 09:50:59 PM - kneaddata.utilities - INFO: Decompressed file created: /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/decompressed_w26kvr6s_67A_R1.fastq 03/02/2023 09:50:59 PM - kneaddata.utilities - INFO: Decompressing gzipped file ... 03/02/2023 09:52:08 PM - kneaddata.utilities - INFO: Decompressed file created: /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/decompressed_3zj1e2qy_67A_R2.fastq 03/02/2023 09:52:08 PM - kneaddata.utilities - INFO: Reformatting file sequence identifiers ... 03/02/2023 09:53:31 PM - kneaddata.utilities - INFO: Reformatting file sequence identifiers ... 03/02/2023 09:55:24 PM - kneaddata.utilities - INFO: READ COUNT: raw pair1 : Initial number of reads ( /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/reformatted_identifierskrzd412d_decompressed_w26kvr6s_67A_R1 ): 50811211.0 03/02/2023 09:55:47 PM - kneaddata.utilities - INFO: READ COUNT: raw pair2 : Initial number of reads ( /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/reformatted_identifiersudssmt8z_decompressed_3zj1e2qy_67A_R2 ): 50811211.0 03/02/2023 09:55:47 PM - kneaddata.utilities - DEBUG: Creating output directory: /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/fastqc 03/02/2023 09:55:47 PM - kneaddata.utilities - DEBUG: Checking input file to fastqc : /home/jsadeghi/project/Javad/Ch4-trans/Chapter4_Transcriptomics/67A_R1.fastq.gz 03/02/2023 09:55:47 PM - kneaddata.utilities - DEBUG: Checking input file to fastqc : /home/jsadeghi/project/Javad/Ch4-trans/Chapter4_Transcriptomics/67A_R2.fastq.gz 03/02/2023 09:55:47 PM - kneaddata.utilities - INFO: Running fastqc ... 03/02/2023 09:55:47 PM - kneaddata.utilities - INFO: Execute command: /home/jsadeghi/scratch/envs/kneaddata/bin/fastqc /home/jsadeghi/project/Javad/Ch4-trans/Chapter4_Transcriptomics/67A_R1.fastq.gz /home/jsadeghi/project/Javad/Ch4-trans/Chapter4_Transcriptomics/67A_R2.fastq.gz --threads 32 --outdir /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/fastqc --extract 03/02/2023 10:00:17 PM - kneaddata.utilities - DEBUG: b'Started analysis of 67A_R1.fastq.gz\nStarted analysis of 67A_R2.fastq.gz\nApprox 5% complete for 67A_R1.fastq.gz\nApprox 5% complete for 67A_R2.fastq.gz\nApprox 10% complete for 67A_R1.fastq.gz\nApprox 10% complete for 67A_R2.fastq.gz\nApprox 15% complete for 67A_R1.fastq.gz\nApprox 15% complete for 67A_R2.fastq.gz\nApprox 20% complete for 67A_R1.fastq.gz\nApprox 20% complete for 67A_R2.fastq.gz\nApprox 25% complete for 67A_R1.fastq.gz\nApprox 25% complete for 67A_R2.fastq.gz\nApprox 30% complete for 67A_R1.fastq.gz\nApprox 30% complete for 67A_R2.fastq.gz\nApprox 35% complete for 67A_R1.fastq.gz\nApprox 35% complete for 67A_R2.fastq.gz\nApprox 40% complete for 67A_R1.fastq.gz\nApprox 40% complete for 67A_R2.fastq.gz\nApprox 45% complete for 67A_R1.fastq.gz\nApprox 45% complete for 67A_R2.fastq.gz\nApprox 50% complete for 67A_R1.fastq.gz\nApprox 50% complete for 67A_R2.fastq.gz\nApprox 55% complete for 67A_R1.fastq.gz\nApprox 55% complete for 67A_R2.fastq.gz\nApprox 60% complete for 67A_R1.fastq.gz\nApprox 60% complete for 67A_R2.fastq.gz\nApprox 65% complete for 67A_R1.fastq.gz\nApprox 65% complete for 67A_R2.fastq.gz\nApprox 70% complete for 67A_R1.fastq.gz\nApprox 70% complete for 67A_R2.fastq.gz\nApprox 75% complete for 67A_R1.fastq.gz\nApprox 75% complete for 67A_R2.fastq.gz\nApprox 80% complete for 67A_R1.fastq.gz\nApprox 80% complete for 67A_R2.fastq.gz\nApprox 85% complete for 67A_R1.fastq.gz\nApprox 85% complete for 67A_R2.fastq.gz\nApprox 90% complete for 67A_R1.fastq.gz\nApprox 90% complete for 67A_R2.fastq.gz\nApprox 95% complete for 67A_R1.fastq.gz\nApprox 95% complete for 67A_R2.fastq.gz\nAnalysis complete for 67A_R1.fastq.gz\nAnalysis complete for 67A_R2.fastq.gz\n' 03/02/2023 10:00:17 PM - kneaddata.utilities - DEBUG: Checking input file to Trimmomatic : /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/reformatted_identifierskrzd412d_decompressed_w26kvr6s_67A_R1 03/02/2023 10:00:17 PM - kneaddata.utilities - DEBUG: Checking input file to Trimmomatic : /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/reformatted_identifiersudssmt8z_decompressed_3zj1e2qy_67A_R2 03/02/2023 10:00:17 PM - kneaddata.utilities - INFO: Running Trimmomatic ... 03/02/2023 10:00:17 PM - kneaddata.utilities - INFO: Execute command: java -Xmx500m -jar /scratch/st-spakpour-1/envs/kneaddata/Trimmomatic-0.39/trimmomatic-0.39.jar PE -threads 32 -phred33 /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/reformatted_identifierskrzd412d_decompressed_w26kvr6s_67A_R1 /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/reformatted_identifiersudssmt8z_decompressed_3zj1e2qy_67A_R2 /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata.trimmed.1.fastq /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata.trimmed.single.1.fastq /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata.trimmed.2.fastq /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata.trimmed.single.2.fastq MINLEN:60 ILLUMINACLIP:/scratch/st-spakpour-1/envs/kneaddata/lib/python3.7/site-packages/kneaddata/adapters/NexteraPE-PE.fa:2:30:10:8:TRUE SLIDINGWINDOW:4:20 MINLEN:50 03/02/2023 10:01:33 PM - kneaddata.utilities - DEBUG: b"TrimmomaticPE: Started with arguments:\n -threads 32 -phred33 /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/reformatted_identifierskrzd412d_decompressed_w26kvr6s_67A_R1 /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/reformatted_identifiersudssmt8z_decompressed_3zj1e2qy_67A_R2 /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata.trimmed.1.fastq /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata.trimmed.single.1.fastq /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata.trimmed.2.fastq /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata.trimmed.single.2.fastq MINLEN:60 ILLUMINACLIP:/scratch/st-spakpour-1/envs/kneaddata/lib/python3.7/site-packages/kneaddata/adapters/NexteraPE-PE.fa:2:30:10:8:TRUE SLIDINGWINDOW:4:20 MINLEN:50\nUsing PrefixPair: 'AGATGTGTATAAGAGACAG' and 'AGATGTGTATAAGAGACAG'\nUsing Long Clipping Sequence: 'GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG'\nUsing Long Clipping Sequence: 'TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG'\nUsing Long Clipping Sequence: 'CTGTCTCTTATACACATCTCCGAGCCCACGAGAC'\nUsing Long Clipping Sequence: 'CTGTCTCTTATACACATCTGACGCTGCCGACGA'\nILLUMINACLIP: Using 1 prefix pairs, 4 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences\nInput Read Pairs: 50811211 Both Surviving: 48574126 (95.60%) Forward Only Surviving: 1152435 (2.27%) Reverse Only Surviving: 627300 (1.23%) Dropped: 457350 (0.90%)\nTrimmomaticPE: Completed successfully\n" 03/02/2023 10:01:33 PM - kneaddata.utilities - DEBUG: Checking output file from Trimmomatic : /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata.trimmed.1.fastq 03/02/2023 10:01:33 PM - kneaddata.utilities - DEBUG: Checking output file from Trimmomatic : /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata.trimmed.single.1.fastq 03/02/2023 10:01:33 PM - kneaddata.utilities - DEBUG: Checking output file from Trimmomatic : /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata.trimmed.2.fastq 03/02/2023 10:01:33 PM - kneaddata.utilities - DEBUG: Checking output file from Trimmomatic : /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata.trimmed.single.2.fastq 03/02/2023 10:01:54 PM - kneaddata.utilities - INFO: READ COUNT: trimmed pair1 : Total reads after trimming ( /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata.trimmed.1.fastq ): 48574126.0 03/02/2023 10:02:16 PM - kneaddata.utilities - INFO: READ COUNT: trimmed pair2 : Total reads after trimming ( /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata.trimmed.2.fastq ): 48574126.0 03/02/2023 10:02:16 PM - kneaddata.utilities - INFO: READ COUNT: trimmed orphan1 : Total reads after trimming ( /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata.trimmed.single.1.fastq ): 1152435.0 03/02/2023 10:02:17 PM - kneaddata.utilities - INFO: READ COUNT: trimmed orphan2 : Total reads after trimming ( /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata.trimmed.single.2.fastq ): 627300.0 03/02/2023 10:17:49 PM - kneaddata.utilities - DEBUG: Checking input file to trf : /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata.trimmed.1.fasta 03/02/2023 10:17:49 PM - kneaddata.utilities - DEBUG: Checking input file to trf : /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata.trimmed.2.fasta 03/02/2023 10:17:49 PM - kneaddata.utilities - INFO: Running trf ... 03/02/2023 10:17:49 PM - kneaddata.utilities - INFO: Running trf ... 03/02/2023 10:17:49 PM - kneaddata.utilities - INFO: Execute command: kneaddata_trf_parallel --input /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata.trimmed.2.fasta --output /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata.trimmed.2.fasta.trf.parameters.2.7.7.80.10.50.500.dat --trf-path /home/jsadeghi/scratch/envs/kneaddata/bin/trf --trf-options '2 7 7 80 10 50 500 -h -ngs' --nproc 32 03/02/2023 10:17:49 PM - kneaddata.utilities - INFO: Execute command: kneaddata_trf_parallel --input /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata.trimmed.1.fasta --output /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata.trimmed.1.fasta.trf.parameters.2.7.7.80.10.50.500.dat --trf-path /home/jsadeghi/scratch/envs/kneaddata/bin/trf --trf-options '2 7 7 80 10 50 500 -h -ngs' --nproc 32 03/02/2023 10:24:41 PM - kneaddata.utilities - DEBUG: 0 03/02/2023 10:24:41 PM - kneaddata.utilities - DEBUG: Checking output file from trf : /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata.trimmed.2.fasta.trf.parameters.2.7.7.80.10.50.500.dat 03/02/2023 10:24:48 PM - kneaddata.utilities - DEBUG: 0 03/02/2023 10:24:48 PM - kneaddata.utilities - DEBUG: Checking output file from trf : /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata.trimmed.1.fasta.trf.parameters.2.7.7.80.10.50.500.dat 03/02/2023 10:26:04 PM - kneaddata.run - INFO: Total number of sequences with repeats removed from file ( /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata.trimmed.1.fastq ): 2058991 03/02/2023 10:27:28 PM - kneaddata.run - INFO: Total number of sequences with repeats removed from file ( /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata.trimmed.2.fastq ): 1935114 03/02/2023 10:27:39 PM - kneaddata.utilities - DEBUG: Checking input file to trf : /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata.trimmed.single.1.fasta 03/02/2023 10:27:39 PM - kneaddata.utilities - INFO: Running trf ... 03/02/2023 10:27:39 PM - kneaddata.utilities - INFO: Execute command: kneaddata_trf_parallel --input /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata.trimmed.single.1.fasta --output /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata.trimmed.single.1.fasta.trf.parameters.2.7.7.80.10.50.500.dat --trf-path /home/jsadeghi/scratch/envs/kneaddata/bin/trf --trf-options '2 7 7 80 10 50 500 -h -ngs' --nproc 32 03/02/2023 10:27:49 PM - kneaddata.utilities - DEBUG: 0 03/02/2023 10:27:49 PM - kneaddata.utilities - DEBUG: Checking output file from trf : /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata.trimmed.single.1.fasta.trf.parameters.2.7.7.80.10.50.500.dat 03/02/2023 10:27:50 PM - kneaddata.run - INFO: Total number of sequences with repeats removed from file ( /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata.trimmed.single.1.fastq ): 163486 03/02/2023 10:27:57 PM - kneaddata.utilities - DEBUG: Checking input file to trf : /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata.trimmed.single.2.fasta 03/02/2023 10:27:57 PM - kneaddata.utilities - INFO: Running trf ... 03/02/2023 10:27:57 PM - kneaddata.utilities - INFO: Execute command: kneaddata_trf_parallel --input /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata.trimmed.single.2.fasta --output /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata.trimmed.single.2.fasta.trf.parameters.2.7.7.80.10.50.500.dat --trf-path /home/jsadeghi/scratch/envs/kneaddata/bin/trf --trf-options '2 7 7 80 10 50 500 -h -ngs' --nproc 32 03/02/2023 10:28:02 PM - kneaddata.utilities - DEBUG: 0 03/02/2023 10:28:02 PM - kneaddata.utilities - DEBUG: Checking output file from trf : /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata.trimmed.single.2.fasta.trf.parameters.2.7.7.80.10.50.500.dat 03/02/2023 10:28:03 PM - kneaddata.run - INFO: Total number of sequences with repeats removed from file ( /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata.trimmed.single.2.fastq ): 66104 03/02/2023 10:28:03 PM - kneaddata.run - INFO: Decontaminating ... 03/02/2023 10:28:03 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata.repeats.removed.1.fastq 03/02/2023 10:28:03 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata.repeats.removed.2.fastq 03/02/2023 10:28:03 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata.repeats.removed.unmatched.1.fastq 03/02/2023 10:28:03 PM - kneaddata.utilities - DEBUG: Checking input file to bowtie2 : /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata.repeats.removed.unmatched.2.fastq 03/02/2023 10:28:03 PM - kneaddata.utilities - INFO: Running bowtie2 ... 03/02/2023 10:28:03 PM - kneaddata.utilities - INFO: Execute command: kneaddata_bowtie2_discordant_pairs --bowtie2 /home/jsadeghi/scratch/envs/kneaddata/bin/bowtie2 --threads 32 -x /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/Ref/Chinook_Trinity --mode strict --bowtie2-options "--very-sensitive-local --phred33" -1 /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata.repeats.removed.1.fastq -2 /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata.repeats.removed.2.fastq --un-pair /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata_Chinook_Trinity_bowtie2_paired_clean_%.fastq --al-pair /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata_Chinook_Trinity_bowtie2_paired_contam_%.fastq -U /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata.repeats.removed.unmatched.1.fastq,/home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata.repeats.removed.unmatched.2.fastq --un-single /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata_Chinook_Trinity_bowtie2_unmatched_%_clean.fastq --al-single /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata_Chinook_Trinity_bowtie2_unmatched_%_contam.fastq -S /dev/null 03/02/2023 10:46:13 PM - kneaddata.utilities - DEBUG: b'94704292 reads; of these:\n 94704292 (100.00%) were unpaired; of these:\n 993505 (1.05%) aligned 0 times\n 9284340 (9.80%) aligned exactly 1 time\n 84426447 (89.15%) aligned >1 times\n98.95% overall alignment rate\npair1_aligned : 0\npair2_aligned : 0\npair1_unaligned : 0\npair2_unaligned : 0\norphan1_aligned : 93930764\norphan2_aligned : 0\norphan1_unaligned : 773528\norphan2_unaligned : 0\n' 03/02/2023 10:46:13 PM - kneaddata.utilities - DEBUG: Checking output file from bowtie2 : /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata_Chinook_Trinity_bowtie2_paired_clean_1.fastq 03/02/2023 10:46:13 PM - kneaddata.utilities - DEBUG: Checking output file from bowtie2 : /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata_Chinook_Trinity_bowtie2_paired_clean_2.fastq 03/02/2023 10:46:13 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata_Chinook_Trinity_bowtie2_paired_contam_1.fastq ) : 0.0 03/02/2023 10:46:13 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata_Chinook_Trinity_bowtie2_paired_contam_2.fastq ) : 0.0 03/02/2023 10:46:51 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata_Chinook_Trinity_bowtie2_unmatched_1_contam.fastq ) : 93930764.0 03/02/2023 10:46:51 PM - kneaddata.run - INFO: Total contaminate sequences in file ( /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata_Chinook_Trinity_bowtie2_unmatched_2_contam.fastq ) : 0.0 03/02/2023 10:46:51 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated Chinook_Trinity pair1 : Total reads after removing those found in reference database ( /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata_Chinook_Trinity_bowtie2_paired_clean_1.fastq ): 0.0 03/02/2023 10:46:51 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated Chinook_Trinity pair2 : Total reads after removing those found in reference database ( /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata_Chinook_Trinity_bowtie2_paired_clean_2.fastq ): 0.0 03/02/2023 10:46:51 PM - kneaddata.utilities - INFO: READ COUNT: final pair1 : Total reads after merging results from multiple databases ( /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata_paired_1.fastq ): 0.0 03/02/2023 10:46:51 PM - kneaddata.utilities - INFO: READ COUNT: final pair2 : Total reads after merging results from multiple databases ( /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata_paired_2.fastq ): 0.0 03/02/2023 10:46:51 PM - kneaddata.utilities - WARNING: Unable to remove file: /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata_Chinook_Trinity_bowtie2_paired_clean_1.fastq 03/02/2023 10:46:51 PM - kneaddata.utilities - WARNING: Unable to remove file: /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata_Chinook_Trinity_bowtie2_paired_clean_2.fastq 03/02/2023 10:46:52 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated Chinook_Trinity orphan1 : Total reads after removing those found in reference database ( /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata_Chinook_Trinity_bowtie2_unmatched_1_clean.fastq ): 773528.0 03/02/2023 10:46:52 PM - kneaddata.utilities - INFO: READ COUNT: final orphan1 : Total reads after merging results from multiple databases ( /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata_unmatched_1.fastq ): 773528.0 03/02/2023 10:46:52 PM - kneaddata.utilities - WARNING: Unable to remove file: /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata_Chinook_Trinity_bowtie2_unmatched_1_clean.fastq 03/02/2023 10:46:52 PM - kneaddata.utilities - INFO: READ COUNT: decontaminated Chinook_Trinity orphan2 : Total reads after removing those found in reference database ( /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata_Chinook_Trinity_bowtie2_unmatched_2_clean.fastq ): 0.0 03/02/2023 10:46:52 PM - kneaddata.utilities - INFO: READ COUNT: final orphan2 : Total reads after merging results from multiple databases ( /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata_unmatched_2.fastq ): 0.0 03/02/2023 10:46:52 PM - kneaddata.utilities - WARNING: Unable to remove file: /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata_Chinook_Trinity_bowtie2_unmatched_2_clean.fastq 03/02/2023 10:46:52 PM - kneaddata.utilities - DEBUG: Checking input file to fastqc : /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata_paired_1.fastq 03/02/2023 10:46:52 PM - kneaddata.utilities - DEBUG: Checking input file to fastqc : /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata_paired_2.fastq 03/02/2023 10:46:52 PM - kneaddata.utilities - DEBUG: Checking input file to fastqc : /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata_unmatched_1.fastq 03/02/2023 10:46:52 PM - kneaddata.utilities - DEBUG: Checking input file to fastqc : /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata_unmatched_2.fastq 03/02/2023 10:46:52 PM - kneaddata.utilities - INFO: Running fastqc ... 03/02/2023 10:46:52 PM - kneaddata.utilities - INFO: Execute command: /home/jsadeghi/scratch/envs/kneaddata/bin/fastqc /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata_paired_1.fastq /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata_paired_2.fastq /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata_unmatched_1.fastq /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata_unmatched_2.fastq --threads 32 --outdir /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/fastqc --extract 03/02/2023 10:47:20 PM - kneaddata.utilities - DEBUG: b'Started analysis of 67A_R1_kneaddata_paired_1.fastq\nAnalysis complete for 67A_R1_kneaddata_paired_1.fastq\nStarted analysis of 67A_R1_kneaddata_paired_2.fastq\nAnalysis complete for 67A_R1_kneaddata_paired_2.fastq\nStarted analysis of 67A_R1_kneaddata_unmatched_1.fastq\nStarted analysis of 67A_R1_kneaddata_unmatched_2.fastq\nAnalysis complete for 67A_R1_kneaddata_unmatched_2.fastq\nApprox 5% complete for 67A_R1_kneaddata_unmatched_1.fastq\nApprox 10% complete for 67A_R1_kneaddata_unmatched_1.fastq\nApprox 15% complete for 67A_R1_kneaddata_unmatched_1.fastq\nApprox 20% complete for 67A_R1_kneaddata_unmatched_1.fastq\nApprox 25% complete for 67A_R1_kneaddata_unmatched_1.fastq\nApprox 30% complete for 67A_R1_kneaddata_unmatched_1.fastq\nApprox 35% complete for 67A_R1_kneaddata_unmatched_1.fastq\nApprox 40% complete for 67A_R1_kneaddata_unmatched_1.fastq\nApprox 45% complete for 67A_R1_kneaddata_unmatched_1.fastq\nApprox 50% complete for 67A_R1_kneaddata_unmatched_1.fastq\nApprox 55% complete for 67A_R1_kneaddata_unmatched_1.fastq\nApprox 60% complete for 67A_R1_kneaddata_unmatched_1.fastq\nApprox 65% complete for 67A_R1_kneaddata_unmatched_1.fastq\nApprox 70% complete for 67A_R1_kneaddata_unmatched_1.fastq\nApprox 75% complete for 67A_R1_kneaddata_unmatched_1.fastq\nApprox 80% complete for 67A_R1_kneaddata_unmatched_1.fastq\nApprox 85% complete for 67A_R1_kneaddata_unmatched_1.fastq\nApprox 90% complete for 67A_R1_kneaddata_unmatched_1.fastq\nApprox 95% complete for 67A_R1_kneaddata_unmatched_1.fastq\nAnalysis complete for 67A_R1_kneaddata_unmatched_1.fastq\n' 03/02/2023 10:47:20 PM - kneaddata.knead_data - INFO: Final output files created: /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata_paired_1.fastq /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata_paired_2.fastq /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata_unmatched_1.fastq /home/jsadeghi/scratch/Javad/Ch4/Kneaddata_practice/kneaddataOutputFastQC/kneaddataOutputFastQCJavad67A/67A_R1_kneaddata_unmatched_2.fastq