Multicore support not enabled. Proceeding with single-core trimming. Path to Cutadapt set as: '/usr/lusers/yaaminiv/.local/bin/cutadapt' (user defined) Cutadapt seems to be working fine (tested command '/usr/lusers/yaaminiv/.local/bin/cutadapt --version') Cutadapt version: 3.1 single-core operation. No quality encoding type selected. Assuming that the data provided uses Sanger encoded Phred scores (default) Output will be written into the directory: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/ Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_1_R1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_1_R1.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j 1 Writing final adapter and quality trimmed output to zr3644_1_R1_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_1_R1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed slurmstepd: error: acct_gather_profile/influxdb _send_data: curl_easy_perform failed to send data (discarded). Reason: Couldn't connect to server 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_1_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1887.98 s (36 µs/read; 1.66 M reads/minute). === Summary === Total reads processed: 52,225,074 Reads with adapters: 22,053,906 (42.2%) Reads written (passing filters): 52,225,074 (100.0%) Total basepairs processed: 6,553,667,817 bp Quality-trimmed: 1,729,636 bp (0.0%) Total written (filtered): 6,525,541,768 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 22053906 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 44.9% C: 10.2% G: 6.6% T: 38.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 19424719 13056268.5 0 19424719 2 1730165 3264067.1 0 1730165 3 461077 816016.8 0 461077 4 305022 204004.2 0 305022 5 70710 51001.0 0 70710 6 17504 12750.3 0 17504 7 12989 3187.6 0 12989 8 10246 796.9 0 10246 9 2676 199.2 0 2190 486 10 17881 49.8 1 16641 1240 11 149 12.5 1 16 133 12 40 3.1 1 8 32 13 4 0.8 1 1 3 14 1 0.8 1 0 1 16 3 0.8 1 1 2 17 2 0.8 1 1 1 18 6 0.8 1 1 5 19 5 0.8 1 2 3 20 1 0.8 1 0 1 21 2 0.8 1 0 2 22 4 0.8 1 0 4 23 4 0.8 1 2 2 24 1 0.8 1 1 25 4 0.8 1 2 2 26 2 0.8 1 1 1 27 4 0.8 1 0 4 28 2 0.8 1 0 2 29 2 0.8 1 1 1 30 3 0.8 1 0 3 31 3 0.8 1 2 1 32 2 0.8 1 0 2 33 3 0.8 1 2 1 34 1 0.8 1 0 1 35 5 0.8 1 5 36 1 0.8 1 1 38 2 0.8 1 2 39 5 0.8 1 2 3 40 3 0.8 1 2 1 41 2 0.8 1 0 2 42 2 0.8 1 2 43 2 0.8 1 1 1 44 2 0.8 1 1 1 45 2 0.8 1 2 46 3 0.8 1 1 2 47 1 0.8 1 1 48 3 0.8 1 1 2 49 8 0.8 1 7 1 50 3 0.8 1 3 52 1 0.8 1 1 53 2 0.8 1 0 2 54 3 0.8 1 2 1 55 2 0.8 1 0 2 56 6 0.8 1 3 3 57 2 0.8 1 2 58 3 0.8 1 2 1 59 2 0.8 1 2 60 2 0.8 1 2 61 1 0.8 1 1 62 2 0.8 1 2 63 1 0.8 1 1 64 4 0.8 1 2 2 65 3 0.8 1 2 1 66 11 0.8 1 9 2 67 3 0.8 1 3 68 2 0.8 1 1 1 70 2 0.8 1 2 71 3 0.8 1 1 2 72 7 0.8 1 7 73 2 0.8 1 1 1 74 6 0.8 1 3 3 75 3 0.8 1 2 1 76 4 0.8 1 3 1 77 1 0.8 1 1 78 4 0.8 1 4 79 4 0.8 1 3 1 80 5 0.8 1 5 81 4 0.8 1 3 1 82 2 0.8 1 2 83 4 0.8 1 4 84 6 0.8 1 6 85 3 0.8 1 2 1 86 5 0.8 1 2 3 87 4 0.8 1 2 2 88 2 0.8 1 2 89 1 0.8 1 0 1 90 2 0.8 1 0 2 91 8 0.8 1 8 92 8 0.8 1 7 1 93 3 0.8 1 2 1 94 5 0.8 1 5 95 11 0.8 1 10 1 96 10 0.8 1 5 5 97 7 0.8 1 3 4 98 11 0.8 1 9 2 99 7 0.8 1 7 100 5 0.8 1 4 1 101 6 0.8 1 5 1 102 5 0.8 1 4 1 103 4 0.8 1 3 1 104 5 0.8 1 2 3 105 8 0.8 1 8 106 4 0.8 1 4 107 13 0.8 1 11 2 108 12 0.8 1 10 2 109 3 0.8 1 3 110 12 0.8 1 10 2 111 9 0.8 1 6 3 112 4 0.8 1 1 3 113 11 0.8 1 8 3 114 12 0.8 1 11 1 115 4 0.8 1 3 1 116 10 0.8 1 9 1 117 10 0.8 1 8 2 118 8 0.8 1 5 3 119 20 0.8 1 14 6 120 14 0.8 1 10 4 121 11 0.8 1 9 2 122 10 0.8 1 6 4 123 7 0.8 1 6 1 124 10 0.8 1 6 4 125 15 0.8 1 13 2 126 11 0.8 1 11 127 6 0.8 1 5 1 128 15 0.8 1 13 2 129 17 0.8 1 12 5 130 24 0.8 1 20 4 131 23 0.8 1 21 2 132 19 0.8 1 18 1 133 25 0.8 1 20 5 134 29 0.8 1 24 5 135 30 0.8 1 15 15 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_1_R1.fq.gz ============================================= 52225074 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_1_R2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_1_R2.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3644_1_R2_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_1_R2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_1_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1774.13 s (34 µs/read; 1.77 M reads/minute). === Summary === Total reads processed: 52,225,074 Reads with adapters: 22,305,466 (42.7%) Reads written (passing filters): 52,225,074 (100.0%) Total basepairs processed: 6,552,607,764 bp Quality-trimmed: 2,651,242 bp (0.0%) Total written (filtered): 6,523,511,397 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 22305466 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.4% C: 10.3% G: 6.3% T: 38.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 19847833 13056268.5 0 19847833 2 1569666 3264067.1 0 1569666 3 455047 816016.8 0 455047 4 309134 204004.2 0 309134 5 65255 51001.0 0 65255 6 16274 12750.3 0 16274 7 12211 3187.6 0 12211 8 9595 796.9 0 9595 9 2853 199.2 0 2440 413 10 16558 49.8 1 15111 1447 11 195 12.5 1 29 166 12 46 3.1 1 7 39 13 8 0.8 1 1 7 14 6 0.8 1 1 5 15 5 0.8 1 1 4 16 1 0.8 1 0 1 17 8 0.8 1 4 4 18 3 0.8 1 2 1 19 3 0.8 1 1 2 21 4 0.8 1 1 3 23 1 0.8 1 1 24 5 0.8 1 1 4 25 5 0.8 1 1 4 26 1 0.8 1 1 27 1 0.8 1 1 28 2 0.8 1 1 1 29 2 0.8 1 2 30 3 0.8 1 2 1 31 3 0.8 1 1 2 32 6 0.8 1 1 5 33 10 0.8 1 6 4 34 4 0.8 1 0 4 35 3 0.8 1 0 3 36 5 0.8 1 4 1 37 1 0.8 1 1 38 1 0.8 1 1 39 4 0.8 1 3 1 40 4 0.8 1 2 2 42 5 0.8 1 1 4 44 4 0.8 1 2 2 45 3 0.8 1 1 2 46 4 0.8 1 3 1 47 9 0.8 1 4 5 48 2 0.8 1 2 49 2 0.8 1 2 50 3 0.8 1 0 3 51 2 0.8 1 2 52 1 0.8 1 1 53 5 0.8 1 3 2 54 2 0.8 1 1 1 55 2 0.8 1 0 2 56 1 0.8 1 1 57 4 0.8 1 3 1 58 1 0.8 1 1 59 2 0.8 1 1 1 60 8 0.8 1 7 1 61 5 0.8 1 4 1 62 4 0.8 1 2 2 63 7 0.8 1 4 3 64 4 0.8 1 2 2 65 4 0.8 1 2 2 66 5 0.8 1 5 67 2 0.8 1 1 1 68 6 0.8 1 5 1 69 3 0.8 1 3 70 3 0.8 1 2 1 71 2 0.8 1 2 72 6 0.8 1 4 2 73 2 0.8 1 2 74 2 0.8 1 1 1 75 6 0.8 1 4 2 76 2 0.8 1 1 1 77 5 0.8 1 3 2 78 5 0.8 1 3 2 79 2 0.8 1 2 80 2 0.8 1 1 1 81 2 0.8 1 2 82 5 0.8 1 3 2 83 4 0.8 1 2 2 84 2 0.8 1 2 85 4 0.8 1 2 2 86 5 0.8 1 3 2 87 4 0.8 1 4 88 7 0.8 1 7 89 8 0.8 1 8 90 1 0.8 1 0 1 91 6 0.8 1 4 2 92 5 0.8 1 3 2 93 8 0.8 1 8 94 7 0.8 1 7 95 6 0.8 1 4 2 96 2 0.8 1 1 1 97 10 0.8 1 7 3 98 7 0.8 1 6 1 99 8 0.8 1 7 1 100 7 0.8 1 6 1 101 8 0.8 1 5 3 102 5 0.8 1 5 103 9 0.8 1 9 104 8 0.8 1 8 105 5 0.8 1 4 1 106 12 0.8 1 11 1 107 10 0.8 1 8 2 108 16 0.8 1 15 1 109 10 0.8 1 10 110 7 0.8 1 5 2 111 7 0.8 1 6 1 112 11 0.8 1 9 2 113 6 0.8 1 2 4 114 11 0.8 1 9 2 115 7 0.8 1 6 1 116 12 0.8 1 12 117 9 0.8 1 7 2 118 11 0.8 1 7 4 119 18 0.8 1 15 3 120 11 0.8 1 8 3 121 14 0.8 1 14 122 17 0.8 1 14 3 123 11 0.8 1 10 1 124 8 0.8 1 7 1 125 16 0.8 1 14 2 126 15 0.8 1 15 127 15 0.8 1 13 2 128 24 0.8 1 22 2 129 14 0.8 1 13 1 130 15 0.8 1 9 6 131 16 0.8 1 13 3 132 25 0.8 1 19 6 133 14 0.8 1 7 7 134 33 0.8 1 20 13 135 25 0.8 1 11 14 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_1_R2.fq.gz ============================================= 52225074 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_1_R1_trimmed.fq.gz and zr3644_1_R2_trimmed.fq.gz file_1: zr3644_1_R1_trimmed.fq.gz, file_2: zr3644_1_R2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_1_R1_trimmed.fq.gz and zr3644_1_R2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_1_R1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_1_R2_val_2.fq.gz Total number of sequences analysed: 52225074 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 274601 (0.53%) >>> Now running FastQC on the validated data zr3644_1_R1_val_1.fq.gz<<< Started analysis of zr3644_1_R1_val_1.fq.gz Approx 5% complete for zr3644_1_R1_val_1.fq.gz Approx 10% complete for zr3644_1_R1_val_1.fq.gz Approx 15% complete for zr3644_1_R1_val_1.fq.gz Approx 20% complete for zr3644_1_R1_val_1.fq.gz Approx 25% complete for zr3644_1_R1_val_1.fq.gz Approx 30% complete for zr3644_1_R1_val_1.fq.gz Approx 35% complete for zr3644_1_R1_val_1.fq.gz Approx 40% complete for zr3644_1_R1_val_1.fq.gz Approx 45% complete for zr3644_1_R1_val_1.fq.gz Approx 50% complete for zr3644_1_R1_val_1.fq.gz Approx 55% complete for zr3644_1_R1_val_1.fq.gz Approx 60% complete for zr3644_1_R1_val_1.fq.gz Approx 65% complete for zr3644_1_R1_val_1.fq.gz Approx 70% complete for zr3644_1_R1_val_1.fq.gz Approx 75% complete for zr3644_1_R1_val_1.fq.gz Approx 80% complete for zr3644_1_R1_val_1.fq.gz Approx 85% complete for zr3644_1_R1_val_1.fq.gz Approx 90% complete for zr3644_1_R1_val_1.fq.gz Approx 95% complete for zr3644_1_R1_val_1.fq.gz Analysis complete for zr3644_1_R1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_1_R2_val_2.fq.gz<<< Started analysis of zr3644_1_R2_val_2.fq.gz Approx 5% complete for zr3644_1_R2_val_2.fq.gz Approx 10% complete for zr3644_1_R2_val_2.fq.gz Approx 15% complete for zr3644_1_R2_val_2.fq.gz Approx 20% complete for zr3644_1_R2_val_2.fq.gz Approx 25% complete for zr3644_1_R2_val_2.fq.gz Approx 30% complete for zr3644_1_R2_val_2.fq.gz Approx 35% complete for zr3644_1_R2_val_2.fq.gz Approx 40% complete for zr3644_1_R2_val_2.fq.gz Approx 45% complete for zr3644_1_R2_val_2.fq.gz Approx 50% complete for zr3644_1_R2_val_2.fq.gz Approx 55% complete for zr3644_1_R2_val_2.fq.gz Approx 60% complete for zr3644_1_R2_val_2.fq.gz Approx 65% complete for zr3644_1_R2_val_2.fq.gz Approx 70% complete for zr3644_1_R2_val_2.fq.gz Approx 75% complete for zr3644_1_R2_val_2.fq.gz Approx 80% complete for zr3644_1_R2_val_2.fq.gz Approx 85% complete for zr3644_1_R2_val_2.fq.gz Approx 90% complete for zr3644_1_R2_val_2.fq.gz Approx 95% complete for zr3644_1_R2_val_2.fq.gz Analysis complete for zr3644_1_R2_val_2.fq.gz Deleting both intermediate output files zr3644_1_R1_trimmed.fq.gz and zr3644_1_R2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_2_R1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_2_R1.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3644_2_R1_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_2_R1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_2_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1826.49 s (33 µs/read; 1.84 M reads/minute). === Summary === Total reads processed: 55,879,313 Reads with adapters: 24,629,147 (44.1%) Reads written (passing filters): 55,879,313 (100.0%) Total basepairs processed: 7,129,414,230 bp Quality-trimmed: 2,033,369 bp (0.0%) Total written (filtered): 7,098,489,333 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 24629147 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.3% C: 10.4% G: 6.2% T: 38.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 21978299 13969828.2 0 21978299 2 1758396 3492457.1 0 1758396 3 499911 873114.3 0 499911 4 296834 218278.6 0 296834 5 49700 54569.6 0 49700 6 12916 13642.4 0 12916 7 9268 3410.6 0 9268 8 6943 852.7 0 6943 9 1916 213.2 0 1464 452 10 13264 53.3 1 12169 1095 11 183 13.3 1 31 152 12 82 3.3 1 20 62 13 15 0.8 1 3 12 14 29 0.8 1 20 9 15 3 0.8 1 2 1 16 23 0.8 1 15 8 17 5 0.8 1 1 4 18 25 0.8 1 17 8 19 33 0.8 1 24 9 20 2 0.8 1 0 2 21 9 0.8 1 4 5 22 4 0.8 1 3 1 23 25 0.8 1 15 10 24 26 0.8 1 14 12 25 5 0.8 1 3 2 26 10 0.8 1 7 3 27 11 0.8 1 9 2 28 2 0.8 1 1 1 29 9 0.8 1 6 3 30 20 0.8 1 12 8 31 23 0.8 1 14 9 32 6 0.8 1 4 2 33 23 0.8 1 22 1 34 9 0.8 1 4 5 35 8 0.8 1 6 2 36 14 0.8 1 12 2 37 12 0.8 1 7 5 38 22 0.8 1 16 6 39 14 0.8 1 12 2 40 11 0.8 1 10 1 41 14 0.8 1 10 4 42 8 0.8 1 5 3 43 17 0.8 1 15 2 44 20 0.8 1 17 3 45 2 0.8 1 0 2 46 6 0.8 1 2 4 47 3 0.8 1 2 1 48 23 0.8 1 19 4 49 15 0.8 1 10 5 50 4 0.8 1 2 2 51 8 0.8 1 6 2 52 16 0.8 1 14 2 53 2 0.8 1 1 1 54 2 0.8 1 2 55 16 0.8 1 12 4 56 14 0.8 1 12 2 57 4 0.8 1 2 2 58 9 0.8 1 8 1 59 12 0.8 1 8 4 60 10 0.8 1 9 1 61 8 0.8 1 8 62 11 0.8 1 9 2 63 6 0.8 1 4 2 64 8 0.8 1 4 4 65 8 0.8 1 8 66 7 0.8 1 6 1 67 7 0.8 1 7 68 9 0.8 1 6 3 69 6 0.8 1 3 3 70 3 0.8 1 2 1 71 7 0.8 1 7 72 3 0.8 1 0 3 73 5 0.8 1 4 1 74 9 0.8 1 7 2 75 5 0.8 1 5 76 4 0.8 1 2 2 77 9 0.8 1 7 2 78 7 0.8 1 5 2 79 8 0.8 1 7 1 80 6 0.8 1 4 2 81 13 0.8 1 11 2 82 6 0.8 1 6 83 6 0.8 1 4 2 84 6 0.8 1 4 2 85 5 0.8 1 5 86 8 0.8 1 4 4 87 7 0.8 1 6 1 88 11 0.8 1 10 1 89 4 0.8 1 4 90 8 0.8 1 6 2 91 8 0.8 1 6 2 92 9 0.8 1 7 2 93 11 0.8 1 7 4 94 6 0.8 1 4 2 95 6 0.8 1 3 3 96 9 0.8 1 8 1 97 10 0.8 1 7 3 98 3 0.8 1 3 99 9 0.8 1 9 100 6 0.8 1 4 2 101 6 0.8 1 5 1 102 9 0.8 1 6 3 103 6 0.8 1 4 2 104 10 0.8 1 8 2 105 20 0.8 1 16 4 106 7 0.8 1 5 2 107 13 0.8 1 13 108 13 0.8 1 8 5 109 8 0.8 1 7 1 110 7 0.8 1 6 1 111 13 0.8 1 11 2 112 14 0.8 1 12 2 113 10 0.8 1 9 1 114 9 0.8 1 6 3 115 13 0.8 1 11 2 116 18 0.8 1 15 3 117 13 0.8 1 11 2 118 16 0.8 1 13 3 119 12 0.8 1 12 120 18 0.8 1 17 1 121 14 0.8 1 12 2 122 8 0.8 1 6 2 123 14 0.8 1 12 2 124 17 0.8 1 15 2 125 12 0.8 1 10 2 126 19 0.8 1 18 1 127 14 0.8 1 13 1 128 23 0.8 1 23 129 24 0.8 1 22 2 130 16 0.8 1 16 131 21 0.8 1 20 1 132 31 0.8 1 24 7 133 29 0.8 1 20 9 134 29 0.8 1 23 6 135 39 0.8 1 17 22 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_2_R1.fq.gz ============================================= 55879313 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_2_R2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_2_R2.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3644_2_R2_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_2_R2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_2_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1877.90 s (34 µs/read; 1.79 M reads/minute). === Summary === Total reads processed: 55,879,313 Reads with adapters: 24,638,835 (44.1%) Reads written (passing filters): 55,879,313 (100.0%) Total basepairs processed: 7,125,459,964 bp Quality-trimmed: 2,371,237 bp (0.0%) Total written (filtered): 7,094,372,704 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 24638835 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.7% C: 10.3% G: 6.0% T: 38.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 22154035 13969828.2 0 22154035 2 1596677 3492457.1 0 1596677 3 490802 873114.3 0 490802 4 304016 218278.6 0 304016 5 49336 54569.6 0 49336 6 12245 13642.4 0 12245 7 8821 3410.6 0 8821 8 6824 852.7 0 6824 9 2088 213.2 0 1647 441 10 12805 53.3 1 11775 1030 11 138 13.3 1 22 116 12 34 3.3 1 6 28 13 6 0.8 1 3 3 14 9 0.8 1 6 3 15 5 0.8 1 3 2 16 1 0.8 1 0 1 17 7 0.8 1 2 5 18 5 0.8 1 4 1 19 6 0.8 1 1 5 20 2 0.8 1 1 1 21 10 0.8 1 6 4 22 3 0.8 1 0 3 23 3 0.8 1 3 24 4 0.8 1 1 3 25 7 0.8 1 5 2 26 1 0.8 1 0 1 27 4 0.8 1 3 1 28 7 0.8 1 4 3 29 3 0.8 1 2 1 30 5 0.8 1 2 3 31 5 0.8 1 4 1 32 8 0.8 1 5 3 33 5 0.8 1 4 1 34 6 0.8 1 3 3 35 5 0.8 1 2 3 36 9 0.8 1 7 2 37 3 0.8 1 1 2 38 3 0.8 1 1 2 39 3 0.8 1 3 40 1 0.8 1 1 42 3 0.8 1 1 2 43 3 0.8 1 1 2 44 6 0.8 1 4 2 45 2 0.8 1 1 1 46 3 0.8 1 1 2 47 9 0.8 1 6 3 48 4 0.8 1 4 49 5 0.8 1 5 50 1 0.8 1 1 51 1 0.8 1 1 52 3 0.8 1 3 53 2 0.8 1 2 54 4 0.8 1 4 55 1 0.8 1 0 1 56 8 0.8 1 2 6 57 2 0.8 1 1 1 58 7 0.8 1 7 59 5 0.8 1 5 60 9 0.8 1 7 2 61 5 0.8 1 3 2 62 6 0.8 1 5 1 63 6 0.8 1 4 2 64 2 0.8 1 2 65 5 0.8 1 5 66 10 0.8 1 3 7 67 1 0.8 1 1 68 5 0.8 1 4 1 69 5 0.8 1 3 2 70 2 0.8 1 2 71 8 0.8 1 6 2 72 9 0.8 1 7 2 73 8 0.8 1 6 2 74 7 0.8 1 5 2 75 5 0.8 1 5 76 4 0.8 1 4 77 4 0.8 1 4 78 6 0.8 1 3 3 79 9 0.8 1 9 80 4 0.8 1 3 1 81 8 0.8 1 5 3 82 9 0.8 1 9 83 9 0.8 1 8 1 84 12 0.8 1 9 3 85 6 0.8 1 4 2 86 4 0.8 1 4 87 5 0.8 1 5 88 7 0.8 1 7 89 7 0.8 1 5 2 90 5 0.8 1 5 91 7 0.8 1 5 2 92 8 0.8 1 6 2 93 8 0.8 1 5 3 94 9 0.8 1 7 2 95 8 0.8 1 5 3 96 6 0.8 1 3 3 97 9 0.8 1 9 98 10 0.8 1 8 2 99 6 0.8 1 6 100 5 0.8 1 5 101 5 0.8 1 4 1 102 3 0.8 1 3 103 4 0.8 1 3 1 104 3 0.8 1 3 105 10 0.8 1 10 106 9 0.8 1 8 1 107 10 0.8 1 9 1 108 15 0.8 1 15 109 15 0.8 1 12 3 110 11 0.8 1 8 3 111 11 0.8 1 8 3 112 13 0.8 1 12 1 113 8 0.8 1 6 2 114 8 0.8 1 7 1 115 14 0.8 1 11 3 116 14 0.8 1 12 2 117 11 0.8 1 10 1 118 20 0.8 1 15 5 119 15 0.8 1 13 2 120 18 0.8 1 16 2 121 14 0.8 1 13 1 122 14 0.8 1 13 1 123 21 0.8 1 18 3 124 22 0.8 1 17 5 125 23 0.8 1 20 3 126 19 0.8 1 15 4 127 16 0.8 1 15 1 128 15 0.8 1 14 1 129 18 0.8 1 17 1 130 28 0.8 1 25 3 131 31 0.8 1 27 4 132 19 0.8 1 14 5 133 20 0.8 1 15 5 134 26 0.8 1 16 10 135 38 0.8 1 17 21 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_2_R2.fq.gz ============================================= 55879313 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_2_R1_trimmed.fq.gz and zr3644_2_R2_trimmed.fq.gz file_1: zr3644_2_R1_trimmed.fq.gz, file_2: zr3644_2_R2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_2_R1_trimmed.fq.gz and zr3644_2_R2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_2_R1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_2_R2_val_2.fq.gz Total number of sequences analysed: 55879313 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 214944 (0.38%) >>> Now running FastQC on the validated data zr3644_2_R1_val_1.fq.gz<<< Started analysis of zr3644_2_R1_val_1.fq.gz Approx 5% complete for zr3644_2_R1_val_1.fq.gz Approx 10% complete for zr3644_2_R1_val_1.fq.gz Approx 15% complete for zr3644_2_R1_val_1.fq.gz Approx 20% complete for zr3644_2_R1_val_1.fq.gz Approx 25% complete for zr3644_2_R1_val_1.fq.gz Approx 30% complete for zr3644_2_R1_val_1.fq.gz Approx 35% complete for zr3644_2_R1_val_1.fq.gz Approx 40% complete for zr3644_2_R1_val_1.fq.gz Approx 45% complete for zr3644_2_R1_val_1.fq.gz Approx 50% complete for zr3644_2_R1_val_1.fq.gz Approx 55% complete for zr3644_2_R1_val_1.fq.gz Approx 60% complete for zr3644_2_R1_val_1.fq.gz Approx 65% complete for zr3644_2_R1_val_1.fq.gz Approx 70% complete for zr3644_2_R1_val_1.fq.gz Approx 75% complete for zr3644_2_R1_val_1.fq.gz Approx 80% complete for zr3644_2_R1_val_1.fq.gz Approx 85% complete for zr3644_2_R1_val_1.fq.gz Approx 90% complete for zr3644_2_R1_val_1.fq.gz Approx 95% complete for zr3644_2_R1_val_1.fq.gz Analysis complete for zr3644_2_R1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_2_R2_val_2.fq.gz<<< Started analysis of zr3644_2_R2_val_2.fq.gz Approx 5% complete for zr3644_2_R2_val_2.fq.gz Approx 10% complete for zr3644_2_R2_val_2.fq.gz Approx 15% complete for zr3644_2_R2_val_2.fq.gz Approx 20% complete for zr3644_2_R2_val_2.fq.gz Approx 25% complete for zr3644_2_R2_val_2.fq.gz Approx 30% complete for zr3644_2_R2_val_2.fq.gz Approx 35% complete for zr3644_2_R2_val_2.fq.gz Approx 40% complete for zr3644_2_R2_val_2.fq.gz Approx 45% complete for zr3644_2_R2_val_2.fq.gz Approx 50% complete for zr3644_2_R2_val_2.fq.gz Approx 55% complete for zr3644_2_R2_val_2.fq.gz Approx 60% complete for zr3644_2_R2_val_2.fq.gz Approx 65% complete for zr3644_2_R2_val_2.fq.gz Approx 70% complete for zr3644_2_R2_val_2.fq.gz Approx 75% complete for zr3644_2_R2_val_2.fq.gz Approx 80% complete for zr3644_2_R2_val_2.fq.gz Approx 85% complete for zr3644_2_R2_val_2.fq.gz Approx 90% complete for zr3644_2_R2_val_2.fq.gz Approx 95% complete for zr3644_2_R2_val_2.fq.gz Analysis complete for zr3644_2_R2_val_2.fq.gz Deleting both intermediate output files zr3644_2_R1_trimmed.fq.gz and zr3644_2_R2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_3_R1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_3_R1.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3644_3_R1_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_3_R1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_3_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1288.01 s (33 µs/read; 1.85 M reads/minute). === Summary === Total reads processed: 39,620,531 Reads with adapters: 17,252,677 (43.5%) Reads written (passing filters): 39,620,531 (100.0%) Total basepairs processed: 5,016,985,237 bp Quality-trimmed: 1,682,604 bp (0.0%) Total written (filtered): 4,994,929,003 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 17252677 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.1% C: 10.5% G: 6.3% T: 38.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 15338331 9905132.8 0 15338331 2 1270264 2476283.2 0 1270264 3 353363 619070.8 0 353363 4 216308 154767.7 0 216308 5 38896 38691.9 0 38896 6 10066 9673.0 0 10066 7 7187 2418.2 0 7187 8 5428 604.6 0 5428 9 1518 151.1 0 1212 306 10 9745 37.8 1 8989 756 11 140 9.4 1 34 106 12 77 2.4 1 29 48 13 13 0.6 1 2 11 14 12 0.6 1 7 5 15 5 0.6 1 3 2 16 15 0.6 1 9 6 17 1 0.6 1 1 18 29 0.6 1 21 8 19 31 0.6 1 22 9 20 4 0.6 1 1 3 21 5 0.6 1 2 3 22 7 0.6 1 4 3 23 22 0.6 1 13 9 24 24 0.6 1 16 8 26 15 0.6 1 10 5 27 12 0.6 1 10 2 28 1 0.6 1 1 29 8 0.6 1 3 5 30 19 0.6 1 13 6 31 21 0.6 1 16 5 32 2 0.6 1 2 33 14 0.6 1 9 5 34 5 0.6 1 3 2 35 13 0.6 1 11 2 36 11 0.6 1 8 3 37 11 0.6 1 4 7 38 8 0.6 1 6 2 39 12 0.6 1 10 2 40 11 0.6 1 9 2 41 13 0.6 1 8 5 42 8 0.6 1 8 43 15 0.6 1 9 6 44 10 0.6 1 9 1 45 5 0.6 1 4 1 46 9 0.6 1 7 2 47 5 0.6 1 3 2 48 12 0.6 1 9 3 49 13 0.6 1 10 3 50 6 0.6 1 4 2 51 8 0.6 1 6 2 52 17 0.6 1 13 4 53 11 0.6 1 10 1 54 6 0.6 1 4 2 55 15 0.6 1 10 5 56 15 0.6 1 13 2 57 4 0.6 1 3 1 58 10 0.6 1 8 2 59 10 0.6 1 7 3 60 4 0.6 1 4 61 1 0.6 1 1 62 8 0.6 1 7 1 63 8 0.6 1 7 1 64 4 0.6 1 3 1 65 7 0.6 1 4 3 66 12 0.6 1 8 4 67 8 0.6 1 7 1 68 4 0.6 1 3 1 69 2 0.6 1 1 1 70 3 0.6 1 2 1 71 12 0.6 1 12 72 2 0.6 1 2 73 10 0.6 1 9 1 74 6 0.6 1 3 3 75 9 0.6 1 6 3 76 6 0.6 1 5 1 77 5 0.6 1 5 78 9 0.6 1 7 2 79 11 0.6 1 11 80 7 0.6 1 6 1 81 8 0.6 1 8 82 7 0.6 1 4 3 83 5 0.6 1 3 2 84 11 0.6 1 10 1 85 10 0.6 1 7 3 86 9 0.6 1 8 1 87 8 0.6 1 6 2 88 6 0.6 1 4 2 89 7 0.6 1 7 90 5 0.6 1 4 1 91 12 0.6 1 11 1 92 7 0.6 1 7 93 11 0.6 1 11 94 11 0.6 1 8 3 95 9 0.6 1 8 1 96 7 0.6 1 4 3 97 7 0.6 1 6 1 98 8 0.6 1 7 1 99 7 0.6 1 7 100 8 0.6 1 8 101 9 0.6 1 8 1 102 10 0.6 1 8 2 103 13 0.6 1 9 4 104 9 0.6 1 8 1 105 9 0.6 1 5 4 106 12 0.6 1 12 107 6 0.6 1 6 108 14 0.6 1 12 2 109 8 0.6 1 7 1 110 11 0.6 1 10 1 111 8 0.6 1 7 1 112 14 0.6 1 14 113 10 0.6 1 10 114 6 0.6 1 5 1 115 12 0.6 1 9 3 116 6 0.6 1 5 1 117 15 0.6 1 13 2 118 10 0.6 1 9 1 119 14 0.6 1 12 2 120 17 0.6 1 17 121 14 0.6 1 13 1 122 14 0.6 1 8 6 123 15 0.6 1 13 2 124 13 0.6 1 13 125 9 0.6 1 5 4 126 26 0.6 1 23 3 127 14 0.6 1 11 3 128 30 0.6 1 30 129 29 0.6 1 28 1 130 26 0.6 1 23 3 131 21 0.6 1 19 2 132 26 0.6 1 19 7 133 20 0.6 1 19 1 134 21 0.6 1 11 10 135 39 0.6 1 16 23 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_3_R1.fq.gz ============================================= 39620531 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_3_R2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_3_R2.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3644_3_R2_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_3_R2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_3_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1300.37 s (33 µs/read; 1.83 M reads/minute). === Summary === Total reads processed: 39,620,531 Reads with adapters: 17,150,562 (43.3%) Reads written (passing filters): 39,620,531 (100.0%) Total basepairs processed: 5,015,593,115 bp Quality-trimmed: 1,602,642 bp (0.0%) Total written (filtered): 4,993,811,589 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 17150562 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.4% C: 10.3% G: 6.2% T: 38.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 15315313 9905132.8 0 15315313 2 1190584 2476283.2 0 1190584 3 348180 619070.8 0 348180 4 222979 154767.7 0 222979 5 38963 38691.9 0 38963 6 9791 9673.0 0 9791 7 7052 2418.2 0 7052 8 5372 604.6 0 5372 9 1533 151.1 0 1257 276 10 9668 37.8 1 8907 761 11 121 9.4 1 16 105 12 32 2.4 1 6 26 13 4 0.6 1 1 3 14 6 0.6 1 1 5 15 8 0.6 1 7 1 16 3 0.6 1 2 1 17 3 0.6 1 2 1 18 3 0.6 1 2 1 19 9 0.6 1 3 6 20 4 0.6 1 3 1 21 5 0.6 1 3 2 22 2 0.6 1 0 2 23 3 0.6 1 1 2 24 9 0.6 1 5 4 25 1 0.6 1 0 1 26 3 0.6 1 1 2 27 1 0.6 1 1 28 6 0.6 1 4 2 29 7 0.6 1 4 3 30 6 0.6 1 5 1 31 9 0.6 1 6 3 32 9 0.6 1 6 3 33 6 0.6 1 6 34 3 0.6 1 2 1 35 12 0.6 1 11 1 36 6 0.6 1 4 2 37 4 0.6 1 4 38 5 0.6 1 5 39 3 0.6 1 2 1 40 10 0.6 1 7 3 41 4 0.6 1 3 1 42 4 0.6 1 3 1 43 7 0.6 1 6 1 44 10 0.6 1 6 4 45 11 0.6 1 5 6 46 9 0.6 1 8 1 47 7 0.6 1 4 3 48 3 0.6 1 1 2 49 5 0.6 1 1 4 50 8 0.6 1 4 4 51 4 0.6 1 4 52 3 0.6 1 3 53 7 0.6 1 6 1 54 5 0.6 1 2 3 55 6 0.6 1 4 2 56 4 0.6 1 2 2 57 7 0.6 1 4 3 58 5 0.6 1 4 1 59 4 0.6 1 3 1 60 3 0.6 1 3 62 5 0.6 1 2 3 63 1 0.6 1 1 64 2 0.6 1 1 1 65 6 0.6 1 4 2 66 2 0.6 1 1 1 67 4 0.6 1 3 1 68 4 0.6 1 4 69 2 0.6 1 2 70 2 0.6 1 2 71 4 0.6 1 3 1 72 2 0.6 1 1 1 73 6 0.6 1 5 1 74 8 0.6 1 6 2 75 6 0.6 1 5 1 76 9 0.6 1 6 3 77 5 0.6 1 4 1 78 4 0.6 1 3 1 79 7 0.6 1 2 5 80 4 0.6 1 3 1 81 5 0.6 1 3 2 82 7 0.6 1 4 3 83 12 0.6 1 10 2 84 3 0.6 1 3 85 6 0.6 1 6 86 7 0.6 1 6 1 87 8 0.6 1 6 2 88 7 0.6 1 5 2 89 6 0.6 1 6 90 7 0.6 1 6 1 91 7 0.6 1 6 1 92 5 0.6 1 5 93 10 0.6 1 10 94 7 0.6 1 6 1 95 5 0.6 1 4 1 96 10 0.6 1 6 4 97 6 0.6 1 4 2 98 10 0.6 1 9 1 99 9 0.6 1 7 2 100 10 0.6 1 9 1 101 3 0.6 1 2 1 102 10 0.6 1 8 2 103 4 0.6 1 3 1 104 8 0.6 1 7 1 105 9 0.6 1 9 106 7 0.6 1 7 107 11 0.6 1 9 2 108 6 0.6 1 6 109 9 0.6 1 7 2 110 12 0.6 1 4 8 111 13 0.6 1 10 3 112 3 0.6 1 2 1 113 7 0.6 1 6 1 114 10 0.6 1 7 3 115 16 0.6 1 15 1 116 10 0.6 1 8 2 117 9 0.6 1 8 1 118 11 0.6 1 9 2 119 14 0.6 1 12 2 120 8 0.6 1 8 121 15 0.6 1 14 1 122 17 0.6 1 17 123 15 0.6 1 10 5 124 13 0.6 1 11 2 125 11 0.6 1 9 2 126 12 0.6 1 9 3 127 17 0.6 1 14 3 128 24 0.6 1 21 3 129 24 0.6 1 21 3 130 17 0.6 1 12 5 131 21 0.6 1 20 1 132 25 0.6 1 21 4 133 20 0.6 1 16 4 134 23 0.6 1 16 7 135 44 0.6 1 16 28 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_3_R2.fq.gz ============================================= 39620531 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_3_R1_trimmed.fq.gz and zr3644_3_R2_trimmed.fq.gz file_1: zr3644_3_R1_trimmed.fq.gz, file_2: zr3644_3_R2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_3_R1_trimmed.fq.gz and zr3644_3_R2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_3_R1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_3_R2_val_2.fq.gz Total number of sequences analysed: 39620531 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 173910 (0.44%) >>> Now running FastQC on the validated data zr3644_3_R1_val_1.fq.gz<<< Started analysis of zr3644_3_R1_val_1.fq.gz Approx 5% complete for zr3644_3_R1_val_1.fq.gz Approx 10% complete for zr3644_3_R1_val_1.fq.gz Approx 15% complete for zr3644_3_R1_val_1.fq.gz Approx 20% complete for zr3644_3_R1_val_1.fq.gz Approx 25% complete for zr3644_3_R1_val_1.fq.gz Approx 30% complete for zr3644_3_R1_val_1.fq.gz Approx 35% complete for zr3644_3_R1_val_1.fq.gz Approx 40% complete for zr3644_3_R1_val_1.fq.gz Approx 45% complete for zr3644_3_R1_val_1.fq.gz Approx 50% complete for zr3644_3_R1_val_1.fq.gz Approx 55% complete for zr3644_3_R1_val_1.fq.gz Approx 60% complete for zr3644_3_R1_val_1.fq.gz Approx 65% complete for zr3644_3_R1_val_1.fq.gz Approx 70% complete for zr3644_3_R1_val_1.fq.gz Approx 75% complete for zr3644_3_R1_val_1.fq.gz Approx 80% complete for zr3644_3_R1_val_1.fq.gz Approx 85% complete for zr3644_3_R1_val_1.fq.gz Approx 90% complete for zr3644_3_R1_val_1.fq.gz Approx 95% complete for zr3644_3_R1_val_1.fq.gz Analysis complete for zr3644_3_R1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_3_R2_val_2.fq.gz<<< Started analysis of zr3644_3_R2_val_2.fq.gz Approx 5% complete for zr3644_3_R2_val_2.fq.gz Approx 10% complete for zr3644_3_R2_val_2.fq.gz Approx 15% complete for zr3644_3_R2_val_2.fq.gz Approx 20% complete for zr3644_3_R2_val_2.fq.gz Approx 25% complete for zr3644_3_R2_val_2.fq.gz Approx 30% complete for zr3644_3_R2_val_2.fq.gz Approx 35% complete for zr3644_3_R2_val_2.fq.gz Approx 40% complete for zr3644_3_R2_val_2.fq.gz Approx 45% complete for zr3644_3_R2_val_2.fq.gz Approx 50% complete for zr3644_3_R2_val_2.fq.gz Approx 55% complete for zr3644_3_R2_val_2.fq.gz Approx 60% complete for zr3644_3_R2_val_2.fq.gz Approx 65% complete for zr3644_3_R2_val_2.fq.gz Approx 70% complete for zr3644_3_R2_val_2.fq.gz Approx 75% complete for zr3644_3_R2_val_2.fq.gz Approx 80% complete for zr3644_3_R2_val_2.fq.gz Approx 85% complete for zr3644_3_R2_val_2.fq.gz Approx 90% complete for zr3644_3_R2_val_2.fq.gz Approx 95% complete for zr3644_3_R2_val_2.fq.gz Analysis complete for zr3644_3_R2_val_2.fq.gz Deleting both intermediate output files zr3644_3_R1_trimmed.fq.gz and zr3644_3_R2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_4_R1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_4_R1.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3644_4_R1_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_4_R1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_4_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1715.97 s (34 µs/read; 1.76 M reads/minute). === Summary === Total reads processed: 50,228,886 Reads with adapters: 21,861,473 (43.5%) Reads written (passing filters): 50,228,886 (100.0%) Total basepairs processed: 6,355,763,675 bp Quality-trimmed: 2,416,042 bp (0.0%) Total written (filtered): 6,327,528,676 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 21861473 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.0% C: 10.5% G: 6.3% T: 38.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 19428633 12557221.5 0 19428633 2 1609452 3139305.4 0 1609452 3 451732 784826.3 0 451732 4 273944 196206.6 0 273944 5 51805 49051.6 0 51805 6 13271 12262.9 0 13271 7 9186 3065.7 0 9186 8 6912 766.4 0 6912 9 2001 191.6 0 1610 391 10 12888 47.9 1 11793 1095 11 152 12.0 1 32 120 12 70 3.0 1 24 46 13 15 0.7 1 3 12 14 25 0.7 1 17 8 15 5 0.7 1 3 2 16 13 0.7 1 10 3 17 3 0.7 1 2 1 18 36 0.7 1 22 14 19 26 0.7 1 16 10 20 5 0.7 1 5 21 2 0.7 1 2 22 9 0.7 1 5 4 23 20 0.7 1 12 8 24 23 0.7 1 12 11 25 3 0.7 1 0 3 26 16 0.7 1 13 3 27 17 0.7 1 12 5 28 9 0.7 1 7 2 29 3 0.7 1 3 30 22 0.7 1 9 13 31 24 0.7 1 14 10 32 2 0.7 1 1 1 33 10 0.7 1 9 1 34 5 0.7 1 3 2 35 6 0.7 1 2 4 36 15 0.7 1 15 37 12 0.7 1 8 4 38 13 0.7 1 10 3 39 8 0.7 1 6 2 40 16 0.7 1 12 4 41 13 0.7 1 10 3 42 17 0.7 1 15 2 43 15 0.7 1 12 3 44 15 0.7 1 8 7 45 4 0.7 1 3 1 46 7 0.7 1 5 2 47 1 0.7 1 1 48 16 0.7 1 9 7 49 3 0.7 1 2 1 50 4 0.7 1 4 51 9 0.7 1 6 3 52 16 0.7 1 13 3 53 10 0.7 1 6 4 54 3 0.7 1 0 3 55 13 0.7 1 10 3 56 16 0.7 1 15 1 57 5 0.7 1 4 1 58 7 0.7 1 5 2 59 14 0.7 1 12 2 60 2 0.7 1 0 2 61 5 0.7 1 3 2 62 10 0.7 1 8 2 63 3 0.7 1 2 1 64 7 0.7 1 6 1 65 8 0.7 1 6 2 66 13 0.7 1 10 3 67 9 0.7 1 6 3 68 3 0.7 1 3 69 6 0.7 1 5 1 70 9 0.7 1 6 3 71 4 0.7 1 3 1 72 6 0.7 1 4 2 73 2 0.7 1 2 74 12 0.7 1 8 4 75 9 0.7 1 8 1 76 6 0.7 1 4 2 77 4 0.7 1 3 1 78 7 0.7 1 4 3 79 4 0.7 1 2 2 80 19 0.7 1 16 3 81 11 0.7 1 6 5 82 7 0.7 1 7 83 8 0.7 1 8 84 10 0.7 1 7 3 85 7 0.7 1 7 86 6 0.7 1 6 87 9 0.7 1 8 1 88 5 0.7 1 5 89 4 0.7 1 4 90 10 0.7 1 7 3 91 10 0.7 1 9 1 92 9 0.7 1 9 93 11 0.7 1 10 1 94 7 0.7 1 6 1 95 7 0.7 1 5 2 96 11 0.7 1 6 5 97 5 0.7 1 2 3 98 6 0.7 1 5 1 99 8 0.7 1 8 100 4 0.7 1 3 1 101 10 0.7 1 9 1 102 10 0.7 1 9 1 103 4 0.7 1 3 1 104 11 0.7 1 7 4 105 13 0.7 1 13 106 9 0.7 1 8 1 107 12 0.7 1 10 2 108 10 0.7 1 9 1 109 12 0.7 1 8 4 110 13 0.7 1 12 1 111 10 0.7 1 7 3 112 7 0.7 1 7 113 12 0.7 1 12 114 13 0.7 1 11 2 115 13 0.7 1 10 3 116 15 0.7 1 12 3 117 18 0.7 1 16 2 118 13 0.7 1 11 2 119 18 0.7 1 16 2 120 13 0.7 1 9 4 121 19 0.7 1 16 3 122 14 0.7 1 12 2 123 18 0.7 1 13 5 124 19 0.7 1 17 2 125 18 0.7 1 14 4 126 25 0.7 1 22 3 127 19 0.7 1 18 1 128 19 0.7 1 16 3 129 26 0.7 1 23 3 130 24 0.7 1 19 5 131 19 0.7 1 18 1 132 26 0.7 1 21 5 133 21 0.7 1 18 3 134 21 0.7 1 17 4 135 49 0.7 1 19 30 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_4_R1.fq.gz ============================================= 50228886 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_4_R2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_4_R2.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3644_4_R2_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_4_R2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_4_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1604.01 s (32 µs/read; 1.88 M reads/minute). === Summary === Total reads processed: 50,228,886 Reads with adapters: 21,636,567 (43.1%) Reads written (passing filters): 50,228,886 (100.0%) Total basepairs processed: 6,352,591,952 bp Quality-trimmed: 1,729,527 bp (0.0%) Total written (filtered): 6,325,433,799 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 21636567 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.6% C: 10.1% G: 6.0% T: 38.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 19340172 12557221.5 0 19340172 2 1494763 3139305.4 0 1494763 3 424673 784826.3 0 424673 4 279671 196206.6 0 279671 5 52568 49051.6 0 52568 6 13090 12262.9 0 13090 7 9143 3065.7 0 9143 8 6874 766.4 0 6874 9 1861 191.6 0 1473 388 10 12512 47.9 1 11560 952 11 148 12.0 1 21 127 12 37 3.0 1 14 23 13 13 0.7 1 5 8 14 7 0.7 1 3 4 15 1 0.7 1 1 16 2 0.7 1 0 2 17 2 0.7 1 0 2 18 2 0.7 1 2 19 10 0.7 1 4 6 20 4 0.7 1 2 2 21 2 0.7 1 2 22 4 0.7 1 3 1 23 7 0.7 1 5 2 24 5 0.7 1 4 1 25 4 0.7 1 2 2 26 1 0.7 1 1 27 1 0.7 1 1 28 3 0.7 1 1 2 29 3 0.7 1 1 2 30 7 0.7 1 5 2 31 3 0.7 1 2 1 32 2 0.7 1 0 2 33 2 0.7 1 2 34 9 0.7 1 5 4 36 3 0.7 1 2 1 37 3 0.7 1 2 1 38 3 0.7 1 2 1 40 11 0.7 1 10 1 41 4 0.7 1 3 1 42 5 0.7 1 4 1 43 2 0.7 1 0 2 44 6 0.7 1 3 3 45 7 0.7 1 6 1 46 1 0.7 1 1 47 5 0.7 1 2 3 48 2 0.7 1 1 1 49 4 0.7 1 2 2 50 3 0.7 1 2 1 51 5 0.7 1 5 52 4 0.7 1 3 1 53 5 0.7 1 2 3 54 6 0.7 1 5 1 55 5 0.7 1 4 1 56 3 0.7 1 2 1 57 4 0.7 1 3 1 58 5 0.7 1 4 1 59 2 0.7 1 1 1 60 5 0.7 1 3 2 61 5 0.7 1 4 1 62 5 0.7 1 4 1 63 6 0.7 1 3 3 64 3 0.7 1 3 65 6 0.7 1 3 3 66 4 0.7 1 3 1 67 1 0.7 1 1 68 5 0.7 1 5 69 4 0.7 1 4 70 7 0.7 1 6 1 71 8 0.7 1 8 72 5 0.7 1 3 2 73 6 0.7 1 3 3 74 9 0.7 1 7 2 75 1 0.7 1 1 76 2 0.7 1 2 77 3 0.7 1 2 1 78 3 0.7 1 3 79 9 0.7 1 5 4 80 11 0.7 1 10 1 81 3 0.7 1 3 82 5 0.7 1 5 83 3 0.7 1 3 84 14 0.7 1 11 3 85 4 0.7 1 4 86 10 0.7 1 8 2 87 5 0.7 1 4 1 88 7 0.7 1 5 2 89 8 0.7 1 8 90 11 0.7 1 7 4 91 6 0.7 1 6 92 7 0.7 1 5 2 93 7 0.7 1 7 94 5 0.7 1 5 95 10 0.7 1 8 2 96 12 0.7 1 9 3 97 9 0.7 1 7 2 98 9 0.7 1 5 4 99 11 0.7 1 10 1 100 10 0.7 1 9 1 101 7 0.7 1 6 1 102 9 0.7 1 7 2 103 13 0.7 1 11 2 104 3 0.7 1 3 105 7 0.7 1 7 106 5 0.7 1 5 107 10 0.7 1 8 2 108 11 0.7 1 8 3 109 16 0.7 1 15 1 110 12 0.7 1 12 111 8 0.7 1 6 2 112 21 0.7 1 19 2 113 11 0.7 1 9 2 114 16 0.7 1 15 1 115 8 0.7 1 8 116 18 0.7 1 17 1 117 10 0.7 1 6 4 118 20 0.7 1 15 5 119 18 0.7 1 15 3 120 11 0.7 1 10 1 121 20 0.7 1 20 122 19 0.7 1 14 5 123 15 0.7 1 14 1 124 32 0.7 1 22 10 125 16 0.7 1 16 126 23 0.7 1 21 2 127 21 0.7 1 15 6 128 15 0.7 1 10 5 129 23 0.7 1 18 5 130 24 0.7 1 19 5 131 26 0.7 1 23 3 132 29 0.7 1 24 5 133 31 0.7 1 24 7 134 33 0.7 1 22 11 135 38 0.7 1 13 25 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_4_R2.fq.gz ============================================= 50228886 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_4_R1_trimmed.fq.gz and zr3644_4_R2_trimmed.fq.gz file_1: zr3644_4_R1_trimmed.fq.gz, file_2: zr3644_4_R2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_4_R1_trimmed.fq.gz and zr3644_4_R2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_4_R1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_4_R2_val_2.fq.gz Total number of sequences analysed: 50228886 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 216426 (0.43%) >>> Now running FastQC on the validated data zr3644_4_R1_val_1.fq.gz<<< Started analysis of zr3644_4_R1_val_1.fq.gz Approx 5% complete for zr3644_4_R1_val_1.fq.gz Approx 10% complete for zr3644_4_R1_val_1.fq.gz Approx 15% complete for zr3644_4_R1_val_1.fq.gz Approx 20% complete for zr3644_4_R1_val_1.fq.gz Approx 25% complete for zr3644_4_R1_val_1.fq.gz Approx 30% complete for zr3644_4_R1_val_1.fq.gz Approx 35% complete for zr3644_4_R1_val_1.fq.gz Approx 40% complete for zr3644_4_R1_val_1.fq.gz Approx 45% complete for zr3644_4_R1_val_1.fq.gz Approx 50% complete for zr3644_4_R1_val_1.fq.gz Approx 55% complete for zr3644_4_R1_val_1.fq.gz Approx 60% complete for zr3644_4_R1_val_1.fq.gz Approx 65% complete for zr3644_4_R1_val_1.fq.gz Approx 70% complete for zr3644_4_R1_val_1.fq.gz Approx 75% complete for zr3644_4_R1_val_1.fq.gz Approx 80% complete for zr3644_4_R1_val_1.fq.gz Approx 85% complete for zr3644_4_R1_val_1.fq.gz Approx 90% complete for zr3644_4_R1_val_1.fq.gz Approx 95% complete for zr3644_4_R1_val_1.fq.gz Analysis complete for zr3644_4_R1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_4_R2_val_2.fq.gz<<< Started analysis of zr3644_4_R2_val_2.fq.gz Approx 5% complete for zr3644_4_R2_val_2.fq.gz Approx 10% complete for zr3644_4_R2_val_2.fq.gz Approx 15% complete for zr3644_4_R2_val_2.fq.gz Approx 20% complete for zr3644_4_R2_val_2.fq.gz Approx 25% complete for zr3644_4_R2_val_2.fq.gz Approx 30% complete for zr3644_4_R2_val_2.fq.gz Approx 35% complete for zr3644_4_R2_val_2.fq.gz Approx 40% complete for zr3644_4_R2_val_2.fq.gz Approx 45% complete for zr3644_4_R2_val_2.fq.gz Approx 50% complete for zr3644_4_R2_val_2.fq.gz Approx 55% complete for zr3644_4_R2_val_2.fq.gz Approx 60% complete for zr3644_4_R2_val_2.fq.gz Approx 65% complete for zr3644_4_R2_val_2.fq.gz Approx 70% complete for zr3644_4_R2_val_2.fq.gz Approx 75% complete for zr3644_4_R2_val_2.fq.gz Approx 80% complete for zr3644_4_R2_val_2.fq.gz Approx 85% complete for zr3644_4_R2_val_2.fq.gz Approx 90% complete for zr3644_4_R2_val_2.fq.gz Approx 95% complete for zr3644_4_R2_val_2.fq.gz Analysis complete for zr3644_4_R2_val_2.fq.gz Deleting both intermediate output files zr3644_4_R1_trimmed.fq.gz and zr3644_4_R2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_5_R1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_5_R1.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3644_5_R1_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_5_R1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_5_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1590.82 s (35 µs/read; 1.69 M reads/minute). === Summary === Total reads processed: 44,881,631 Reads with adapters: 19,722,224 (43.9%) Reads written (passing filters): 44,881,631 (100.0%) Total basepairs processed: 5,692,356,532 bp Quality-trimmed: 2,683,556 bp (0.0%) Total written (filtered): 5,666,410,901 bp (99.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 19722224 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 44.7% C: 10.8% G: 6.4% T: 38.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 17528792 11220407.8 0 17528792 2 1454610 2805101.9 0 1454610 3 418340 701275.5 0 418340 4 240375 175318.9 0 240375 5 41021 43829.7 0 41021 6 11374 10957.4 0 11374 7 7886 2739.4 0 7886 8 5720 684.8 0 5720 9 1679 171.2 0 1298 381 10 11099 42.8 1 10017 1082 11 132 10.7 1 24 108 12 49 2.7 1 16 33 13 7 0.7 1 2 5 14 10 0.7 1 3 7 15 2 0.7 1 1 1 16 11 0.7 1 9 2 17 1 0.7 1 0 1 18 12 0.7 1 6 6 19 15 0.7 1 9 6 20 3 0.7 1 1 2 21 3 0.7 1 1 2 22 4 0.7 1 2 2 23 8 0.7 1 7 1 24 4 0.7 1 4 25 2 0.7 1 1 1 26 6 0.7 1 4 2 27 10 0.7 1 7 3 28 5 0.7 1 2 3 29 5 0.7 1 4 1 30 6 0.7 1 2 4 31 6 0.7 1 4 2 32 5 0.7 1 4 1 33 8 0.7 1 4 4 34 2 0.7 1 0 2 35 6 0.7 1 4 2 36 11 0.7 1 5 6 37 3 0.7 1 2 1 38 8 0.7 1 5 3 39 6 0.7 1 6 40 3 0.7 1 3 41 4 0.7 1 2 2 42 4 0.7 1 3 1 43 8 0.7 1 7 1 44 9 0.7 1 7 2 45 3 0.7 1 2 1 46 7 0.7 1 3 4 47 2 0.7 1 1 1 48 6 0.7 1 4 2 49 11 0.7 1 7 4 50 5 0.7 1 5 51 4 0.7 1 3 1 52 8 0.7 1 5 3 53 6 0.7 1 4 2 54 4 0.7 1 3 1 55 11 0.7 1 8 3 56 7 0.7 1 3 4 57 4 0.7 1 4 58 3 0.7 1 2 1 59 6 0.7 1 5 1 61 3 0.7 1 1 2 62 5 0.7 1 5 63 3 0.7 1 3 64 2 0.7 1 2 65 7 0.7 1 5 2 66 6 0.7 1 4 2 67 6 0.7 1 6 68 5 0.7 1 5 69 4 0.7 1 4 70 2 0.7 1 2 71 2 0.7 1 1 1 72 3 0.7 1 3 73 9 0.7 1 8 1 74 8 0.7 1 4 4 75 6 0.7 1 6 76 11 0.7 1 10 1 77 3 0.7 1 2 1 78 11 0.7 1 7 4 79 6 0.7 1 5 1 81 2 0.7 1 2 82 9 0.7 1 7 2 83 7 0.7 1 7 84 6 0.7 1 3 3 85 8 0.7 1 8 86 9 0.7 1 6 3 87 12 0.7 1 11 1 88 4 0.7 1 3 1 89 9 0.7 1 8 1 90 13 0.7 1 13 91 4 0.7 1 4 92 7 0.7 1 5 2 93 3 0.7 1 3 94 8 0.7 1 7 1 95 9 0.7 1 9 96 10 0.7 1 9 1 97 9 0.7 1 8 1 98 13 0.7 1 11 2 99 14 0.7 1 11 3 100 14 0.7 1 13 1 101 8 0.7 1 5 3 102 11 0.7 1 10 1 103 7 0.7 1 6 1 104 10 0.7 1 9 1 105 8 0.7 1 7 1 106 7 0.7 1 6 1 107 12 0.7 1 11 1 108 10 0.7 1 10 109 10 0.7 1 9 1 110 18 0.7 1 16 2 111 14 0.7 1 13 1 112 14 0.7 1 11 3 113 13 0.7 1 11 2 114 13 0.7 1 9 4 115 13 0.7 1 10 3 116 4 0.7 1 3 1 117 10 0.7 1 8 2 118 12 0.7 1 10 2 119 14 0.7 1 11 3 120 12 0.7 1 12 121 21 0.7 1 17 4 122 17 0.7 1 16 1 123 15 0.7 1 9 6 124 22 0.7 1 21 1 125 12 0.7 1 12 126 33 0.7 1 28 5 127 27 0.7 1 22 5 128 30 0.7 1 26 4 129 26 0.7 1 22 4 130 28 0.7 1 25 3 131 26 0.7 1 20 6 132 26 0.7 1 24 2 133 27 0.7 1 19 8 134 28 0.7 1 18 10 135 33 0.7 1 15 18 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_5_R1.fq.gz ============================================= 44881631 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_5_R2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_5_R2.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3644_5_R2_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_5_R2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_5_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1444.28 s (32 µs/read; 1.86 M reads/minute). === Summary === Total reads processed: 44,881,631 Reads with adapters: 19,396,540 (43.2%) Reads written (passing filters): 44,881,631 (100.0%) Total basepairs processed: 5,690,565,908 bp Quality-trimmed: 1,400,281 bp (0.0%) Total written (filtered): 5,666,348,897 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 19396540 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.5% C: 10.1% G: 6.1% T: 38.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 17327604 11220407.8 0 17327604 2 1345332 2805101.9 0 1345332 3 389691 701275.5 0 389691 4 250075 175318.9 0 250075 5 44626 43829.7 0 44626 6 11196 10957.4 0 11196 7 8027 2739.4 0 8027 8 5938 684.8 0 5938 9 1618 171.2 0 1293 325 10 11157 42.8 1 10293 864 11 122 10.7 1 19 103 12 35 2.7 1 6 29 13 12 0.7 1 5 7 14 4 0.7 1 1 3 15 2 0.7 1 2 16 1 0.7 1 0 1 17 4 0.7 1 3 1 18 2 0.7 1 1 1 19 4 0.7 1 2 2 20 4 0.7 1 2 2 21 3 0.7 1 3 22 4 0.7 1 1 3 23 5 0.7 1 2 3 24 4 0.7 1 3 1 25 4 0.7 1 3 1 26 4 0.7 1 3 1 27 3 0.7 1 3 28 5 0.7 1 2 3 29 2 0.7 1 1 1 30 2 0.7 1 2 31 11 0.7 1 6 5 32 6 0.7 1 3 3 33 8 0.7 1 5 3 34 3 0.7 1 3 35 3 0.7 1 1 2 36 2 0.7 1 2 37 9 0.7 1 6 3 38 7 0.7 1 6 1 39 4 0.7 1 3 1 40 3 0.7 1 3 41 3 0.7 1 1 2 42 1 0.7 1 1 43 3 0.7 1 1 2 44 5 0.7 1 3 2 45 5 0.7 1 5 46 3 0.7 1 3 47 5 0.7 1 5 48 1 0.7 1 1 49 4 0.7 1 4 50 6 0.7 1 4 2 51 7 0.7 1 7 52 3 0.7 1 2 1 53 14 0.7 1 11 3 54 2 0.7 1 2 55 7 0.7 1 5 2 56 7 0.7 1 4 3 57 1 0.7 1 0 1 59 4 0.7 1 4 60 8 0.7 1 5 3 61 2 0.7 1 0 2 62 3 0.7 1 3 63 14 0.7 1 12 2 64 6 0.7 1 6 65 7 0.7 1 7 66 5 0.7 1 5 67 5 0.7 1 2 3 68 6 0.7 1 6 69 14 0.7 1 8 6 70 3 0.7 1 1 2 71 2 0.7 1 2 72 7 0.7 1 6 1 73 1 0.7 1 1 74 6 0.7 1 4 2 75 6 0.7 1 5 1 76 6 0.7 1 3 3 77 6 0.7 1 6 78 8 0.7 1 8 79 6 0.7 1 5 1 80 5 0.7 1 5 81 6 0.7 1 5 1 82 9 0.7 1 7 2 83 10 0.7 1 9 1 84 4 0.7 1 3 1 85 8 0.7 1 7 1 86 3 0.7 1 2 1 87 6 0.7 1 6 88 5 0.7 1 3 2 89 7 0.7 1 7 90 8 0.7 1 7 1 91 4 0.7 1 4 92 9 0.7 1 8 1 93 9 0.7 1 8 1 94 14 0.7 1 12 2 95 12 0.7 1 11 1 96 8 0.7 1 7 1 97 16 0.7 1 16 98 11 0.7 1 8 3 99 14 0.7 1 14 100 13 0.7 1 12 1 101 4 0.7 1 3 1 102 9 0.7 1 8 1 103 12 0.7 1 9 3 104 10 0.7 1 9 1 105 9 0.7 1 7 2 106 8 0.7 1 7 1 107 15 0.7 1 15 108 16 0.7 1 16 109 7 0.7 1 6 1 110 10 0.7 1 9 1 111 12 0.7 1 8 4 112 9 0.7 1 9 113 4 0.7 1 4 114 17 0.7 1 14 3 115 17 0.7 1 13 4 116 12 0.7 1 9 3 117 15 0.7 1 8 7 118 11 0.7 1 10 1 119 22 0.7 1 18 4 120 23 0.7 1 15 8 121 21 0.7 1 16 5 122 14 0.7 1 12 2 123 16 0.7 1 15 1 124 19 0.7 1 17 2 125 21 0.7 1 20 1 126 21 0.7 1 18 3 127 19 0.7 1 14 5 128 28 0.7 1 22 6 129 28 0.7 1 26 2 130 23 0.7 1 22 1 131 19 0.7 1 12 7 132 27 0.7 1 20 7 133 37 0.7 1 30 7 134 28 0.7 1 20 8 135 48 0.7 1 19 29 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_5_R2.fq.gz ============================================= 44881631 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_5_R1_trimmed.fq.gz and zr3644_5_R2_trimmed.fq.gz file_1: zr3644_5_R1_trimmed.fq.gz, file_2: zr3644_5_R2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_5_R1_trimmed.fq.gz and zr3644_5_R2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_5_R1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_5_R2_val_2.fq.gz Total number of sequences analysed: 44881631 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 187536 (0.42%) >>> Now running FastQC on the validated data zr3644_5_R1_val_1.fq.gz<<< Started analysis of zr3644_5_R1_val_1.fq.gz Approx 5% complete for zr3644_5_R1_val_1.fq.gz Approx 10% complete for zr3644_5_R1_val_1.fq.gz Approx 15% complete for zr3644_5_R1_val_1.fq.gz Approx 20% complete for zr3644_5_R1_val_1.fq.gz Approx 25% complete for zr3644_5_R1_val_1.fq.gz Approx 30% complete for zr3644_5_R1_val_1.fq.gz Approx 35% complete for zr3644_5_R1_val_1.fq.gz Approx 40% complete for zr3644_5_R1_val_1.fq.gz Approx 45% complete for zr3644_5_R1_val_1.fq.gz Approx 50% complete for zr3644_5_R1_val_1.fq.gz Approx 55% complete for zr3644_5_R1_val_1.fq.gz Approx 60% complete for zr3644_5_R1_val_1.fq.gz Approx 65% complete for zr3644_5_R1_val_1.fq.gz Approx 70% complete for zr3644_5_R1_val_1.fq.gz Approx 75% complete for zr3644_5_R1_val_1.fq.gz Approx 80% complete for zr3644_5_R1_val_1.fq.gz Approx 85% complete for zr3644_5_R1_val_1.fq.gz Approx 90% complete for zr3644_5_R1_val_1.fq.gz Approx 95% complete for zr3644_5_R1_val_1.fq.gz Analysis complete for zr3644_5_R1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_5_R2_val_2.fq.gz<<< Started analysis of zr3644_5_R2_val_2.fq.gz Approx 5% complete for zr3644_5_R2_val_2.fq.gz Approx 10% complete for zr3644_5_R2_val_2.fq.gz Approx 15% complete for zr3644_5_R2_val_2.fq.gz Approx 20% complete for zr3644_5_R2_val_2.fq.gz Approx 25% complete for zr3644_5_R2_val_2.fq.gz Approx 30% complete for zr3644_5_R2_val_2.fq.gz Approx 35% complete for zr3644_5_R2_val_2.fq.gz Approx 40% complete for zr3644_5_R2_val_2.fq.gz Approx 45% complete for zr3644_5_R2_val_2.fq.gz Approx 50% complete for zr3644_5_R2_val_2.fq.gz Approx 55% complete for zr3644_5_R2_val_2.fq.gz Approx 60% complete for zr3644_5_R2_val_2.fq.gz Approx 65% complete for zr3644_5_R2_val_2.fq.gz Approx 70% complete for zr3644_5_R2_val_2.fq.gz Approx 75% complete for zr3644_5_R2_val_2.fq.gz Approx 80% complete for zr3644_5_R2_val_2.fq.gz Approx 85% complete for zr3644_5_R2_val_2.fq.gz Approx 90% complete for zr3644_5_R2_val_2.fq.gz Approx 95% complete for zr3644_5_R2_val_2.fq.gz Analysis complete for zr3644_5_R2_val_2.fq.gz Deleting both intermediate output files zr3644_5_R1_trimmed.fq.gz and zr3644_5_R2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_6_R1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_6_R1.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3644_6_R1_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_6_R1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_6_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1752.19 s (32 µs/read; 1.86 M reads/minute). === Summary === Total reads processed: 54,279,403 Reads with adapters: 23,503,336 (43.3%) Reads written (passing filters): 54,279,403 (100.0%) Total basepairs processed: 6,866,266,970 bp Quality-trimmed: 2,331,881 bp (0.0%) Total written (filtered): 6,836,138,023 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 23503336 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.1% C: 10.4% G: 6.4% T: 38.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 20859514 13569850.8 0 20859514 2 1750993 3392462.7 0 1750993 3 487441 848115.7 0 487441 4 299944 212028.9 0 299944 5 55176 53007.2 0 55176 6 14518 13251.8 0 14518 7 10342 3313.0 0 10342 8 7594 828.2 0 7594 9 2061 207.1 0 1612 449 10 14212 51.8 1 13087 1125 11 164 12.9 1 37 127 12 66 3.2 1 24 42 13 6 0.8 1 1 5 14 13 0.8 1 7 6 15 4 0.8 1 3 1 16 11 0.8 1 7 4 18 32 0.8 1 17 15 19 26 0.8 1 18 8 20 8 0.8 1 5 3 21 6 0.8 1 5 1 22 1 0.8 1 0 1 23 11 0.8 1 7 4 24 18 0.8 1 13 5 25 1 0.8 1 0 1 26 8 0.8 1 5 3 27 7 0.8 1 5 2 28 4 0.8 1 3 1 29 5 0.8 1 2 3 30 14 0.8 1 9 5 31 15 0.8 1 11 4 32 3 0.8 1 3 33 17 0.8 1 12 5 34 4 0.8 1 1 3 35 7 0.8 1 4 3 36 5 0.8 1 5 37 8 0.8 1 2 6 38 6 0.8 1 3 3 39 5 0.8 1 3 2 40 10 0.8 1 9 1 41 7 0.8 1 2 5 42 11 0.8 1 5 6 43 11 0.8 1 8 3 44 7 0.8 1 5 2 45 4 0.8 1 2 2 46 4 0.8 1 4 47 4 0.8 1 3 1 48 10 0.8 1 5 5 49 8 0.8 1 6 2 50 4 0.8 1 3 1 51 4 0.8 1 3 1 52 11 0.8 1 6 5 53 8 0.8 1 6 2 54 6 0.8 1 6 55 14 0.8 1 8 6 56 15 0.8 1 11 4 57 8 0.8 1 4 4 58 2 0.8 1 2 59 4 0.8 1 4 60 2 0.8 1 1 1 61 3 0.8 1 3 62 12 0.8 1 9 3 63 3 0.8 1 3 64 3 0.8 1 3 65 10 0.8 1 8 2 66 9 0.8 1 7 2 67 2 0.8 1 2 68 8 0.8 1 6 2 69 5 0.8 1 2 3 70 5 0.8 1 4 1 71 3 0.8 1 3 72 9 0.8 1 8 1 73 3 0.8 1 3 74 5 0.8 1 2 3 75 6 0.8 1 6 76 10 0.8 1 8 2 77 4 0.8 1 3 1 78 9 0.8 1 7 2 79 6 0.8 1 5 1 80 5 0.8 1 4 1 81 9 0.8 1 9 82 5 0.8 1 4 1 83 8 0.8 1 4 4 84 7 0.8 1 6 1 85 8 0.8 1 7 1 86 9 0.8 1 9 87 8 0.8 1 7 1 88 9 0.8 1 8 1 89 4 0.8 1 4 90 9 0.8 1 8 1 91 12 0.8 1 8 4 92 6 0.8 1 6 93 6 0.8 1 4 2 94 8 0.8 1 5 3 95 7 0.8 1 5 2 96 10 0.8 1 7 3 97 11 0.8 1 5 6 98 6 0.8 1 5 1 99 8 0.8 1 7 1 100 10 0.8 1 8 2 101 8 0.8 1 6 2 102 5 0.8 1 5 103 8 0.8 1 7 1 104 8 0.8 1 6 2 105 10 0.8 1 8 2 106 14 0.8 1 12 2 107 12 0.8 1 10 2 108 19 0.8 1 13 6 109 11 0.8 1 8 3 110 8 0.8 1 5 3 111 9 0.8 1 7 2 112 14 0.8 1 13 1 113 15 0.8 1 13 2 114 16 0.8 1 14 2 115 9 0.8 1 8 1 116 7 0.8 1 7 117 17 0.8 1 15 2 118 9 0.8 1 9 119 11 0.8 1 9 2 120 23 0.8 1 21 2 121 25 0.8 1 25 122 20 0.8 1 17 3 123 23 0.8 1 19 4 124 19 0.8 1 18 1 125 25 0.8 1 22 3 126 18 0.8 1 16 2 127 17 0.8 1 14 3 128 33 0.8 1 30 3 129 26 0.8 1 25 1 130 23 0.8 1 20 3 131 26 0.8 1 20 6 132 29 0.8 1 23 6 133 34 0.8 1 26 8 134 39 0.8 1 29 10 135 42 0.8 1 19 23 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_6_R1.fq.gz ============================================= 54279403 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_6_R2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_6_R2.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3644_6_R2_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_6_R2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_6_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1753.56 s (32 µs/read; 1.86 M reads/minute). === Summary === Total reads processed: 54,279,403 Reads with adapters: 23,389,569 (43.1%) Reads written (passing filters): 54,279,403 (100.0%) Total basepairs processed: 6,864,471,929 bp Quality-trimmed: 1,982,834 bp (0.0%) Total written (filtered): 6,834,977,157 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 23389569 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.5% C: 10.2% G: 6.1% T: 38.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 20894172 13569850.8 0 20894172 2 1616291 3392462.7 0 1616291 3 469462 848115.7 0 469462 4 305433 212028.9 0 305433 5 55463 53007.2 0 55463 6 13979 13251.8 0 13979 7 9891 3313.0 0 9891 8 7745 828.2 0 7745 9 2130 207.1 0 1675 455 10 13659 51.8 1 12616 1043 11 191 12.9 1 20 171 12 40 3.2 1 14 26 13 9 0.8 1 3 6 14 2 0.8 1 0 2 15 1 0.8 1 0 1 16 7 0.8 1 4 3 17 5 0.8 1 3 2 18 1 0.8 1 1 19 6 0.8 1 4 2 20 7 0.8 1 5 2 22 3 0.8 1 2 1 23 2 0.8 1 2 24 6 0.8 1 2 4 25 3 0.8 1 2 1 26 7 0.8 1 3 4 27 6 0.8 1 6 28 8 0.8 1 4 4 29 6 0.8 1 3 3 30 5 0.8 1 1 4 32 4 0.8 1 1 3 33 2 0.8 1 1 1 34 7 0.8 1 1 6 35 7 0.8 1 3 4 36 6 0.8 1 6 37 5 0.8 1 2 3 38 3 0.8 1 2 1 39 3 0.8 1 2 1 40 8 0.8 1 5 3 41 4 0.8 1 3 1 42 8 0.8 1 5 3 43 8 0.8 1 6 2 44 3 0.8 1 1 2 45 8 0.8 1 6 2 46 7 0.8 1 3 4 47 7 0.8 1 4 3 48 4 0.8 1 4 49 4 0.8 1 4 50 5 0.8 1 5 51 4 0.8 1 2 2 52 1 0.8 1 0 1 53 3 0.8 1 2 1 54 2 0.8 1 1 1 55 12 0.8 1 6 6 56 5 0.8 1 4 1 57 2 0.8 1 2 58 6 0.8 1 5 1 59 5 0.8 1 2 3 60 2 0.8 1 1 1 61 2 0.8 1 1 1 62 5 0.8 1 5 63 1 0.8 1 1 64 9 0.8 1 9 65 4 0.8 1 4 66 5 0.8 1 3 2 67 4 0.8 1 4 68 2 0.8 1 2 69 8 0.8 1 7 1 70 5 0.8 1 3 2 71 7 0.8 1 4 3 72 4 0.8 1 3 1 73 8 0.8 1 5 3 74 11 0.8 1 9 2 75 9 0.8 1 8 1 76 7 0.8 1 6 1 77 9 0.8 1 6 3 78 11 0.8 1 7 4 79 6 0.8 1 5 1 80 5 0.8 1 4 1 81 10 0.8 1 6 4 82 5 0.8 1 4 1 83 8 0.8 1 7 1 84 10 0.8 1 8 2 85 6 0.8 1 6 86 5 0.8 1 4 1 87 13 0.8 1 9 4 88 7 0.8 1 6 1 89 13 0.8 1 10 3 90 9 0.8 1 6 3 91 7 0.8 1 6 1 92 4 0.8 1 4 93 5 0.8 1 3 2 94 11 0.8 1 10 1 95 12 0.8 1 10 2 96 8 0.8 1 8 97 7 0.8 1 6 1 98 12 0.8 1 11 1 99 11 0.8 1 9 2 100 7 0.8 1 6 1 101 8 0.8 1 6 2 102 6 0.8 1 6 103 12 0.8 1 12 104 6 0.8 1 6 105 16 0.8 1 15 1 106 16 0.8 1 11 5 107 6 0.8 1 5 1 108 18 0.8 1 13 5 109 13 0.8 1 13 110 14 0.8 1 13 1 111 14 0.8 1 12 2 112 11 0.8 1 11 113 20 0.8 1 20 114 12 0.8 1 10 2 115 13 0.8 1 9 4 116 17 0.8 1 15 2 117 17 0.8 1 17 118 19 0.8 1 19 119 20 0.8 1 15 5 120 19 0.8 1 17 2 121 23 0.8 1 20 3 122 12 0.8 1 9 3 123 13 0.8 1 9 4 124 9 0.8 1 8 1 125 16 0.8 1 13 3 126 19 0.8 1 14 5 127 12 0.8 1 10 2 128 16 0.8 1 14 2 129 28 0.8 1 26 2 130 19 0.8 1 16 3 131 28 0.8 1 28 132 31 0.8 1 27 4 133 25 0.8 1 22 3 134 29 0.8 1 17 12 135 35 0.8 1 7 28 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_6_R2.fq.gz ============================================= 54279403 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_6_R1_trimmed.fq.gz and zr3644_6_R2_trimmed.fq.gz file_1: zr3644_6_R1_trimmed.fq.gz, file_2: zr3644_6_R2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_6_R1_trimmed.fq.gz and zr3644_6_R2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_6_R1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_6_R2_val_2.fq.gz Total number of sequences analysed: 54279403 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 246739 (0.45%) >>> Now running FastQC on the validated data zr3644_6_R1_val_1.fq.gz<<< Started analysis of zr3644_6_R1_val_1.fq.gz Approx 5% complete for zr3644_6_R1_val_1.fq.gz Approx 10% complete for zr3644_6_R1_val_1.fq.gz Approx 15% complete for zr3644_6_R1_val_1.fq.gz Approx 20% complete for zr3644_6_R1_val_1.fq.gz Approx 25% complete for zr3644_6_R1_val_1.fq.gz Approx 30% complete for zr3644_6_R1_val_1.fq.gz Approx 35% complete for zr3644_6_R1_val_1.fq.gz Approx 40% complete for zr3644_6_R1_val_1.fq.gz Approx 45% complete for zr3644_6_R1_val_1.fq.gz Approx 50% complete for zr3644_6_R1_val_1.fq.gz Approx 55% complete for zr3644_6_R1_val_1.fq.gz Approx 60% complete for zr3644_6_R1_val_1.fq.gz Approx 65% complete for zr3644_6_R1_val_1.fq.gz Approx 70% complete for zr3644_6_R1_val_1.fq.gz Approx 75% complete for zr3644_6_R1_val_1.fq.gz Approx 80% complete for zr3644_6_R1_val_1.fq.gz Approx 85% complete for zr3644_6_R1_val_1.fq.gz Approx 90% complete for zr3644_6_R1_val_1.fq.gz Approx 95% complete for zr3644_6_R1_val_1.fq.gz Analysis complete for zr3644_6_R1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_6_R2_val_2.fq.gz<<< Started analysis of zr3644_6_R2_val_2.fq.gz Approx 5% complete for zr3644_6_R2_val_2.fq.gz Approx 10% complete for zr3644_6_R2_val_2.fq.gz Approx 15% complete for zr3644_6_R2_val_2.fq.gz Approx 20% complete for zr3644_6_R2_val_2.fq.gz Approx 25% complete for zr3644_6_R2_val_2.fq.gz Approx 30% complete for zr3644_6_R2_val_2.fq.gz Approx 35% complete for zr3644_6_R2_val_2.fq.gz Approx 40% complete for zr3644_6_R2_val_2.fq.gz Approx 45% complete for zr3644_6_R2_val_2.fq.gz Approx 50% complete for zr3644_6_R2_val_2.fq.gz Approx 55% complete for zr3644_6_R2_val_2.fq.gz Approx 60% complete for zr3644_6_R2_val_2.fq.gz Approx 65% complete for zr3644_6_R2_val_2.fq.gz Approx 70% complete for zr3644_6_R2_val_2.fq.gz Approx 75% complete for zr3644_6_R2_val_2.fq.gz Approx 80% complete for zr3644_6_R2_val_2.fq.gz Approx 85% complete for zr3644_6_R2_val_2.fq.gz Approx 90% complete for zr3644_6_R2_val_2.fq.gz Approx 95% complete for zr3644_6_R2_val_2.fq.gz Analysis complete for zr3644_6_R2_val_2.fq.gz Deleting both intermediate output files zr3644_6_R1_trimmed.fq.gz and zr3644_6_R2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_7_R1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_7_R1.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3644_7_R1_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_7_R1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_7_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 2655.20 s (32 µs/read; 1.87 M reads/minute). === Summary === Total reads processed: 82,933,633 Reads with adapters: 36,177,192 (43.6%) Reads written (passing filters): 82,933,633 (100.0%) Total basepairs processed: 10,519,950,530 bp Quality-trimmed: 2,898,401 bp (0.0%) Total written (filtered): 10,474,395,775 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 36177192 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.3% C: 10.3% G: 6.2% T: 38.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 32189614 20733408.2 0 32189614 2 2643851 5183352.1 0 2643851 3 730512 1295838.0 0 730512 4 454107 323959.5 0 454107 5 83925 80989.9 0 83925 6 21891 20247.5 0 21891 7 15266 5061.9 0 15266 8 11574 1265.5 0 11574 9 3140 316.4 0 2517 623 10 20789 79.1 1 19181 1608 11 274 19.8 1 43 231 12 104 4.9 1 32 72 13 11 1.2 1 3 8 14 18 1.2 1 10 8 15 7 1.2 1 4 3 16 21 1.2 1 15 6 17 2 1.2 1 1 1 18 35 1.2 1 24 11 19 53 1.2 1 34 19 20 5 1.2 1 2 3 21 5 1.2 1 3 2 22 10 1.2 1 6 4 23 21 1.2 1 15 6 24 33 1.2 1 19 14 25 7 1.2 1 5 2 26 10 1.2 1 6 4 27 14 1.2 1 10 4 28 4 1.2 1 3 1 29 11 1.2 1 8 3 30 28 1.2 1 22 6 31 20 1.2 1 12 8 32 10 1.2 1 6 4 33 35 1.2 1 22 13 34 12 1.2 1 10 2 35 12 1.2 1 8 4 36 15 1.2 1 10 5 37 16 1.2 1 13 3 38 9 1.2 1 7 2 39 17 1.2 1 12 5 40 12 1.2 1 7 5 41 8 1.2 1 6 2 42 15 1.2 1 8 7 43 19 1.2 1 12 7 44 22 1.2 1 17 5 45 6 1.2 1 6 46 10 1.2 1 6 4 47 5 1.2 1 5 48 26 1.2 1 20 6 49 7 1.2 1 5 2 50 6 1.2 1 3 3 51 17 1.2 1 9 8 52 18 1.2 1 14 4 53 15 1.2 1 13 2 54 6 1.2 1 3 3 55 27 1.2 1 21 6 56 17 1.2 1 10 7 57 8 1.2 1 5 3 58 8 1.2 1 6 2 59 8 1.2 1 6 2 60 6 1.2 1 5 1 61 11 1.2 1 9 2 62 18 1.2 1 15 3 63 6 1.2 1 6 64 11 1.2 1 9 2 65 11 1.2 1 11 66 17 1.2 1 8 9 67 13 1.2 1 9 4 68 7 1.2 1 5 2 69 13 1.2 1 13 70 12 1.2 1 10 2 71 6 1.2 1 6 72 13 1.2 1 10 3 73 18 1.2 1 15 3 74 6 1.2 1 6 75 15 1.2 1 11 4 76 8 1.2 1 7 1 77 10 1.2 1 7 3 78 12 1.2 1 9 3 79 14 1.2 1 12 2 80 9 1.2 1 8 1 81 11 1.2 1 11 82 11 1.2 1 9 2 83 13 1.2 1 11 2 84 12 1.2 1 12 85 7 1.2 1 6 1 86 4 1.2 1 4 87 9 1.2 1 6 3 88 10 1.2 1 8 2 89 13 1.2 1 9 4 90 15 1.2 1 14 1 91 21 1.2 1 18 3 92 13 1.2 1 12 1 93 17 1.2 1 16 1 94 23 1.2 1 21 2 95 10 1.2 1 9 1 96 9 1.2 1 9 97 12 1.2 1 12 98 15 1.2 1 12 3 99 18 1.2 1 16 2 100 13 1.2 1 9 4 101 12 1.2 1 10 2 102 14 1.2 1 12 2 103 15 1.2 1 13 2 104 11 1.2 1 9 2 105 16 1.2 1 13 3 106 12 1.2 1 9 3 107 19 1.2 1 17 2 108 22 1.2 1 19 3 109 23 1.2 1 20 3 110 14 1.2 1 13 1 111 31 1.2 1 24 7 112 16 1.2 1 11 5 113 22 1.2 1 19 3 114 16 1.2 1 13 3 115 20 1.2 1 18 2 116 27 1.2 1 25 2 117 14 1.2 1 13 1 118 27 1.2 1 25 2 119 28 1.2 1 22 6 120 38 1.2 1 35 3 121 22 1.2 1 21 1 122 30 1.2 1 26 4 123 25 1.2 1 23 2 124 26 1.2 1 23 3 125 40 1.2 1 33 7 126 25 1.2 1 23 2 127 25 1.2 1 22 3 128 24 1.2 1 21 3 129 27 1.2 1 23 4 130 47 1.2 1 41 6 131 53 1.2 1 46 7 132 45 1.2 1 38 7 133 67 1.2 1 52 15 134 46 1.2 1 25 21 135 53 1.2 1 30 23 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_7_R1.fq.gz ============================================= 82933633 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_7_R2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_7_R2.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3644_7_R2_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_7_R2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_7_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 2765.69 s (33 µs/read; 1.80 M reads/minute). === Summary === Total reads processed: 82,933,633 Reads with adapters: 36,117,516 (43.5%) Reads written (passing filters): 82,933,633 (100.0%) Total basepairs processed: 10,515,361,816 bp Quality-trimmed: 3,279,955 bp (0.0%) Total written (filtered): 10,469,702,809 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 36117516 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.7% C: 10.2% G: 6.1% T: 38.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 32338767 20733408.2 0 32338767 2 2433358 5183352.1 0 2433358 3 726050 1295838.0 0 726050 4 462161 323959.5 0 462161 5 84776 80989.9 0 84776 6 20704 20247.5 0 20704 7 15079 5061.9 0 15079 8 11270 1265.5 0 11270 9 3227 316.4 0 2607 620 10 19965 79.1 1 18231 1734 11 257 19.8 1 28 229 12 62 4.9 1 14 48 13 20 1.2 1 10 10 14 8 1.2 1 1 7 15 7 1.2 1 4 3 16 4 1.2 1 2 2 17 7 1.2 1 2 5 18 4 1.2 1 3 1 19 8 1.2 1 4 4 20 10 1.2 1 7 3 21 5 1.2 1 3 2 22 11 1.2 1 4 7 23 12 1.2 1 7 5 24 12 1.2 1 7 5 25 3 1.2 1 3 26 11 1.2 1 7 4 27 12 1.2 1 6 6 28 17 1.2 1 9 8 29 5 1.2 1 4 1 30 3 1.2 1 2 1 31 2 1.2 1 1 1 32 8 1.2 1 4 4 33 8 1.2 1 4 4 34 7 1.2 1 6 1 35 8 1.2 1 6 2 36 15 1.2 1 9 6 37 3 1.2 1 1 2 38 7 1.2 1 6 1 39 3 1.2 1 2 1 40 10 1.2 1 6 4 41 8 1.2 1 6 2 42 8 1.2 1 6 2 43 7 1.2 1 6 1 44 7 1.2 1 4 3 45 9 1.2 1 8 1 46 8 1.2 1 6 2 47 5 1.2 1 2 3 48 12 1.2 1 10 2 49 10 1.2 1 7 3 50 13 1.2 1 7 6 51 8 1.2 1 7 1 52 4 1.2 1 3 1 53 8 1.2 1 6 2 54 3 1.2 1 2 1 55 13 1.2 1 11 2 56 4 1.2 1 4 57 11 1.2 1 7 4 58 4 1.2 1 4 59 10 1.2 1 6 4 60 11 1.2 1 8 3 61 5 1.2 1 5 62 9 1.2 1 7 2 63 9 1.2 1 8 1 64 13 1.2 1 12 1 65 6 1.2 1 5 1 66 9 1.2 1 7 2 67 6 1.2 1 6 68 12 1.2 1 12 69 10 1.2 1 7 3 70 20 1.2 1 15 5 71 11 1.2 1 6 5 72 9 1.2 1 7 2 73 14 1.2 1 14 74 10 1.2 1 7 3 75 12 1.2 1 10 2 76 8 1.2 1 7 1 77 11 1.2 1 10 1 78 14 1.2 1 11 3 79 11 1.2 1 10 1 80 10 1.2 1 9 1 81 16 1.2 1 16 82 9 1.2 1 8 1 83 17 1.2 1 13 4 84 17 1.2 1 15 2 85 17 1.2 1 12 5 86 18 1.2 1 14 4 87 11 1.2 1 8 3 88 16 1.2 1 16 89 15 1.2 1 11 4 90 13 1.2 1 13 91 9 1.2 1 6 3 92 10 1.2 1 10 93 13 1.2 1 13 94 17 1.2 1 14 3 95 12 1.2 1 11 1 96 20 1.2 1 16 4 97 18 1.2 1 13 5 98 14 1.2 1 11 3 99 12 1.2 1 9 3 100 16 1.2 1 12 4 101 21 1.2 1 16 5 102 15 1.2 1 12 3 103 13 1.2 1 10 3 104 13 1.2 1 10 3 105 26 1.2 1 23 3 106 12 1.2 1 9 3 107 18 1.2 1 15 3 108 18 1.2 1 12 6 109 18 1.2 1 17 1 110 21 1.2 1 19 2 111 21 1.2 1 19 2 112 19 1.2 1 16 3 113 19 1.2 1 15 4 114 24 1.2 1 20 4 115 12 1.2 1 10 2 116 35 1.2 1 29 6 117 21 1.2 1 17 4 118 17 1.2 1 15 2 119 34 1.2 1 29 5 120 18 1.2 1 15 3 121 20 1.2 1 18 2 122 33 1.2 1 28 5 123 20 1.2 1 16 4 124 21 1.2 1 20 1 125 22 1.2 1 18 4 126 33 1.2 1 28 5 127 45 1.2 1 36 9 128 36 1.2 1 32 4 129 37 1.2 1 28 9 130 43 1.2 1 41 2 131 43 1.2 1 36 7 132 39 1.2 1 34 5 133 47 1.2 1 33 14 134 50 1.2 1 38 12 135 64 1.2 1 35 29 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_7_R2.fq.gz ============================================= 82933633 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_7_R1_trimmed.fq.gz and zr3644_7_R2_trimmed.fq.gz file_1: zr3644_7_R1_trimmed.fq.gz, file_2: zr3644_7_R2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_7_R1_trimmed.fq.gz and zr3644_7_R2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_7_R1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_7_R2_val_2.fq.gz Total number of sequences analysed: 82933633 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 357666 (0.43%) >>> Now running FastQC on the validated data zr3644_7_R1_val_1.fq.gz<<< Started analysis of zr3644_7_R1_val_1.fq.gz Approx 5% complete for zr3644_7_R1_val_1.fq.gz Approx 10% complete for zr3644_7_R1_val_1.fq.gz Approx 15% complete for zr3644_7_R1_val_1.fq.gz Approx 20% complete for zr3644_7_R1_val_1.fq.gz Approx 25% complete for zr3644_7_R1_val_1.fq.gz Approx 30% complete for zr3644_7_R1_val_1.fq.gz Approx 35% complete for zr3644_7_R1_val_1.fq.gz Approx 40% complete for zr3644_7_R1_val_1.fq.gz Approx 45% complete for zr3644_7_R1_val_1.fq.gz Approx 50% complete for zr3644_7_R1_val_1.fq.gz Approx 55% complete for zr3644_7_R1_val_1.fq.gz Approx 60% complete for zr3644_7_R1_val_1.fq.gz Approx 65% complete for zr3644_7_R1_val_1.fq.gz Approx 70% complete for zr3644_7_R1_val_1.fq.gz Approx 75% complete for zr3644_7_R1_val_1.fq.gz Approx 80% complete for zr3644_7_R1_val_1.fq.gz Approx 85% complete for zr3644_7_R1_val_1.fq.gz Approx 90% complete for zr3644_7_R1_val_1.fq.gz Approx 95% complete for zr3644_7_R1_val_1.fq.gz Analysis complete for zr3644_7_R1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_7_R2_val_2.fq.gz<<< Started analysis of zr3644_7_R2_val_2.fq.gz Approx 5% complete for zr3644_7_R2_val_2.fq.gz Approx 10% complete for zr3644_7_R2_val_2.fq.gz Approx 15% complete for zr3644_7_R2_val_2.fq.gz Approx 20% complete for zr3644_7_R2_val_2.fq.gz Approx 25% complete for zr3644_7_R2_val_2.fq.gz Approx 30% complete for zr3644_7_R2_val_2.fq.gz Approx 35% complete for zr3644_7_R2_val_2.fq.gz Approx 40% complete for zr3644_7_R2_val_2.fq.gz Approx 45% complete for zr3644_7_R2_val_2.fq.gz Approx 50% complete for zr3644_7_R2_val_2.fq.gz Approx 55% complete for zr3644_7_R2_val_2.fq.gz Approx 60% complete for zr3644_7_R2_val_2.fq.gz Approx 65% complete for zr3644_7_R2_val_2.fq.gz Approx 70% complete for zr3644_7_R2_val_2.fq.gz Approx 75% complete for zr3644_7_R2_val_2.fq.gz Approx 80% complete for zr3644_7_R2_val_2.fq.gz Approx 85% complete for zr3644_7_R2_val_2.fq.gz Approx 90% complete for zr3644_7_R2_val_2.fq.gz Approx 95% complete for zr3644_7_R2_val_2.fq.gz Analysis complete for zr3644_7_R2_val_2.fq.gz Deleting both intermediate output files zr3644_7_R1_trimmed.fq.gz and zr3644_7_R2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_8_R1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_8_R1.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3644_8_R1_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_8_R1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_8_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1699.97 s (39 µs/read; 1.52 M reads/minute). === Summary === Total reads processed: 43,149,301 Reads with adapters: 18,575,513 (43.0%) Reads written (passing filters): 43,149,301 (100.0%) Total basepairs processed: 5,444,670,140 bp Quality-trimmed: 1,595,123 bp (0.0%) Total written (filtered): 5,421,008,525 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 18575513 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.0% C: 10.5% G: 6.4% T: 38.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 16448696 10787325.2 0 16448696 2 1401414 2696831.3 0 1401414 3 388555 674207.8 0 388555 4 244595 168552.0 0 244595 5 49532 42138.0 0 49532 6 12305 10534.5 0 12305 7 8768 2633.6 0 8768 8 6717 658.4 0 6717 9 1780 164.6 0 1436 344 10 11939 41.2 1 11083 856 11 130 10.3 1 21 109 12 38 2.6 1 12 26 13 8 0.6 1 3 5 14 4 0.6 1 3 1 15 2 0.6 1 1 1 16 7 0.6 1 3 4 17 3 0.6 1 2 1 18 9 0.6 1 6 3 19 15 0.6 1 9 6 20 4 0.6 1 4 21 2 0.6 1 2 22 4 0.6 1 3 1 23 8 0.6 1 5 3 24 2 0.6 1 2 25 3 0.6 1 3 26 4 0.6 1 2 2 27 7 0.6 1 6 1 28 3 0.6 1 2 1 29 6 0.6 1 4 2 30 4 0.6 1 3 1 31 11 0.6 1 6 5 32 3 0.6 1 3 33 5 0.6 1 3 2 34 3 0.6 1 2 1 35 1 0.6 1 0 1 36 2 0.6 1 1 1 37 6 0.6 1 3 3 38 5 0.6 1 4 1 39 2 0.6 1 2 40 3 0.6 1 2 1 41 2 0.6 1 1 1 42 1 0.6 1 1 43 11 0.6 1 7 4 44 4 0.6 1 3 1 45 3 0.6 1 2 1 46 5 0.6 1 3 2 47 4 0.6 1 2 2 48 5 0.6 1 5 49 7 0.6 1 3 4 50 5 0.6 1 3 2 51 4 0.6 1 4 52 3 0.6 1 3 53 7 0.6 1 4 3 54 3 0.6 1 2 1 55 5 0.6 1 5 56 5 0.6 1 3 2 57 9 0.6 1 8 1 58 1 0.6 1 1 59 6 0.6 1 5 1 60 9 0.6 1 6 3 61 4 0.6 1 4 62 7 0.6 1 6 1 63 3 0.6 1 3 64 4 0.6 1 4 65 4 0.6 1 3 1 66 7 0.6 1 6 1 67 2 0.6 1 1 1 68 5 0.6 1 3 2 69 8 0.6 1 5 3 70 6 0.6 1 6 71 3 0.6 1 3 72 13 0.6 1 8 5 73 6 0.6 1 5 1 74 6 0.6 1 4 2 75 9 0.6 1 2 7 76 8 0.6 1 4 4 77 4 0.6 1 4 78 6 0.6 1 6 79 1 0.6 1 1 80 9 0.6 1 5 4 81 6 0.6 1 4 2 82 8 0.6 1 7 1 83 6 0.6 1 4 2 84 7 0.6 1 6 1 85 12 0.6 1 9 3 86 2 0.6 1 1 1 87 4 0.6 1 2 2 88 11 0.6 1 9 2 89 11 0.6 1 10 1 90 12 0.6 1 10 2 91 7 0.6 1 6 1 92 8 0.6 1 7 1 93 7 0.6 1 7 94 8 0.6 1 6 2 95 5 0.6 1 5 96 9 0.6 1 8 1 97 8 0.6 1 5 3 98 3 0.6 1 3 99 6 0.6 1 4 2 100 5 0.6 1 5 101 5 0.6 1 4 1 102 9 0.6 1 5 4 103 5 0.6 1 5 104 9 0.6 1 6 3 105 8 0.6 1 6 2 106 8 0.6 1 6 2 107 10 0.6 1 5 5 108 10 0.6 1 8 2 109 9 0.6 1 7 2 110 7 0.6 1 7 111 11 0.6 1 7 4 112 21 0.6 1 18 3 113 11 0.6 1 9 2 114 11 0.6 1 10 1 115 9 0.6 1 8 1 116 11 0.6 1 8 3 117 20 0.6 1 19 1 118 8 0.6 1 6 2 119 8 0.6 1 7 1 120 11 0.6 1 10 1 121 15 0.6 1 14 1 122 21 0.6 1 16 5 123 17 0.6 1 13 4 124 15 0.6 1 15 125 19 0.6 1 16 3 126 21 0.6 1 19 2 127 23 0.6 1 20 3 128 21 0.6 1 18 3 129 25 0.6 1 21 4 130 23 0.6 1 20 3 131 23 0.6 1 22 1 132 24 0.6 1 21 3 133 37 0.6 1 28 9 134 25 0.6 1 16 9 135 39 0.6 1 14 25 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_8_R1.fq.gz ============================================= 43149301 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_8_R2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_8_R2.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3644_8_R2_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_8_R2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_8_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1447.08 s (34 µs/read; 1.79 M reads/minute). === Summary === Total reads processed: 43,149,301 Reads with adapters: 18,631,147 (43.2%) Reads written (passing filters): 43,149,301 (100.0%) Total basepairs processed: 5,443,153,167 bp Quality-trimmed: 1,812,726 bp (0.0%) Total written (filtered): 5,419,360,965 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 18631147 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.4% C: 10.3% G: 6.3% T: 38.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 16618768 10787325.2 0 16618768 2 1296734 2696831.3 0 1296734 3 379833 674207.8 0 379833 4 245864 168552.0 0 245864 5 48781 42138.0 0 48781 6 11644 10534.5 0 11644 7 8534 2633.6 0 8534 8 6628 658.4 0 6628 9 1831 164.6 0 1474 357 10 11430 41.2 1 10505 925 11 149 10.3 1 20 129 12 42 2.6 1 11 31 13 14 0.6 1 3 11 14 3 0.6 1 1 2 15 7 0.6 1 3 4 16 1 0.6 1 1 17 4 0.6 1 1 3 19 3 0.6 1 3 20 1 0.6 1 0 1 21 4 0.6 1 3 1 22 3 0.6 1 1 2 23 6 0.6 1 2 4 24 6 0.6 1 2 4 25 3 0.6 1 1 2 26 7 0.6 1 4 3 27 2 0.6 1 0 2 28 4 0.6 1 3 1 29 3 0.6 1 1 2 30 3 0.6 1 3 31 3 0.6 1 2 1 32 4 0.6 1 2 2 33 2 0.6 1 2 34 2 0.6 1 1 1 35 6 0.6 1 3 3 36 4 0.6 1 2 2 37 2 0.6 1 2 38 1 0.6 1 1 39 5 0.6 1 4 1 40 5 0.6 1 4 1 41 5 0.6 1 4 1 42 7 0.6 1 5 2 43 7 0.6 1 5 2 44 7 0.6 1 2 5 45 3 0.6 1 2 1 46 2 0.6 1 2 47 9 0.6 1 5 4 48 5 0.6 1 3 2 49 5 0.6 1 3 2 50 2 0.6 1 2 51 3 0.6 1 1 2 52 8 0.6 1 6 2 53 5 0.6 1 4 1 54 5 0.6 1 3 2 55 3 0.6 1 3 56 6 0.6 1 5 1 57 10 0.6 1 9 1 58 5 0.6 1 3 2 59 6 0.6 1 6 60 9 0.6 1 7 2 61 3 0.6 1 3 62 1 0.6 1 1 63 3 0.6 1 3 64 4 0.6 1 2 2 65 4 0.6 1 2 2 66 7 0.6 1 4 3 67 2 0.6 1 2 68 4 0.6 1 4 69 6 0.6 1 4 2 70 4 0.6 1 4 72 1 0.6 1 0 1 73 4 0.6 1 3 1 74 1 0.6 1 1 75 6 0.6 1 6 76 7 0.6 1 7 77 5 0.6 1 5 78 5 0.6 1 3 2 79 7 0.6 1 7 80 3 0.6 1 3 81 10 0.6 1 4 6 83 5 0.6 1 5 84 10 0.6 1 8 2 85 5 0.6 1 5 86 6 0.6 1 2 4 87 5 0.6 1 5 88 10 0.6 1 9 1 89 3 0.6 1 2 1 90 4 0.6 1 3 1 91 6 0.6 1 4 2 92 2 0.6 1 2 93 8 0.6 1 8 94 4 0.6 1 3 1 95 4 0.6 1 3 1 96 3 0.6 1 3 97 7 0.6 1 3 4 98 17 0.6 1 13 4 99 13 0.6 1 10 3 100 6 0.6 1 6 101 8 0.6 1 6 2 102 9 0.6 1 6 3 103 4 0.6 1 4 104 6 0.6 1 5 1 105 5 0.6 1 3 2 106 13 0.6 1 11 2 107 7 0.6 1 7 108 6 0.6 1 5 1 109 9 0.6 1 8 1 110 3 0.6 1 3 111 7 0.6 1 5 2 112 12 0.6 1 11 1 113 10 0.6 1 9 1 114 12 0.6 1 8 4 115 8 0.6 1 8 116 14 0.6 1 12 2 117 18 0.6 1 18 118 18 0.6 1 16 2 119 16 0.6 1 15 1 120 15 0.6 1 11 4 121 13 0.6 1 13 122 13 0.6 1 10 3 123 11 0.6 1 10 1 124 13 0.6 1 11 2 125 14 0.6 1 12 2 126 15 0.6 1 10 5 127 16 0.6 1 11 5 128 14 0.6 1 13 1 129 24 0.6 1 22 2 130 18 0.6 1 14 4 131 22 0.6 1 18 4 132 31 0.6 1 23 8 133 25 0.6 1 16 9 134 24 0.6 1 17 7 135 31 0.6 1 10 21 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_8_R2.fq.gz ============================================= 43149301 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_8_R1_trimmed.fq.gz and zr3644_8_R2_trimmed.fq.gz file_1: zr3644_8_R1_trimmed.fq.gz, file_2: zr3644_8_R2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_8_R1_trimmed.fq.gz and zr3644_8_R2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_8_R1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_8_R2_val_2.fq.gz Total number of sequences analysed: 43149301 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 205242 (0.48%) >>> Now running FastQC on the validated data zr3644_8_R1_val_1.fq.gz<<< Started analysis of zr3644_8_R1_val_1.fq.gz Approx 5% complete for zr3644_8_R1_val_1.fq.gz Approx 10% complete for zr3644_8_R1_val_1.fq.gz Approx 15% complete for zr3644_8_R1_val_1.fq.gz Approx 20% complete for zr3644_8_R1_val_1.fq.gz Approx 25% complete for zr3644_8_R1_val_1.fq.gz Approx 30% complete for zr3644_8_R1_val_1.fq.gz Approx 35% complete for zr3644_8_R1_val_1.fq.gz Approx 40% complete for zr3644_8_R1_val_1.fq.gz Approx 45% complete for zr3644_8_R1_val_1.fq.gz Approx 50% complete for zr3644_8_R1_val_1.fq.gz Approx 55% complete for zr3644_8_R1_val_1.fq.gz Approx 60% complete for zr3644_8_R1_val_1.fq.gz Approx 65% complete for zr3644_8_R1_val_1.fq.gz Approx 70% complete for zr3644_8_R1_val_1.fq.gz Approx 75% complete for zr3644_8_R1_val_1.fq.gz Approx 80% complete for zr3644_8_R1_val_1.fq.gz Approx 85% complete for zr3644_8_R1_val_1.fq.gz Approx 90% complete for zr3644_8_R1_val_1.fq.gz Approx 95% complete for zr3644_8_R1_val_1.fq.gz Analysis complete for zr3644_8_R1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_8_R2_val_2.fq.gz<<< Started analysis of zr3644_8_R2_val_2.fq.gz Approx 5% complete for zr3644_8_R2_val_2.fq.gz Approx 10% complete for zr3644_8_R2_val_2.fq.gz Approx 15% complete for zr3644_8_R2_val_2.fq.gz Approx 20% complete for zr3644_8_R2_val_2.fq.gz Approx 25% complete for zr3644_8_R2_val_2.fq.gz Approx 30% complete for zr3644_8_R2_val_2.fq.gz Approx 35% complete for zr3644_8_R2_val_2.fq.gz Approx 40% complete for zr3644_8_R2_val_2.fq.gz Approx 45% complete for zr3644_8_R2_val_2.fq.gz Approx 50% complete for zr3644_8_R2_val_2.fq.gz Approx 55% complete for zr3644_8_R2_val_2.fq.gz Approx 60% complete for zr3644_8_R2_val_2.fq.gz Approx 65% complete for zr3644_8_R2_val_2.fq.gz Approx 70% complete for zr3644_8_R2_val_2.fq.gz Approx 75% complete for zr3644_8_R2_val_2.fq.gz Approx 80% complete for zr3644_8_R2_val_2.fq.gz Approx 85% complete for zr3644_8_R2_val_2.fq.gz Approx 90% complete for zr3644_8_R2_val_2.fq.gz Approx 95% complete for zr3644_8_R2_val_2.fq.gz Analysis complete for zr3644_8_R2_val_2.fq.gz Deleting both intermediate output files zr3644_8_R1_trimmed.fq.gz and zr3644_8_R2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_9_R1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_9_R1.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3644_9_R1_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_9_R1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_9_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1528.07 s (31 µs/read; 1.93 M reads/minute). === Summary === Total reads processed: 49,101,606 Reads with adapters: 20,209,348 (41.2%) Reads written (passing filters): 49,101,606 (100.0%) Total basepairs processed: 6,079,740,279 bp Quality-trimmed: 1,919,505 bp (0.0%) Total written (filtered): 6,053,388,645 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 20209348 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 44.8% C: 10.1% G: 6.8% T: 38.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 17670933 12275401.5 0 17670933 2 1676774 3068850.4 0 1676774 3 435504 767212.6 0 435504 4 294070 191803.1 0 294070 5 71211 47950.8 0 71211 6 17963 11987.7 0 17963 7 13193 2996.9 0 13193 8 9913 749.2 0 9913 9 2386 187.3 0 1891 495 10 15816 46.8 1 14684 1132 11 180 11.7 1 37 143 12 79 2.9 1 24 55 13 11 0.7 1 2 9 14 21 0.7 1 9 12 15 3 0.7 1 1 2 16 16 0.7 1 9 7 17 2 0.7 1 0 2 18 28 0.7 1 13 15 19 35 0.7 1 25 10 20 2 0.7 1 1 1 21 3 0.7 1 3 22 7 0.7 1 5 2 23 13 0.7 1 10 3 24 19 0.7 1 12 7 25 1 0.7 1 1 26 12 0.7 1 8 4 27 14 0.7 1 8 6 28 8 0.7 1 5 3 29 7 0.7 1 7 30 16 0.7 1 11 5 31 18 0.7 1 11 7 32 3 0.7 1 1 2 33 19 0.7 1 15 4 34 3 0.7 1 3 35 14 0.7 1 11 3 36 8 0.7 1 4 4 37 15 0.7 1 12 3 38 7 0.7 1 5 2 39 9 0.7 1 7 2 40 11 0.7 1 8 3 41 15 0.7 1 12 3 42 12 0.7 1 9 3 43 10 0.7 1 8 2 44 11 0.7 1 9 2 45 2 0.7 1 1 1 46 2 0.7 1 0 2 47 5 0.7 1 2 3 48 14 0.7 1 9 5 49 7 0.7 1 4 3 50 8 0.7 1 7 1 51 14 0.7 1 9 5 52 11 0.7 1 8 3 53 5 0.7 1 4 1 54 2 0.7 1 2 55 12 0.7 1 10 2 56 14 0.7 1 12 2 57 4 0.7 1 3 1 58 4 0.7 1 3 1 59 6 0.7 1 5 1 60 4 0.7 1 3 1 61 8 0.7 1 4 4 62 9 0.7 1 7 2 63 3 0.7 1 3 64 5 0.7 1 4 1 65 6 0.7 1 5 1 66 17 0.7 1 14 3 67 4 0.7 1 4 68 9 0.7 1 9 69 6 0.7 1 6 70 6 0.7 1 5 1 71 4 0.7 1 4 72 8 0.7 1 5 3 73 4 0.7 1 4 74 8 0.7 1 8 75 4 0.7 1 4 76 9 0.7 1 7 2 77 11 0.7 1 9 2 78 4 0.7 1 3 1 79 7 0.7 1 5 2 80 9 0.7 1 7 2 81 5 0.7 1 5 82 8 0.7 1 5 3 83 7 0.7 1 6 1 84 6 0.7 1 2 4 85 4 0.7 1 3 1 86 7 0.7 1 7 87 4 0.7 1 4 88 7 0.7 1 7 89 4 0.7 1 2 2 90 4 0.7 1 3 1 91 7 0.7 1 5 2 92 12 0.7 1 8 4 93 10 0.7 1 5 5 94 10 0.7 1 10 95 2 0.7 1 2 96 11 0.7 1 11 97 10 0.7 1 8 2 98 6 0.7 1 3 3 99 10 0.7 1 10 100 14 0.7 1 13 1 101 4 0.7 1 4 102 13 0.7 1 9 4 103 9 0.7 1 8 1 104 8 0.7 1 6 2 105 11 0.7 1 8 3 106 14 0.7 1 14 107 7 0.7 1 6 1 108 13 0.7 1 12 1 109 7 0.7 1 4 3 110 9 0.7 1 7 2 111 14 0.7 1 14 112 11 0.7 1 10 1 113 11 0.7 1 11 114 9 0.7 1 8 1 115 11 0.7 1 8 3 116 13 0.7 1 10 3 117 13 0.7 1 11 2 118 12 0.7 1 12 119 13 0.7 1 12 1 120 17 0.7 1 15 2 121 17 0.7 1 15 2 122 19 0.7 1 11 8 123 16 0.7 1 13 3 124 34 0.7 1 33 1 125 14 0.7 1 10 4 126 19 0.7 1 12 7 127 22 0.7 1 19 3 128 22 0.7 1 17 5 129 20 0.7 1 14 6 130 24 0.7 1 23 1 131 18 0.7 1 17 1 132 24 0.7 1 19 5 133 24 0.7 1 23 1 134 25 0.7 1 18 7 135 33 0.7 1 8 25 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_9_R1.fq.gz ============================================= 49101606 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_9_R2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_9_R2.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3644_9_R2_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_9_R2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_9_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1536.59 s (31 µs/read; 1.92 M reads/minute). === Summary === Total reads processed: 49,101,606 Reads with adapters: 20,297,822 (41.3%) Reads written (passing filters): 49,101,606 (100.0%) Total basepairs processed: 6,078,278,717 bp Quality-trimmed: 2,099,959 bp (0.0%) Total written (filtered): 6,051,789,039 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 20297822 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.3% C: 10.1% G: 6.5% T: 38.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 17869930 12275401.5 0 17869930 2 1574910 3068850.4 0 1574910 3 427072 767212.6 0 427072 4 296533 191803.1 0 296533 5 70445 47950.8 0 70445 6 17079 11987.7 0 17079 7 12905 2996.9 0 12905 8 9863 749.2 0 9863 9 2451 187.3 0 1954 497 10 15313 46.8 1 14170 1143 11 152 11.7 1 25 127 12 46 2.9 1 12 34 13 10 0.7 1 2 8 14 7 0.7 1 4 3 15 7 0.7 1 3 4 16 6 0.7 1 1 5 17 11 0.7 1 6 5 18 5 0.7 1 4 1 19 8 0.7 1 4 4 20 4 0.7 1 3 1 21 3 0.7 1 2 1 22 2 0.7 1 1 1 23 7 0.7 1 5 2 24 4 0.7 1 3 1 25 7 0.7 1 4 3 26 5 0.7 1 2 3 27 7 0.7 1 4 3 28 8 0.7 1 5 3 29 5 0.7 1 3 2 30 3 0.7 1 2 1 31 4 0.7 1 3 1 32 9 0.7 1 4 5 33 6 0.7 1 3 3 34 4 0.7 1 2 2 35 6 0.7 1 4 2 36 5 0.7 1 3 2 38 2 0.7 1 0 2 39 6 0.7 1 4 2 40 6 0.7 1 4 2 41 7 0.7 1 7 42 4 0.7 1 2 2 43 6 0.7 1 4 2 44 10 0.7 1 5 5 45 5 0.7 1 5 46 4 0.7 1 3 1 47 3 0.7 1 1 2 48 9 0.7 1 7 2 49 5 0.7 1 5 50 2 0.7 1 2 51 10 0.7 1 5 5 52 4 0.7 1 3 1 53 9 0.7 1 6 3 54 9 0.7 1 5 4 55 4 0.7 1 3 1 56 6 0.7 1 5 1 57 11 0.7 1 6 5 58 6 0.7 1 5 1 59 4 0.7 1 4 60 2 0.7 1 1 1 61 6 0.7 1 5 1 62 5 0.7 1 3 2 63 7 0.7 1 5 2 64 11 0.7 1 8 3 65 7 0.7 1 6 1 66 10 0.7 1 7 3 67 5 0.7 1 4 1 68 6 0.7 1 4 2 69 8 0.7 1 7 1 70 1 0.7 1 1 71 3 0.7 1 1 2 72 3 0.7 1 1 2 73 5 0.7 1 3 2 74 2 0.7 1 2 75 6 0.7 1 3 3 76 8 0.7 1 8 77 8 0.7 1 8 78 6 0.7 1 4 2 79 10 0.7 1 6 4 80 12 0.7 1 11 1 81 4 0.7 1 1 3 82 8 0.7 1 6 2 83 11 0.7 1 9 2 84 8 0.7 1 7 1 85 6 0.7 1 4 2 86 10 0.7 1 9 1 87 3 0.7 1 3 88 8 0.7 1 7 1 89 4 0.7 1 4 90 8 0.7 1 6 2 91 4 0.7 1 3 1 92 6 0.7 1 4 2 93 8 0.7 1 6 2 94 8 0.7 1 8 95 18 0.7 1 16 2 96 11 0.7 1 11 97 10 0.7 1 10 98 7 0.7 1 4 3 99 7 0.7 1 6 1 100 9 0.7 1 6 3 101 11 0.7 1 7 4 102 10 0.7 1 10 103 6 0.7 1 5 1 104 10 0.7 1 7 3 105 9 0.7 1 6 3 106 15 0.7 1 13 2 107 10 0.7 1 9 1 108 14 0.7 1 12 2 109 13 0.7 1 11 2 110 14 0.7 1 10 4 111 8 0.7 1 8 112 11 0.7 1 10 1 113 18 0.7 1 15 3 114 14 0.7 1 9 5 115 5 0.7 1 4 1 116 17 0.7 1 14 3 117 10 0.7 1 7 3 118 21 0.7 1 17 4 119 16 0.7 1 15 1 120 23 0.7 1 22 1 121 24 0.7 1 20 4 122 10 0.7 1 9 1 123 9 0.7 1 7 2 124 15 0.7 1 11 4 125 17 0.7 1 14 3 126 20 0.7 1 19 1 127 16 0.7 1 13 3 128 21 0.7 1 20 1 129 20 0.7 1 19 1 130 19 0.7 1 15 4 131 9 0.7 1 8 1 132 21 0.7 1 17 4 133 31 0.7 1 18 13 134 29 0.7 1 19 10 135 43 0.7 1 22 21 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_9_R2.fq.gz ============================================= 49101606 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_9_R1_trimmed.fq.gz and zr3644_9_R2_trimmed.fq.gz file_1: zr3644_9_R1_trimmed.fq.gz, file_2: zr3644_9_R2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_9_R1_trimmed.fq.gz and zr3644_9_R2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_9_R1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_9_R2_val_2.fq.gz Total number of sequences analysed: 49101606 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 341760 (0.70%) >>> Now running FastQC on the validated data zr3644_9_R1_val_1.fq.gz<<< Started analysis of zr3644_9_R1_val_1.fq.gz Approx 5% complete for zr3644_9_R1_val_1.fq.gz Approx 10% complete for zr3644_9_R1_val_1.fq.gz Approx 15% complete for zr3644_9_R1_val_1.fq.gz Approx 20% complete for zr3644_9_R1_val_1.fq.gz Approx 25% complete for zr3644_9_R1_val_1.fq.gz Approx 30% complete for zr3644_9_R1_val_1.fq.gz Approx 35% complete for zr3644_9_R1_val_1.fq.gz Approx 40% complete for zr3644_9_R1_val_1.fq.gz Approx 45% complete for zr3644_9_R1_val_1.fq.gz Approx 50% complete for zr3644_9_R1_val_1.fq.gz Approx 55% complete for zr3644_9_R1_val_1.fq.gz Approx 60% complete for zr3644_9_R1_val_1.fq.gz Approx 65% complete for zr3644_9_R1_val_1.fq.gz Approx 70% complete for zr3644_9_R1_val_1.fq.gz Approx 75% complete for zr3644_9_R1_val_1.fq.gz Approx 80% complete for zr3644_9_R1_val_1.fq.gz Approx 85% complete for zr3644_9_R1_val_1.fq.gz Approx 90% complete for zr3644_9_R1_val_1.fq.gz Approx 95% complete for zr3644_9_R1_val_1.fq.gz Analysis complete for zr3644_9_R1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_9_R2_val_2.fq.gz<<< Started analysis of zr3644_9_R2_val_2.fq.gz Approx 5% complete for zr3644_9_R2_val_2.fq.gz Approx 10% complete for zr3644_9_R2_val_2.fq.gz Approx 15% complete for zr3644_9_R2_val_2.fq.gz Approx 20% complete for zr3644_9_R2_val_2.fq.gz Approx 25% complete for zr3644_9_R2_val_2.fq.gz Approx 30% complete for zr3644_9_R2_val_2.fq.gz Approx 35% complete for zr3644_9_R2_val_2.fq.gz Approx 40% complete for zr3644_9_R2_val_2.fq.gz Approx 45% complete for zr3644_9_R2_val_2.fq.gz Approx 50% complete for zr3644_9_R2_val_2.fq.gz Approx 55% complete for zr3644_9_R2_val_2.fq.gz Approx 60% complete for zr3644_9_R2_val_2.fq.gz Approx 65% complete for zr3644_9_R2_val_2.fq.gz Approx 70% complete for zr3644_9_R2_val_2.fq.gz Approx 75% complete for zr3644_9_R2_val_2.fq.gz Approx 80% complete for zr3644_9_R2_val_2.fq.gz Approx 85% complete for zr3644_9_R2_val_2.fq.gz Approx 90% complete for zr3644_9_R2_val_2.fq.gz Approx 95% complete for zr3644_9_R2_val_2.fq.gz Analysis complete for zr3644_9_R2_val_2.fq.gz Deleting both intermediate output files zr3644_9_R1_trimmed.fq.gz and zr3644_9_R2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_10_R1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_10_R1.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3644_10_R1_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_10_R1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_10_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 2087.48 s (39 µs/read; 1.52 M reads/minute). === Summary === Total reads processed: 52,847,841 Reads with adapters: 22,764,641 (43.1%) Reads written (passing filters): 52,847,841 (100.0%) Total basepairs processed: 6,663,716,444 bp Quality-trimmed: 2,077,880 bp (0.0%) Total written (filtered): 6,634,572,674 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 22764641 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.0% C: 10.4% G: 6.5% T: 38.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 20139970 13211960.2 0 20139970 2 1741524 3302990.1 0 1741524 3 474041 825747.5 0 474041 4 299082 206436.9 0 299082 5 57704 51609.2 0 57704 6 15545 12902.3 0 15545 7 10772 3225.6 0 10772 8 8021 806.4 0 8021 9 2063 201.6 0 1607 456 10 13825 50.4 1 12748 1077 11 200 12.6 1 31 169 12 82 3.1 1 29 53 13 7 0.8 1 1 6 14 28 0.8 1 19 9 15 8 0.8 1 2 6 16 21 0.8 1 14 7 17 4 0.8 1 3 1 18 34 0.8 1 21 13 19 37 0.8 1 23 14 20 6 0.8 1 5 1 21 4 0.8 1 4 22 9 0.8 1 7 2 23 23 0.8 1 18 5 24 37 0.8 1 22 15 25 5 0.8 1 4 1 26 16 0.8 1 12 4 27 18 0.8 1 15 3 28 5 0.8 1 5 29 14 0.8 1 12 2 30 20 0.8 1 9 11 31 29 0.8 1 23 6 32 8 0.8 1 7 1 33 26 0.8 1 19 7 34 6 0.8 1 4 2 35 15 0.8 1 13 2 36 9 0.8 1 5 4 37 17 0.8 1 12 5 38 17 0.8 1 16 1 39 11 0.8 1 7 4 40 12 0.8 1 9 3 41 12 0.8 1 8 4 42 17 0.8 1 10 7 43 15 0.8 1 12 3 44 19 0.8 1 14 5 45 8 0.8 1 6 2 46 8 0.8 1 7 1 47 3 0.8 1 3 48 20 0.8 1 13 7 49 13 0.8 1 10 3 50 9 0.8 1 7 2 51 11 0.8 1 9 2 52 18 0.8 1 14 4 53 10 0.8 1 6 4 54 6 0.8 1 6 55 25 0.8 1 17 8 56 18 0.8 1 15 3 57 12 0.8 1 10 2 58 7 0.8 1 5 2 59 14 0.8 1 12 2 60 5 0.8 1 2 3 61 11 0.8 1 11 62 16 0.8 1 15 1 63 6 0.8 1 5 1 64 9 0.8 1 8 1 65 10 0.8 1 9 1 66 16 0.8 1 11 5 67 8 0.8 1 8 68 9 0.8 1 7 2 69 12 0.8 1 8 4 70 11 0.8 1 10 1 71 12 0.8 1 12 72 10 0.8 1 7 3 73 6 0.8 1 4 2 74 8 0.8 1 6 2 75 13 0.8 1 9 4 76 10 0.8 1 10 77 8 0.8 1 7 1 78 7 0.8 1 7 79 9 0.8 1 8 1 80 10 0.8 1 9 1 81 4 0.8 1 1 3 82 15 0.8 1 13 2 83 3 0.8 1 3 84 7 0.8 1 5 2 85 15 0.8 1 12 3 86 11 0.8 1 10 1 87 6 0.8 1 6 88 7 0.8 1 6 1 89 8 0.8 1 7 1 90 13 0.8 1 11 2 91 11 0.8 1 8 3 92 12 0.8 1 11 1 93 14 0.8 1 12 2 94 14 0.8 1 12 2 95 14 0.8 1 14 96 14 0.8 1 13 1 97 14 0.8 1 13 1 98 9 0.8 1 8 1 99 10 0.8 1 9 1 100 12 0.8 1 11 1 101 14 0.8 1 12 2 102 11 0.8 1 8 3 103 11 0.8 1 8 3 104 12 0.8 1 9 3 105 12 0.8 1 9 3 106 8 0.8 1 5 3 107 7 0.8 1 6 1 108 15 0.8 1 13 2 109 15 0.8 1 10 5 110 11 0.8 1 10 1 111 12 0.8 1 12 112 12 0.8 1 9 3 113 10 0.8 1 7 3 114 27 0.8 1 21 6 115 13 0.8 1 8 5 116 22 0.8 1 20 2 117 26 0.8 1 21 5 118 15 0.8 1 13 2 119 29 0.8 1 27 2 120 20 0.8 1 19 1 121 20 0.8 1 17 3 122 23 0.8 1 19 4 123 20 0.8 1 17 3 124 21 0.8 1 14 7 125 26 0.8 1 22 4 126 20 0.8 1 16 4 127 25 0.8 1 20 5 128 25 0.8 1 23 2 129 25 0.8 1 23 2 130 26 0.8 1 22 4 131 22 0.8 1 21 1 132 30 0.8 1 27 3 133 35 0.8 1 20 15 134 37 0.8 1 26 11 135 45 0.8 1 21 24 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_10_R1.fq.gz ============================================= 52847841 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_10_R2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_10_R2.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3644_10_R2_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_10_R2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_10_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1730.29 s (33 µs/read; 1.83 M reads/minute). === Summary === Total reads processed: 52,847,841 Reads with adapters: 22,781,010 (43.1%) Reads written (passing filters): 52,847,841 (100.0%) Total basepairs processed: 6,661,118,919 bp Quality-trimmed: 2,209,762 bp (0.0%) Total written (filtered): 6,632,042,202 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 22781010 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.4% C: 10.2% G: 6.2% T: 38.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 20322773 13211960.2 0 20322773 2 1590779 3302990.1 0 1590779 3 459662 825747.5 0 459662 4 302784 206436.9 0 302784 5 55915 51609.2 0 55915 6 14196 12902.3 0 14196 7 10464 3225.6 0 10464 8 7831 806.4 0 7831 9 2067 201.6 0 1683 384 10 13009 50.4 1 11893 1116 11 172 12.6 1 26 146 12 53 3.1 1 10 43 13 9 0.8 1 6 3 14 6 0.8 1 5 1 15 7 0.8 1 6 1 16 1 0.8 1 1 17 6 0.8 1 5 1 18 5 0.8 1 4 1 19 11 0.8 1 8 3 20 5 0.8 1 2 3 21 4 0.8 1 2 2 22 7 0.8 1 1 6 23 9 0.8 1 3 6 24 7 0.8 1 2 5 25 2 0.8 1 1 1 26 1 0.8 1 1 27 7 0.8 1 3 4 28 5 0.8 1 3 2 29 7 0.8 1 6 1 30 11 0.8 1 7 4 31 3 0.8 1 3 32 7 0.8 1 2 5 33 10 0.8 1 7 3 34 6 0.8 1 4 2 35 5 0.8 1 2 3 36 7 0.8 1 6 1 37 1 0.8 1 1 38 6 0.8 1 3 3 39 5 0.8 1 3 2 40 9 0.8 1 6 3 41 3 0.8 1 2 1 42 6 0.8 1 5 1 43 4 0.8 1 2 2 44 3 0.8 1 1 2 45 3 0.8 1 1 2 46 6 0.8 1 6 47 5 0.8 1 3 2 48 8 0.8 1 7 1 49 8 0.8 1 4 4 50 7 0.8 1 3 4 51 4 0.8 1 3 1 52 4 0.8 1 4 53 8 0.8 1 5 3 54 7 0.8 1 7 55 6 0.8 1 4 2 56 15 0.8 1 11 4 57 12 0.8 1 8 4 58 6 0.8 1 6 59 4 0.8 1 4 60 12 0.8 1 9 3 61 6 0.8 1 4 2 62 7 0.8 1 7 63 7 0.8 1 4 3 64 11 0.8 1 9 2 65 2 0.8 1 2 66 9 0.8 1 7 2 67 5 0.8 1 5 68 11 0.8 1 8 3 69 3 0.8 1 2 1 70 4 0.8 1 1 3 71 5 0.8 1 4 1 72 5 0.8 1 4 1 73 11 0.8 1 11 74 9 0.8 1 8 1 75 6 0.8 1 6 76 3 0.8 1 3 77 4 0.8 1 4 78 12 0.8 1 9 3 79 9 0.8 1 7 2 80 8 0.8 1 5 3 81 12 0.8 1 11 1 82 1 0.8 1 0 1 83 10 0.8 1 9 1 84 7 0.8 1 4 3 85 8 0.8 1 5 3 86 10 0.8 1 8 2 87 11 0.8 1 11 88 10 0.8 1 10 89 7 0.8 1 7 90 18 0.8 1 17 1 91 9 0.8 1 8 1 92 9 0.8 1 9 93 8 0.8 1 5 3 94 19 0.8 1 18 1 95 9 0.8 1 9 96 8 0.8 1 7 1 97 9 0.8 1 5 4 98 8 0.8 1 7 1 99 12 0.8 1 11 1 100 11 0.8 1 11 101 10 0.8 1 7 3 102 10 0.8 1 7 3 103 9 0.8 1 9 104 11 0.8 1 11 105 4 0.8 1 3 1 106 12 0.8 1 10 2 107 13 0.8 1 12 1 108 27 0.8 1 25 2 109 10 0.8 1 9 1 110 10 0.8 1 10 111 11 0.8 1 10 1 112 15 0.8 1 12 3 113 15 0.8 1 14 1 114 16 0.8 1 14 2 115 17 0.8 1 15 2 116 22 0.8 1 18 4 117 18 0.8 1 16 2 118 21 0.8 1 16 5 119 11 0.8 1 9 2 120 17 0.8 1 16 1 121 27 0.8 1 20 7 122 17 0.8 1 13 4 123 21 0.8 1 18 3 124 20 0.8 1 16 4 125 22 0.8 1 20 2 126 18 0.8 1 15 3 127 25 0.8 1 23 2 128 21 0.8 1 20 1 129 31 0.8 1 24 7 130 25 0.8 1 19 6 131 26 0.8 1 25 1 132 29 0.8 1 22 7 133 32 0.8 1 26 6 134 33 0.8 1 20 13 135 46 0.8 1 17 29 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_10_R2.fq.gz ============================================= 52847841 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_10_R1_trimmed.fq.gz and zr3644_10_R2_trimmed.fq.gz file_1: zr3644_10_R1_trimmed.fq.gz, file_2: zr3644_10_R2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_10_R1_trimmed.fq.gz and zr3644_10_R2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_10_R1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_10_R2_val_2.fq.gz Total number of sequences analysed: 52847841 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 254964 (0.48%) >>> Now running FastQC on the validated data zr3644_10_R1_val_1.fq.gz<<< Started analysis of zr3644_10_R1_val_1.fq.gz Approx 5% complete for zr3644_10_R1_val_1.fq.gz Approx 10% complete for zr3644_10_R1_val_1.fq.gz Approx 15% complete for zr3644_10_R1_val_1.fq.gz Approx 20% complete for zr3644_10_R1_val_1.fq.gz Approx 25% complete for zr3644_10_R1_val_1.fq.gz Approx 30% complete for zr3644_10_R1_val_1.fq.gz Approx 35% complete for zr3644_10_R1_val_1.fq.gz Approx 40% complete for zr3644_10_R1_val_1.fq.gz Approx 45% complete for zr3644_10_R1_val_1.fq.gz Approx 50% complete for zr3644_10_R1_val_1.fq.gz Approx 55% complete for zr3644_10_R1_val_1.fq.gz Approx 60% complete for zr3644_10_R1_val_1.fq.gz Approx 65% complete for zr3644_10_R1_val_1.fq.gz Approx 70% complete for zr3644_10_R1_val_1.fq.gz Approx 75% complete for zr3644_10_R1_val_1.fq.gz Approx 80% complete for zr3644_10_R1_val_1.fq.gz Approx 85% complete for zr3644_10_R1_val_1.fq.gz Approx 90% complete for zr3644_10_R1_val_1.fq.gz Approx 95% complete for zr3644_10_R1_val_1.fq.gz Analysis complete for zr3644_10_R1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_10_R2_val_2.fq.gz<<< Started analysis of zr3644_10_R2_val_2.fq.gz Approx 5% complete for zr3644_10_R2_val_2.fq.gz Approx 10% complete for zr3644_10_R2_val_2.fq.gz Approx 15% complete for zr3644_10_R2_val_2.fq.gz Approx 20% complete for zr3644_10_R2_val_2.fq.gz Approx 25% complete for zr3644_10_R2_val_2.fq.gz Approx 30% complete for zr3644_10_R2_val_2.fq.gz Approx 35% complete for zr3644_10_R2_val_2.fq.gz Approx 40% complete for zr3644_10_R2_val_2.fq.gz Approx 45% complete for zr3644_10_R2_val_2.fq.gz Approx 50% complete for zr3644_10_R2_val_2.fq.gz Approx 55% complete for zr3644_10_R2_val_2.fq.gz Approx 60% complete for zr3644_10_R2_val_2.fq.gz Approx 65% complete for zr3644_10_R2_val_2.fq.gz Approx 70% complete for zr3644_10_R2_val_2.fq.gz Approx 75% complete for zr3644_10_R2_val_2.fq.gz Approx 80% complete for zr3644_10_R2_val_2.fq.gz Approx 85% complete for zr3644_10_R2_val_2.fq.gz Approx 90% complete for zr3644_10_R2_val_2.fq.gz Approx 95% complete for zr3644_10_R2_val_2.fq.gz Analysis complete for zr3644_10_R2_val_2.fq.gz Deleting both intermediate output files zr3644_10_R1_trimmed.fq.gz and zr3644_10_R2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_11_R1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_11_R1.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3644_11_R1_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_11_R1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_11_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1820.98 s (32 µs/read; 1.88 M reads/minute). === Summary === Total reads processed: 57,092,207 Reads with adapters: 24,564,038 (43.0%) Reads written (passing filters): 57,092,207 (100.0%) Total basepairs processed: 7,194,811,854 bp Quality-trimmed: 2,160,013 bp (0.0%) Total written (filtered): 7,163,488,585 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 24564038 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.1% C: 10.4% G: 6.4% T: 38.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 21756752 14273051.8 0 21756752 2 1861665 3568262.9 0 1861665 3 507444 892065.7 0 507444 4 321170 223016.4 0 321170 5 62573 55754.1 0 62573 6 16175 13938.5 0 16175 7 11234 3484.6 0 11234 8 8549 871.2 0 8549 9 2068 217.8 0 1619 449 10 14386 54.4 1 13213 1173 11 164 13.6 1 27 137 12 70 3.4 1 15 55 13 10 0.9 1 3 7 14 18 0.9 1 14 4 15 8 0.9 1 5 3 16 16 0.9 1 9 7 17 9 0.9 1 7 2 18 24 0.9 1 11 13 19 24 0.9 1 18 6 20 6 0.9 1 3 3 21 3 0.9 1 3 22 13 0.9 1 5 8 23 9 0.9 1 9 24 20 0.9 1 14 6 25 4 0.9 1 1 3 26 12 0.9 1 9 3 27 9 0.9 1 8 1 28 5 0.9 1 4 1 29 10 0.9 1 7 3 30 15 0.9 1 8 7 31 10 0.9 1 7 3 32 4 0.9 1 2 2 33 14 0.9 1 11 3 34 6 0.9 1 5 1 35 11 0.9 1 10 1 36 6 0.9 1 4 2 37 12 0.9 1 8 4 38 15 0.9 1 11 4 39 8 0.9 1 5 3 40 8 0.9 1 7 1 41 9 0.9 1 4 5 42 20 0.9 1 11 9 43 14 0.9 1 6 8 44 19 0.9 1 14 5 45 3 0.9 1 1 2 46 8 0.9 1 6 2 47 5 0.9 1 4 1 48 16 0.9 1 12 4 49 9 0.9 1 8 1 50 14 0.9 1 10 4 51 6 0.9 1 6 52 13 0.9 1 8 5 53 5 0.9 1 3 2 54 3 0.9 1 2 1 55 15 0.9 1 11 4 56 6 0.9 1 4 2 57 7 0.9 1 7 58 11 0.9 1 9 2 59 7 0.9 1 6 1 60 6 0.9 1 6 61 14 0.9 1 11 3 62 18 0.9 1 11 7 63 7 0.9 1 5 2 64 8 0.9 1 6 2 65 4 0.9 1 3 1 66 10 0.9 1 9 1 67 12 0.9 1 9 3 68 19 0.9 1 16 3 69 11 0.9 1 10 1 70 8 0.9 1 7 1 71 8 0.9 1 7 1 72 14 0.9 1 7 7 73 9 0.9 1 9 74 11 0.9 1 7 4 75 8 0.9 1 7 1 76 14 0.9 1 9 5 77 14 0.9 1 12 2 78 14 0.9 1 12 2 79 11 0.9 1 8 3 80 9 0.9 1 8 1 81 14 0.9 1 14 82 8 0.9 1 7 1 83 20 0.9 1 18 2 84 13 0.9 1 13 85 17 0.9 1 13 4 86 4 0.9 1 4 87 10 0.9 1 8 2 88 18 0.9 1 12 6 89 12 0.9 1 10 2 90 14 0.9 1 12 2 91 13 0.9 1 12 1 92 12 0.9 1 8 4 93 9 0.9 1 7 2 94 12 0.9 1 8 4 95 15 0.9 1 12 3 96 8 0.9 1 6 2 97 12 0.9 1 9 3 98 15 0.9 1 11 4 99 10 0.9 1 8 2 100 13 0.9 1 10 3 101 11 0.9 1 9 2 102 14 0.9 1 13 1 103 10 0.9 1 10 104 18 0.9 1 17 1 105 16 0.9 1 16 106 8 0.9 1 6 2 107 12 0.9 1 11 1 108 23 0.9 1 20 3 109 23 0.9 1 19 4 110 11 0.9 1 10 1 111 19 0.9 1 17 2 112 9 0.9 1 7 2 113 18 0.9 1 13 5 114 22 0.9 1 21 1 115 15 0.9 1 11 4 116 21 0.9 1 18 3 117 22 0.9 1 18 4 118 31 0.9 1 29 2 119 21 0.9 1 17 4 120 32 0.9 1 27 5 121 30 0.9 1 21 9 122 24 0.9 1 23 1 123 29 0.9 1 24 5 124 21 0.9 1 18 3 125 21 0.9 1 18 3 126 27 0.9 1 25 2 127 26 0.9 1 20 6 128 28 0.9 1 22 6 129 20 0.9 1 18 2 130 47 0.9 1 41 6 131 45 0.9 1 35 10 132 31 0.9 1 28 3 133 31 0.9 1 24 7 134 36 0.9 1 22 14 135 39 0.9 1 17 22 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_11_R1.fq.gz ============================================= 57092207 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_11_R2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_11_R2.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3644_11_R2_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_11_R2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_11_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1850.90 s (32 µs/read; 1.85 M reads/minute). === Summary === Total reads processed: 57,092,207 Reads with adapters: 24,597,705 (43.1%) Reads written (passing filters): 57,092,207 (100.0%) Total basepairs processed: 7,192,359,667 bp Quality-trimmed: 2,438,054 bp (0.0%) Total written (filtered): 7,160,901,486 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 24597705 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.5% C: 10.1% G: 6.2% T: 38.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 21938947 14273051.8 0 21938947 2 1725533 3568262.9 0 1725533 3 494996 892065.7 0 494996 4 325612 223016.4 0 325612 5 60444 55754.1 0 60444 6 15122 13938.5 0 15122 7 10970 3484.6 0 10970 8 8166 871.2 0 8166 9 2181 217.8 0 1742 439 10 13918 54.4 1 12775 1143 11 184 13.6 1 37 147 12 57 3.4 1 17 40 13 14 0.9 1 6 8 14 5 0.9 1 2 3 15 9 0.9 1 7 2 16 3 0.9 1 2 1 17 3 0.9 1 0 3 18 6 0.9 1 4 2 19 9 0.9 1 6 3 20 9 0.9 1 7 2 21 10 0.9 1 4 6 22 8 0.9 1 4 4 23 4 0.9 1 3 1 24 8 0.9 1 6 2 25 12 0.9 1 8 4 26 4 0.9 1 3 1 27 7 0.9 1 6 1 28 5 0.9 1 4 1 29 6 0.9 1 4 2 30 7 0.9 1 3 4 31 8 0.9 1 6 2 32 6 0.9 1 4 2 33 5 0.9 1 3 2 34 6 0.9 1 5 1 35 7 0.9 1 2 5 36 5 0.9 1 3 2 37 8 0.9 1 7 1 38 9 0.9 1 5 4 39 7 0.9 1 3 4 40 8 0.9 1 7 1 41 3 0.9 1 2 1 42 4 0.9 1 3 1 43 7 0.9 1 6 1 44 8 0.9 1 6 2 45 9 0.9 1 7 2 46 8 0.9 1 6 2 47 4 0.9 1 3 1 48 2 0.9 1 1 1 49 16 0.9 1 14 2 50 8 0.9 1 7 1 51 6 0.9 1 4 2 52 9 0.9 1 4 5 53 9 0.9 1 8 1 54 6 0.9 1 3 3 55 5 0.9 1 3 2 56 17 0.9 1 12 5 57 12 0.9 1 8 4 58 9 0.9 1 8 1 59 5 0.9 1 5 60 8 0.9 1 8 61 7 0.9 1 6 1 62 7 0.9 1 5 2 63 9 0.9 1 6 3 64 7 0.9 1 6 1 65 8 0.9 1 5 3 66 13 0.9 1 9 4 67 9 0.9 1 5 4 68 6 0.9 1 5 1 69 15 0.9 1 13 2 70 10 0.9 1 8 2 71 8 0.9 1 5 3 72 6 0.9 1 4 2 73 9 0.9 1 5 4 74 8 0.9 1 7 1 75 9 0.9 1 9 76 13 0.9 1 10 3 77 6 0.9 1 5 1 78 10 0.9 1 4 6 79 12 0.9 1 11 1 80 18 0.9 1 16 2 81 7 0.9 1 7 82 1 0.9 1 1 83 12 0.9 1 8 4 84 3 0.9 1 3 85 14 0.9 1 12 2 86 10 0.9 1 9 1 87 7 0.9 1 6 1 88 9 0.9 1 9 89 12 0.9 1 11 1 90 10 0.9 1 9 1 91 18 0.9 1 16 2 92 17 0.9 1 11 6 93 8 0.9 1 7 1 94 18 0.9 1 14 4 95 10 0.9 1 7 3 96 17 0.9 1 12 5 97 13 0.9 1 11 2 98 17 0.9 1 17 99 11 0.9 1 11 100 5 0.9 1 5 101 13 0.9 1 11 2 102 19 0.9 1 16 3 103 9 0.9 1 8 1 104 15 0.9 1 14 1 105 13 0.9 1 9 4 106 12 0.9 1 12 107 15 0.9 1 13 2 108 12 0.9 1 11 1 109 9 0.9 1 7 2 110 18 0.9 1 16 2 111 21 0.9 1 19 2 112 9 0.9 1 7 2 113 27 0.9 1 18 9 114 21 0.9 1 16 5 115 22 0.9 1 18 4 116 15 0.9 1 13 2 117 17 0.9 1 15 2 118 20 0.9 1 19 1 119 17 0.9 1 14 3 120 17 0.9 1 14 3 121 25 0.9 1 19 6 122 22 0.9 1 17 5 123 21 0.9 1 19 2 124 20 0.9 1 14 6 125 24 0.9 1 22 2 126 20 0.9 1 16 4 127 31 0.9 1 28 3 128 29 0.9 1 25 4 129 33 0.9 1 27 6 130 41 0.9 1 34 7 131 41 0.9 1 37 4 132 32 0.9 1 30 2 133 52 0.9 1 40 12 134 45 0.9 1 34 11 135 56 0.9 1 31 25 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_11_R2.fq.gz ============================================= 57092207 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_11_R1_trimmed.fq.gz and zr3644_11_R2_trimmed.fq.gz file_1: zr3644_11_R1_trimmed.fq.gz, file_2: zr3644_11_R2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_11_R1_trimmed.fq.gz and zr3644_11_R2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_11_R1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_11_R2_val_2.fq.gz Total number of sequences analysed: 57092207 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 284658 (0.50%) >>> Now running FastQC on the validated data zr3644_11_R1_val_1.fq.gz<<< Started analysis of zr3644_11_R1_val_1.fq.gz Approx 5% complete for zr3644_11_R1_val_1.fq.gz Approx 10% complete for zr3644_11_R1_val_1.fq.gz Approx 15% complete for zr3644_11_R1_val_1.fq.gz Approx 20% complete for zr3644_11_R1_val_1.fq.gz Approx 25% complete for zr3644_11_R1_val_1.fq.gz Approx 30% complete for zr3644_11_R1_val_1.fq.gz Approx 35% complete for zr3644_11_R1_val_1.fq.gz Approx 40% complete for zr3644_11_R1_val_1.fq.gz Approx 45% complete for zr3644_11_R1_val_1.fq.gz Approx 50% complete for zr3644_11_R1_val_1.fq.gz Approx 55% complete for zr3644_11_R1_val_1.fq.gz Approx 60% complete for zr3644_11_R1_val_1.fq.gz Approx 65% complete for zr3644_11_R1_val_1.fq.gz Approx 70% complete for zr3644_11_R1_val_1.fq.gz Approx 75% complete for zr3644_11_R1_val_1.fq.gz Approx 80% complete for zr3644_11_R1_val_1.fq.gz Approx 85% complete for zr3644_11_R1_val_1.fq.gz Approx 90% complete for zr3644_11_R1_val_1.fq.gz Approx 95% complete for zr3644_11_R1_val_1.fq.gz Analysis complete for zr3644_11_R1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_11_R2_val_2.fq.gz<<< Started analysis of zr3644_11_R2_val_2.fq.gz Approx 5% complete for zr3644_11_R2_val_2.fq.gz Approx 10% complete for zr3644_11_R2_val_2.fq.gz Approx 15% complete for zr3644_11_R2_val_2.fq.gz Approx 20% complete for zr3644_11_R2_val_2.fq.gz Approx 25% complete for zr3644_11_R2_val_2.fq.gz Approx 30% complete for zr3644_11_R2_val_2.fq.gz Approx 35% complete for zr3644_11_R2_val_2.fq.gz Approx 40% complete for zr3644_11_R2_val_2.fq.gz Approx 45% complete for zr3644_11_R2_val_2.fq.gz Approx 50% complete for zr3644_11_R2_val_2.fq.gz Approx 55% complete for zr3644_11_R2_val_2.fq.gz Approx 60% complete for zr3644_11_R2_val_2.fq.gz Approx 65% complete for zr3644_11_R2_val_2.fq.gz Approx 70% complete for zr3644_11_R2_val_2.fq.gz Approx 75% complete for zr3644_11_R2_val_2.fq.gz Approx 80% complete for zr3644_11_R2_val_2.fq.gz Approx 85% complete for zr3644_11_R2_val_2.fq.gz Approx 90% complete for zr3644_11_R2_val_2.fq.gz Approx 95% complete for zr3644_11_R2_val_2.fq.gz Analysis complete for zr3644_11_R2_val_2.fq.gz Deleting both intermediate output files zr3644_11_R1_trimmed.fq.gz and zr3644_11_R2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_12_R1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_12_R1.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3644_12_R1_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_12_R1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_12_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1515.62 s (32 µs/read; 1.90 M reads/minute). === Summary === Total reads processed: 47,871,006 Reads with adapters: 20,609,022 (43.1%) Reads written (passing filters): 47,871,006 (100.0%) Total basepairs processed: 6,044,965,124 bp Quality-trimmed: 1,661,047 bp (0.0%) Total written (filtered): 6,019,036,550 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 20609022 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.5% C: 10.1% G: 5.9% T: 38.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 18389974 11967751.5 0 18389974 2 1462519 2991937.9 0 1462519 3 393984 747984.5 0 393984 4 261257 186996.1 0 261257 5 55110 46749.0 0 55110 6 13822 11687.3 0 13822 7 9340 2921.8 0 9340 8 6830 730.5 0 6830 9 1917 182.6 0 1555 362 10 12674 45.7 1 11706 968 11 132 11.4 1 27 105 12 57 2.9 1 22 35 13 11 0.7 1 4 7 14 26 0.7 1 12 14 15 6 0.7 1 3 3 16 14 0.7 1 10 4 17 6 0.7 1 2 4 18 43 0.7 1 27 16 19 53 0.7 1 38 15 20 5 0.7 1 3 2 21 4 0.7 1 3 1 22 5 0.7 1 1 4 23 19 0.7 1 10 9 24 28 0.7 1 21 7 25 3 0.7 1 3 26 25 0.7 1 18 7 27 11 0.7 1 4 7 28 4 0.7 1 3 1 29 14 0.7 1 8 6 30 26 0.7 1 18 8 31 32 0.7 1 21 11 32 6 0.7 1 2 4 33 26 0.7 1 17 9 34 16 0.7 1 11 5 35 19 0.7 1 18 1 36 24 0.7 1 18 6 37 4 0.7 1 4 38 13 0.7 1 9 4 39 10 0.7 1 8 2 40 12 0.7 1 5 7 41 16 0.7 1 13 3 42 13 0.7 1 9 4 43 12 0.7 1 9 3 44 14 0.7 1 11 3 45 4 0.7 1 2 2 46 11 0.7 1 6 5 47 2 0.7 1 1 1 48 22 0.7 1 14 8 49 14 0.7 1 12 2 50 2 0.7 1 0 2 51 11 0.7 1 9 2 52 15 0.7 1 11 4 53 5 0.7 1 3 2 54 7 0.7 1 6 1 55 22 0.7 1 15 7 56 17 0.7 1 12 5 57 5 0.7 1 2 3 58 9 0.7 1 7 2 59 14 0.7 1 11 3 60 5 0.7 1 4 1 61 3 0.7 1 2 1 62 11 0.7 1 9 2 63 4 0.7 1 2 2 64 4 0.7 1 3 1 65 5 0.7 1 4 1 66 8 0.7 1 6 2 67 7 0.7 1 7 68 8 0.7 1 7 1 69 4 0.7 1 2 2 70 4 0.7 1 4 71 5 0.7 1 5 72 8 0.7 1 8 73 2 0.7 1 2 74 3 0.7 1 2 1 75 6 0.7 1 3 3 76 7 0.7 1 6 1 77 6 0.7 1 3 3 78 2 0.7 1 1 1 79 2 0.7 1 1 1 80 7 0.7 1 6 1 81 10 0.7 1 8 2 82 6 0.7 1 5 1 83 7 0.7 1 6 1 84 4 0.7 1 4 85 10 0.7 1 8 2 86 11 0.7 1 10 1 87 5 0.7 1 5 88 6 0.7 1 5 1 89 4 0.7 1 3 1 90 5 0.7 1 3 2 91 8 0.7 1 7 1 92 6 0.7 1 5 1 93 9 0.7 1 9 94 4 0.7 1 3 1 95 6 0.7 1 4 2 96 8 0.7 1 8 97 5 0.7 1 5 98 3 0.7 1 3 99 9 0.7 1 7 2 100 9 0.7 1 8 1 101 10 0.7 1 8 2 102 13 0.7 1 9 4 103 10 0.7 1 9 1 104 10 0.7 1 10 105 9 0.7 1 9 106 7 0.7 1 6 1 107 7 0.7 1 5 2 108 3 0.7 1 1 2 109 12 0.7 1 8 4 110 8 0.7 1 8 111 8 0.7 1 8 112 10 0.7 1 7 3 113 9 0.7 1 9 114 8 0.7 1 7 1 115 10 0.7 1 7 3 116 11 0.7 1 8 3 117 10 0.7 1 8 2 118 16 0.7 1 10 6 119 21 0.7 1 18 3 120 15 0.7 1 15 121 16 0.7 1 13 3 122 13 0.7 1 12 1 123 18 0.7 1 18 124 12 0.7 1 11 1 125 9 0.7 1 7 2 126 19 0.7 1 18 1 127 15 0.7 1 14 1 128 20 0.7 1 19 1 129 25 0.7 1 23 2 130 20 0.7 1 19 1 131 18 0.7 1 17 1 132 21 0.7 1 19 2 133 23 0.7 1 17 6 134 18 0.7 1 15 3 135 26 0.7 1 10 16 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_12_R1.fq.gz ============================================= 47871006 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_12_R2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_12_R2.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3644_12_R2_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_12_R2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_12_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1548.34 s (32 µs/read; 1.86 M reads/minute). === Summary === Total reads processed: 47,871,006 Reads with adapters: 20,525,648 (42.9%) Reads written (passing filters): 47,871,006 (100.0%) Total basepairs processed: 6,042,854,501 bp Quality-trimmed: 1,702,355 bp (0.0%) Total written (filtered): 6,017,085,430 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 20525648 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.8% C: 9.9% G: 5.8% T: 38.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 18406616 11967751.5 0 18406616 2 1361487 2991937.9 0 1361487 3 391002 747984.5 0 391002 4 266858 186996.1 0 266858 5 55111 46749.0 0 55111 6 13358 11687.3 0 13358 7 9112 2921.8 0 9112 8 6597 730.5 0 6597 9 2003 182.6 0 1676 327 10 12450 45.7 1 11470 980 11 128 11.4 1 23 105 12 41 2.9 1 10 31 13 12 0.7 1 3 9 14 6 0.7 1 1 5 15 6 0.7 1 3 3 16 1 0.7 1 1 17 6 0.7 1 3 3 18 2 0.7 1 0 2 19 9 0.7 1 6 3 20 5 0.7 1 3 2 21 4 0.7 1 3 1 22 7 0.7 1 6 1 23 1 0.7 1 0 1 24 9 0.7 1 4 5 25 4 0.7 1 3 1 26 3 0.7 1 3 27 4 0.7 1 0 4 28 4 0.7 1 2 2 29 2 0.7 1 2 30 6 0.7 1 5 1 31 1 0.7 1 0 1 32 9 0.7 1 6 3 33 3 0.7 1 2 1 34 3 0.7 1 3 35 6 0.7 1 2 4 36 5 0.7 1 2 3 37 7 0.7 1 5 2 38 4 0.7 1 2 2 39 5 0.7 1 3 2 40 5 0.7 1 4 1 41 2 0.7 1 1 1 42 5 0.7 1 3 2 43 4 0.7 1 3 1 44 5 0.7 1 4 1 45 6 0.7 1 5 1 46 1 0.7 1 1 47 7 0.7 1 5 2 48 6 0.7 1 4 2 49 5 0.7 1 4 1 50 4 0.7 1 3 1 51 2 0.7 1 2 52 4 0.7 1 3 1 53 7 0.7 1 4 3 54 6 0.7 1 4 2 55 7 0.7 1 6 1 56 5 0.7 1 4 1 57 6 0.7 1 2 4 58 5 0.7 1 3 2 59 1 0.7 1 0 1 60 12 0.7 1 8 4 61 2 0.7 1 2 62 2 0.7 1 2 63 6 0.7 1 5 1 64 1 0.7 1 1 65 3 0.7 1 1 2 66 13 0.7 1 12 1 67 3 0.7 1 3 68 5 0.7 1 2 3 69 3 0.7 1 2 1 70 3 0.7 1 3 71 1 0.7 1 0 1 72 3 0.7 1 3 73 1 0.7 1 1 74 4 0.7 1 3 1 75 6 0.7 1 4 2 76 7 0.7 1 5 2 77 7 0.7 1 2 5 78 4 0.7 1 4 79 4 0.7 1 4 80 7 0.7 1 5 2 81 1 0.7 1 0 1 82 3 0.7 1 2 1 83 4 0.7 1 2 2 84 6 0.7 1 4 2 85 8 0.7 1 8 86 6 0.7 1 6 87 2 0.7 1 2 88 3 0.7 1 3 89 3 0.7 1 3 90 4 0.7 1 2 2 91 4 0.7 1 3 1 92 5 0.7 1 3 2 93 6 0.7 1 4 2 94 3 0.7 1 3 95 3 0.7 1 3 96 13 0.7 1 10 3 97 13 0.7 1 11 2 98 4 0.7 1 3 1 99 6 0.7 1 4 2 100 7 0.7 1 4 3 101 6 0.7 1 6 102 7 0.7 1 6 1 103 5 0.7 1 2 3 104 9 0.7 1 7 2 105 7 0.7 1 5 2 106 8 0.7 1 8 107 8 0.7 1 7 1 108 7 0.7 1 6 1 109 9 0.7 1 9 110 9 0.7 1 9 111 4 0.7 1 3 1 112 5 0.7 1 5 113 13 0.7 1 11 2 114 7 0.7 1 7 115 16 0.7 1 16 116 16 0.7 1 15 1 117 25 0.7 1 22 3 118 11 0.7 1 10 1 119 24 0.7 1 22 2 120 9 0.7 1 8 1 121 14 0.7 1 13 1 122 10 0.7 1 8 2 123 13 0.7 1 11 2 124 11 0.7 1 8 3 125 13 0.7 1 10 3 126 10 0.7 1 9 1 127 14 0.7 1 14 128 10 0.7 1 9 1 129 25 0.7 1 22 3 130 13 0.7 1 10 3 131 15 0.7 1 14 1 132 33 0.7 1 26 7 133 24 0.7 1 22 2 134 17 0.7 1 10 7 135 30 0.7 1 13 17 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_12_R2.fq.gz ============================================= 47871006 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_12_R1_trimmed.fq.gz and zr3644_12_R2_trimmed.fq.gz file_1: zr3644_12_R1_trimmed.fq.gz, file_2: zr3644_12_R2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_12_R1_trimmed.fq.gz and zr3644_12_R2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_12_R1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_12_R2_val_2.fq.gz Total number of sequences analysed: 47871006 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 198066 (0.41%) >>> Now running FastQC on the validated data zr3644_12_R1_val_1.fq.gz<<< Started analysis of zr3644_12_R1_val_1.fq.gz Approx 5% complete for zr3644_12_R1_val_1.fq.gz Approx 10% complete for zr3644_12_R1_val_1.fq.gz Approx 15% complete for zr3644_12_R1_val_1.fq.gz Approx 20% complete for zr3644_12_R1_val_1.fq.gz Approx 25% complete for zr3644_12_R1_val_1.fq.gz Approx 30% complete for zr3644_12_R1_val_1.fq.gz Approx 35% complete for zr3644_12_R1_val_1.fq.gz Approx 40% complete for zr3644_12_R1_val_1.fq.gz Approx 45% complete for zr3644_12_R1_val_1.fq.gz Approx 50% complete for zr3644_12_R1_val_1.fq.gz Approx 55% complete for zr3644_12_R1_val_1.fq.gz Approx 60% complete for zr3644_12_R1_val_1.fq.gz Approx 65% complete for zr3644_12_R1_val_1.fq.gz Approx 70% complete for zr3644_12_R1_val_1.fq.gz Approx 75% complete for zr3644_12_R1_val_1.fq.gz Approx 80% complete for zr3644_12_R1_val_1.fq.gz Approx 85% complete for zr3644_12_R1_val_1.fq.gz Approx 90% complete for zr3644_12_R1_val_1.fq.gz Approx 95% complete for zr3644_12_R1_val_1.fq.gz Analysis complete for zr3644_12_R1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_12_R2_val_2.fq.gz<<< Started analysis of zr3644_12_R2_val_2.fq.gz Approx 5% complete for zr3644_12_R2_val_2.fq.gz Approx 10% complete for zr3644_12_R2_val_2.fq.gz Approx 15% complete for zr3644_12_R2_val_2.fq.gz Approx 20% complete for zr3644_12_R2_val_2.fq.gz Approx 25% complete for zr3644_12_R2_val_2.fq.gz Approx 30% complete for zr3644_12_R2_val_2.fq.gz Approx 35% complete for zr3644_12_R2_val_2.fq.gz Approx 40% complete for zr3644_12_R2_val_2.fq.gz Approx 45% complete for zr3644_12_R2_val_2.fq.gz Approx 50% complete for zr3644_12_R2_val_2.fq.gz Approx 55% complete for zr3644_12_R2_val_2.fq.gz Approx 60% complete for zr3644_12_R2_val_2.fq.gz Approx 65% complete for zr3644_12_R2_val_2.fq.gz Approx 70% complete for zr3644_12_R2_val_2.fq.gz Approx 75% complete for zr3644_12_R2_val_2.fq.gz Approx 80% complete for zr3644_12_R2_val_2.fq.gz Approx 85% complete for zr3644_12_R2_val_2.fq.gz Approx 90% complete for zr3644_12_R2_val_2.fq.gz Approx 95% complete for zr3644_12_R2_val_2.fq.gz Analysis complete for zr3644_12_R2_val_2.fq.gz Deleting both intermediate output files zr3644_12_R1_trimmed.fq.gz and zr3644_12_R2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_13_R1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_13_R1.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3644_13_R1_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_13_R1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_13_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 2073.70 s (38 µs/read; 1.57 M reads/minute). === Summary === Total reads processed: 54,135,312 Reads with adapters: 23,721,761 (43.8%) Reads written (passing filters): 54,135,312 (100.0%) Total basepairs processed: 6,877,739,495 bp Quality-trimmed: 2,137,120 bp (0.0%) Total written (filtered): 6,847,681,076 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 23721761 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.2% C: 10.4% G: 6.3% T: 38.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 21118975 13533828.0 0 21118975 2 1726136 3383457.0 0 1726136 3 485217 845864.2 0 485217 4 294326 211466.1 0 294326 5 50975 52866.5 0 50975 6 13477 13216.6 0 13477 7 9619 3304.2 0 9619 8 7050 826.0 0 7050 9 1973 206.5 0 1544 429 10 12595 51.6 1 11537 1058 11 162 12.9 1 26 136 12 46 3.2 1 15 31 13 5 0.8 1 3 2 14 10 0.8 1 6 4 15 4 0.8 1 1 3 16 11 0.8 1 6 5 17 2 0.8 1 2 18 15 0.8 1 9 6 19 14 0.8 1 7 7 20 3 0.8 1 2 1 21 9 0.8 1 7 2 22 3 0.8 1 1 2 23 13 0.8 1 10 3 24 9 0.8 1 4 5 25 3 0.8 1 2 1 26 5 0.8 1 2 3 27 3 0.8 1 3 28 5 0.8 1 3 2 29 6 0.8 1 5 1 30 9 0.8 1 4 5 31 12 0.8 1 7 5 32 4 0.8 1 2 2 33 4 0.8 1 2 2 34 2 0.8 1 2 35 6 0.8 1 3 3 36 9 0.8 1 6 3 37 3 0.8 1 3 38 7 0.8 1 2 5 39 9 0.8 1 9 40 7 0.8 1 5 2 41 5 0.8 1 3 2 42 3 0.8 1 3 43 6 0.8 1 4 2 44 6 0.8 1 3 3 45 6 0.8 1 2 4 46 5 0.8 1 2 3 47 4 0.8 1 3 1 48 4 0.8 1 3 1 49 4 0.8 1 4 50 6 0.8 1 5 1 51 3 0.8 1 3 52 10 0.8 1 9 1 53 3 0.8 1 2 1 54 7 0.8 1 5 2 55 5 0.8 1 3 2 56 8 0.8 1 6 2 57 6 0.8 1 5 1 58 3 0.8 1 3 59 6 0.8 1 4 2 60 3 0.8 1 2 1 61 8 0.8 1 5 3 62 5 0.8 1 4 1 63 2 0.8 1 1 1 64 5 0.8 1 3 2 65 4 0.8 1 3 1 66 6 0.8 1 4 2 67 6 0.8 1 4 2 68 3 0.8 1 2 1 69 6 0.8 1 5 1 70 8 0.8 1 7 1 71 4 0.8 1 2 2 72 5 0.8 1 5 73 5 0.8 1 4 1 74 5 0.8 1 4 1 75 6 0.8 1 6 76 1 0.8 1 1 77 5 0.8 1 3 2 78 5 0.8 1 4 1 79 1 0.8 1 0 1 80 5 0.8 1 4 1 81 10 0.8 1 7 3 82 2 0.8 1 2 83 6 0.8 1 5 1 84 8 0.8 1 7 1 85 7 0.8 1 7 86 9 0.8 1 7 2 87 10 0.8 1 8 2 88 14 0.8 1 9 5 89 9 0.8 1 7 2 90 15 0.8 1 11 4 91 11 0.8 1 5 6 92 9 0.8 1 8 1 93 5 0.8 1 5 94 13 0.8 1 12 1 95 13 0.8 1 11 2 96 4 0.8 1 4 97 6 0.8 1 2 4 98 6 0.8 1 3 3 99 13 0.8 1 11 2 100 8 0.8 1 8 101 12 0.8 1 11 1 102 8 0.8 1 7 1 103 11 0.8 1 6 5 104 6 0.8 1 5 1 105 12 0.8 1 12 106 15 0.8 1 15 107 7 0.8 1 6 1 108 13 0.8 1 13 109 8 0.8 1 8 110 14 0.8 1 13 1 111 12 0.8 1 11 1 112 17 0.8 1 15 2 113 15 0.8 1 13 2 114 8 0.8 1 8 115 10 0.8 1 9 1 116 9 0.8 1 8 1 117 10 0.8 1 9 1 118 28 0.8 1 24 4 119 13 0.8 1 12 1 120 22 0.8 1 16 6 121 10 0.8 1 6 4 122 25 0.8 1 21 4 123 25 0.8 1 18 7 124 16 0.8 1 14 2 125 19 0.8 1 18 1 126 13 0.8 1 12 1 127 14 0.8 1 13 1 128 28 0.8 1 27 1 129 29 0.8 1 25 4 130 38 0.8 1 33 5 131 22 0.8 1 17 5 132 32 0.8 1 30 2 133 28 0.8 1 22 6 134 34 0.8 1 23 11 135 59 0.8 1 22 37 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_13_R1.fq.gz ============================================= 54135312 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_13_R2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_13_R2.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3644_13_R2_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_13_R2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_13_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1773.29 s (33 µs/read; 1.83 M reads/minute). === Summary === Total reads processed: 54,135,312 Reads with adapters: 23,601,218 (43.6%) Reads written (passing filters): 54,135,312 (100.0%) Total basepairs processed: 6,875,391,122 bp Quality-trimmed: 1,991,084 bp (0.0%) Total written (filtered): 6,845,788,397 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 23601218 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.7% C: 10.2% G: 6.0% T: 38.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 21164011 13533828.0 0 21164011 2 1571912 3383457.0 0 1571912 3 470038 845864.2 0 470038 4 299695 211466.1 0 299695 5 52176 52866.5 0 52176 6 12427 13216.6 0 12427 7 8880 3304.2 0 8880 8 6830 826.0 0 6830 9 1975 206.5 0 1582 393 10 12006 51.6 1 10968 1038 11 151 12.9 1 14 137 12 29 3.2 1 7 22 13 6 0.8 1 4 2 14 8 0.8 1 6 2 15 4 0.8 1 3 1 16 3 0.8 1 1 2 17 2 0.8 1 1 1 18 3 0.8 1 1 2 19 5 0.8 1 0 5 20 3 0.8 1 2 1 21 6 0.8 1 2 4 22 5 0.8 1 1 4 23 5 0.8 1 3 2 24 8 0.8 1 7 1 25 12 0.8 1 6 6 26 3 0.8 1 2 1 27 3 0.8 1 1 2 28 12 0.8 1 6 6 29 3 0.8 1 1 2 30 3 0.8 1 3 31 3 0.8 1 1 2 32 12 0.8 1 4 8 33 7 0.8 1 5 2 34 3 0.8 1 1 2 35 4 0.8 1 1 3 36 5 0.8 1 4 1 37 6 0.8 1 4 2 38 5 0.8 1 1 4 39 7 0.8 1 6 1 40 5 0.8 1 5 41 6 0.8 1 3 3 42 7 0.8 1 4 3 43 2 0.8 1 2 44 4 0.8 1 2 2 45 6 0.8 1 3 3 46 8 0.8 1 7 1 47 6 0.8 1 3 3 48 5 0.8 1 3 2 49 6 0.8 1 6 50 7 0.8 1 6 1 51 1 0.8 1 1 52 4 0.8 1 3 1 53 6 0.8 1 6 54 2 0.8 1 2 55 1 0.8 1 1 56 2 0.8 1 1 1 57 6 0.8 1 3 3 58 12 0.8 1 9 3 60 6 0.8 1 3 3 61 4 0.8 1 3 1 62 2 0.8 1 2 63 7 0.8 1 5 2 64 4 0.8 1 4 65 4 0.8 1 3 1 66 6 0.8 1 4 2 67 2 0.8 1 2 68 7 0.8 1 5 2 69 5 0.8 1 5 70 5 0.8 1 3 2 71 2 0.8 1 2 72 2 0.8 1 2 73 9 0.8 1 6 3 74 7 0.8 1 5 2 75 3 0.8 1 1 2 76 6 0.8 1 5 1 77 2 0.8 1 2 78 4 0.8 1 3 1 79 9 0.8 1 9 80 4 0.8 1 2 2 81 4 0.8 1 3 1 82 9 0.8 1 5 4 83 9 0.8 1 7 2 84 7 0.8 1 5 2 85 12 0.8 1 8 4 86 7 0.8 1 5 2 87 3 0.8 1 3 88 2 0.8 1 1 1 89 10 0.8 1 9 1 90 5 0.8 1 3 2 91 2 0.8 1 1 1 92 5 0.8 1 5 93 6 0.8 1 6 94 9 0.8 1 7 2 95 5 0.8 1 4 1 96 3 0.8 1 3 97 13 0.8 1 8 5 98 7 0.8 1 5 2 99 8 0.8 1 6 2 100 5 0.8 1 4 1 101 10 0.8 1 8 2 102 9 0.8 1 5 4 103 10 0.8 1 8 2 104 5 0.8 1 2 3 105 8 0.8 1 4 4 106 8 0.8 1 7 1 107 4 0.8 1 4 108 11 0.8 1 8 3 109 13 0.8 1 11 2 110 9 0.8 1 9 111 17 0.8 1 15 2 112 9 0.8 1 9 113 10 0.8 1 8 2 114 16 0.8 1 15 1 115 11 0.8 1 10 1 116 14 0.8 1 12 2 117 11 0.8 1 10 1 118 6 0.8 1 5 1 119 26 0.8 1 20 6 120 16 0.8 1 11 5 121 26 0.8 1 19 7 122 19 0.8 1 19 123 24 0.8 1 19 5 124 20 0.8 1 19 1 125 24 0.8 1 19 5 126 26 0.8 1 22 4 127 25 0.8 1 24 1 128 20 0.8 1 18 2 129 23 0.8 1 17 6 130 23 0.8 1 17 6 131 20 0.8 1 18 2 132 36 0.8 1 28 8 133 29 0.8 1 27 2 134 34 0.8 1 25 9 135 43 0.8 1 27 16 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_13_R2.fq.gz ============================================= 54135312 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_13_R1_trimmed.fq.gz and zr3644_13_R2_trimmed.fq.gz file_1: zr3644_13_R1_trimmed.fq.gz, file_2: zr3644_13_R2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_13_R1_trimmed.fq.gz and zr3644_13_R2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_13_R1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_13_R2_val_2.fq.gz Total number of sequences analysed: 54135312 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 223746 (0.41%) >>> Now running FastQC on the validated data zr3644_13_R1_val_1.fq.gz<<< Started analysis of zr3644_13_R1_val_1.fq.gz Approx 5% complete for zr3644_13_R1_val_1.fq.gz Approx 10% complete for zr3644_13_R1_val_1.fq.gz Approx 15% complete for zr3644_13_R1_val_1.fq.gz Approx 20% complete for zr3644_13_R1_val_1.fq.gz Approx 25% complete for zr3644_13_R1_val_1.fq.gz Approx 30% complete for zr3644_13_R1_val_1.fq.gz Approx 35% complete for zr3644_13_R1_val_1.fq.gz Approx 40% complete for zr3644_13_R1_val_1.fq.gz Approx 45% complete for zr3644_13_R1_val_1.fq.gz Approx 50% complete for zr3644_13_R1_val_1.fq.gz Approx 55% complete for zr3644_13_R1_val_1.fq.gz Approx 60% complete for zr3644_13_R1_val_1.fq.gz Approx 65% complete for zr3644_13_R1_val_1.fq.gz Approx 70% complete for zr3644_13_R1_val_1.fq.gz Approx 75% complete for zr3644_13_R1_val_1.fq.gz Approx 80% complete for zr3644_13_R1_val_1.fq.gz Approx 85% complete for zr3644_13_R1_val_1.fq.gz Approx 90% complete for zr3644_13_R1_val_1.fq.gz Approx 95% complete for zr3644_13_R1_val_1.fq.gz Analysis complete for zr3644_13_R1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_13_R2_val_2.fq.gz<<< Started analysis of zr3644_13_R2_val_2.fq.gz Approx 5% complete for zr3644_13_R2_val_2.fq.gz Approx 10% complete for zr3644_13_R2_val_2.fq.gz Approx 15% complete for zr3644_13_R2_val_2.fq.gz Approx 20% complete for zr3644_13_R2_val_2.fq.gz Approx 25% complete for zr3644_13_R2_val_2.fq.gz Approx 30% complete for zr3644_13_R2_val_2.fq.gz Approx 35% complete for zr3644_13_R2_val_2.fq.gz Approx 40% complete for zr3644_13_R2_val_2.fq.gz Approx 45% complete for zr3644_13_R2_val_2.fq.gz Approx 50% complete for zr3644_13_R2_val_2.fq.gz Approx 55% complete for zr3644_13_R2_val_2.fq.gz Approx 60% complete for zr3644_13_R2_val_2.fq.gz Approx 65% complete for zr3644_13_R2_val_2.fq.gz Approx 70% complete for zr3644_13_R2_val_2.fq.gz Approx 75% complete for zr3644_13_R2_val_2.fq.gz Approx 80% complete for zr3644_13_R2_val_2.fq.gz Approx 85% complete for zr3644_13_R2_val_2.fq.gz Approx 90% complete for zr3644_13_R2_val_2.fq.gz Approx 95% complete for zr3644_13_R2_val_2.fq.gz Analysis complete for zr3644_13_R2_val_2.fq.gz Deleting both intermediate output files zr3644_13_R1_trimmed.fq.gz and zr3644_13_R2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_14_R1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_14_R1.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3644_14_R1_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_14_R1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_14_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1317.25 s (36 µs/read; 1.69 M reads/minute). === Summary === Total reads processed: 37,045,803 Reads with adapters: 16,116,353 (43.5%) Reads written (passing filters): 37,045,803 (100.0%) Total basepairs processed: 4,679,181,409 bp Quality-trimmed: 2,133,036 bp (0.0%) Total written (filtered): 4,657,981,637 bp (99.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 16116353 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 44.6% C: 10.7% G: 6.5% T: 38.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 14285260 9261450.8 0 14285260 2 1214770 2315362.7 0 1214770 3 342924 578840.7 0 342924 4 202583 144710.2 0 202583 5 37095 36177.5 0 37095 6 9891 9044.4 0 9891 7 7025 2261.1 0 7025 8 5226 565.3 0 5226 9 1458 141.3 0 1143 315 10 9219 35.3 1 8384 835 11 98 8.8 1 13 85 12 36 2.2 1 3 33 13 11 0.6 1 2 9 14 7 0.6 1 4 3 15 3 0.6 1 0 3 16 9 0.6 1 7 2 17 2 0.6 1 2 18 7 0.6 1 4 3 19 7 0.6 1 2 5 20 1 0.6 1 1 21 4 0.6 1 2 2 22 1 0.6 1 1 23 8 0.6 1 6 2 24 4 0.6 1 2 2 25 2 0.6 1 2 26 8 0.6 1 6 2 27 2 0.6 1 0 2 30 2 0.6 1 2 31 3 0.6 1 1 2 32 2 0.6 1 1 1 33 6 0.6 1 2 4 34 3 0.6 1 2 1 35 3 0.6 1 2 1 36 5 0.6 1 4 1 37 9 0.6 1 3 6 38 5 0.6 1 4 1 39 6 0.6 1 6 40 4 0.6 1 4 41 1 0.6 1 1 42 7 0.6 1 3 4 43 4 0.6 1 2 2 44 4 0.6 1 1 3 45 1 0.6 1 1 46 3 0.6 1 1 2 47 2 0.6 1 2 48 1 0.6 1 1 49 1 0.6 1 1 50 6 0.6 1 4 2 51 3 0.6 1 2 1 52 2 0.6 1 1 1 53 1 0.6 1 1 54 3 0.6 1 3 55 1 0.6 1 0 1 56 3 0.6 1 3 57 3 0.6 1 3 58 3 0.6 1 3 59 1 0.6 1 1 61 3 0.6 1 1 2 62 5 0.6 1 5 63 7 0.6 1 5 2 64 4 0.6 1 3 1 65 5 0.6 1 4 1 66 5 0.6 1 4 1 67 6 0.6 1 5 1 68 5 0.6 1 4 1 69 8 0.6 1 4 4 70 2 0.6 1 2 71 2 0.6 1 2 72 3 0.6 1 2 1 73 5 0.6 1 2 3 74 4 0.6 1 4 75 7 0.6 1 5 2 76 6 0.6 1 6 77 3 0.6 1 2 1 78 7 0.6 1 7 79 3 0.6 1 2 1 80 5 0.6 1 5 81 4 0.6 1 3 1 82 5 0.6 1 5 83 5 0.6 1 2 3 84 4 0.6 1 3 1 85 5 0.6 1 4 1 86 2 0.6 1 2 87 7 0.6 1 6 1 88 3 0.6 1 2 1 89 6 0.6 1 5 1 90 5 0.6 1 2 3 91 1 0.6 1 1 92 3 0.6 1 2 1 93 8 0.6 1 7 1 94 4 0.6 1 3 1 95 8 0.6 1 6 2 96 9 0.6 1 8 1 97 3 0.6 1 2 1 98 5 0.6 1 4 1 99 6 0.6 1 4 2 100 7 0.6 1 6 1 101 6 0.6 1 5 1 102 5 0.6 1 3 2 103 7 0.6 1 7 104 2 0.6 1 1 1 105 3 0.6 1 3 106 7 0.6 1 6 1 107 10 0.6 1 10 108 10 0.6 1 7 3 109 3 0.6 1 3 110 2 0.6 1 2 111 6 0.6 1 4 2 112 10 0.6 1 8 2 113 12 0.6 1 11 1 114 13 0.6 1 9 4 115 9 0.6 1 7 2 116 10 0.6 1 10 117 4 0.6 1 3 1 118 13 0.6 1 12 1 119 17 0.6 1 15 2 120 15 0.6 1 14 1 121 6 0.6 1 5 1 122 14 0.6 1 12 2 123 16 0.6 1 14 2 124 9 0.6 1 6 3 125 9 0.6 1 9 126 10 0.6 1 10 127 20 0.6 1 20 128 13 0.6 1 11 2 129 17 0.6 1 17 130 20 0.6 1 20 131 19 0.6 1 15 4 132 24 0.6 1 21 3 133 21 0.6 1 16 5 134 16 0.6 1 14 2 135 21 0.6 1 11 10 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_14_R1.fq.gz ============================================= 37045803 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_14_R2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_14_R2.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3644_14_R2_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_14_R2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_14_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1183.34 s (32 µs/read; 1.88 M reads/minute). === Summary === Total reads processed: 37,045,803 Reads with adapters: 15,901,700 (42.9%) Reads written (passing filters): 37,045,803 (100.0%) Total basepairs processed: 4,677,677,552 bp Quality-trimmed: 1,158,321 bp (0.0%) Total written (filtered): 4,657,794,991 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 15901700 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.4% C: 10.1% G: 6.2% T: 38.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 14192161 9261450.8 0 14192161 2 1108291 2315362.7 0 1108291 3 317814 578840.7 0 317814 4 209516 144710.2 0 209516 5 40045 36177.5 0 40045 6 9813 9044.4 0 9813 7 7173 2261.1 0 7173 8 5447 565.3 0 5447 9 1388 141.3 0 1097 291 10 9275 35.3 1 8582 693 11 112 8.8 1 17 95 12 20 2.2 1 7 13 13 3 0.6 1 0 3 14 2 0.6 1 0 2 16 3 0.6 1 1 2 17 2 0.6 1 2 18 1 0.6 1 0 1 19 3 0.6 1 0 3 21 2 0.6 1 1 1 22 1 0.6 1 1 23 2 0.6 1 1 1 24 1 0.6 1 1 25 1 0.6 1 1 26 2 0.6 1 1 1 27 3 0.6 1 3 29 1 0.6 1 0 1 30 2 0.6 1 1 1 31 2 0.6 1 1 1 32 6 0.6 1 4 2 33 6 0.6 1 4 2 34 2 0.6 1 1 1 35 3 0.6 1 3 37 1 0.6 1 1 38 1 0.6 1 1 39 2 0.6 1 2 40 1 0.6 1 0 1 41 1 0.6 1 1 42 2 0.6 1 2 43 3 0.6 1 1 2 45 2 0.6 1 2 46 2 0.6 1 1 1 47 1 0.6 1 0 1 48 4 0.6 1 2 2 49 3 0.6 1 2 1 51 3 0.6 1 3 52 2 0.6 1 2 53 4 0.6 1 4 54 3 0.6 1 3 55 4 0.6 1 3 1 56 2 0.6 1 2 57 4 0.6 1 3 1 58 3 0.6 1 2 1 59 1 0.6 1 0 1 60 7 0.6 1 5 2 61 3 0.6 1 2 1 62 3 0.6 1 2 1 63 8 0.6 1 6 2 64 5 0.6 1 4 1 65 2 0.6 1 2 66 1 0.6 1 1 67 3 0.6 1 3 68 1 0.6 1 1 70 1 0.6 1 1 71 3 0.6 1 3 72 4 0.6 1 3 1 73 3 0.6 1 1 2 74 2 0.6 1 2 75 4 0.6 1 3 1 76 1 0.6 1 0 1 77 2 0.6 1 2 78 6 0.6 1 5 1 79 3 0.6 1 3 80 6 0.6 1 5 1 81 3 0.6 1 3 82 5 0.6 1 5 83 2 0.6 1 1 1 84 2 0.6 1 2 85 3 0.6 1 2 1 86 7 0.6 1 6 1 87 2 0.6 1 2 88 8 0.6 1 6 2 89 8 0.6 1 8 90 3 0.6 1 3 91 4 0.6 1 4 92 4 0.6 1 4 93 9 0.6 1 5 4 94 2 0.6 1 2 95 3 0.6 1 3 96 1 0.6 1 1 97 5 0.6 1 2 3 98 7 0.6 1 6 1 99 6 0.6 1 6 100 7 0.6 1 6 1 101 7 0.6 1 5 2 102 2 0.6 1 1 1 103 3 0.6 1 3 104 6 0.6 1 5 1 105 5 0.6 1 4 1 106 5 0.6 1 5 107 7 0.6 1 7 108 3 0.6 1 3 109 6 0.6 1 5 1 110 5 0.6 1 4 1 111 5 0.6 1 5 112 10 0.6 1 10 113 10 0.6 1 10 114 7 0.6 1 7 115 15 0.6 1 13 2 116 11 0.6 1 9 2 117 7 0.6 1 7 118 11 0.6 1 9 2 119 16 0.6 1 16 120 12 0.6 1 11 1 121 9 0.6 1 8 1 122 14 0.6 1 13 1 123 15 0.6 1 13 2 124 7 0.6 1 5 2 125 9 0.6 1 6 3 126 13 0.6 1 13 127 19 0.6 1 17 2 128 17 0.6 1 13 4 129 20 0.6 1 16 4 130 23 0.6 1 21 2 131 10 0.6 1 9 1 132 20 0.6 1 17 3 133 14 0.6 1 11 3 134 15 0.6 1 11 4 135 31 0.6 1 16 15 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_14_R2.fq.gz ============================================= 37045803 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_14_R1_trimmed.fq.gz and zr3644_14_R2_trimmed.fq.gz file_1: zr3644_14_R1_trimmed.fq.gz, file_2: zr3644_14_R2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_14_R1_trimmed.fq.gz and zr3644_14_R2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_14_R1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_14_R2_val_2.fq.gz Total number of sequences analysed: 37045803 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 174047 (0.47%) >>> Now running FastQC on the validated data zr3644_14_R1_val_1.fq.gz<<< Started analysis of zr3644_14_R1_val_1.fq.gz Approx 5% complete for zr3644_14_R1_val_1.fq.gz Approx 10% complete for zr3644_14_R1_val_1.fq.gz Approx 15% complete for zr3644_14_R1_val_1.fq.gz Approx 20% complete for zr3644_14_R1_val_1.fq.gz Approx 25% complete for zr3644_14_R1_val_1.fq.gz Approx 30% complete for zr3644_14_R1_val_1.fq.gz Approx 35% complete for zr3644_14_R1_val_1.fq.gz Approx 40% complete for zr3644_14_R1_val_1.fq.gz Approx 45% complete for zr3644_14_R1_val_1.fq.gz Approx 50% complete for zr3644_14_R1_val_1.fq.gz Approx 55% complete for zr3644_14_R1_val_1.fq.gz Approx 60% complete for zr3644_14_R1_val_1.fq.gz Approx 65% complete for zr3644_14_R1_val_1.fq.gz Approx 70% complete for zr3644_14_R1_val_1.fq.gz Approx 75% complete for zr3644_14_R1_val_1.fq.gz Approx 80% complete for zr3644_14_R1_val_1.fq.gz Approx 85% complete for zr3644_14_R1_val_1.fq.gz Approx 90% complete for zr3644_14_R1_val_1.fq.gz Approx 95% complete for zr3644_14_R1_val_1.fq.gz Analysis complete for zr3644_14_R1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_14_R2_val_2.fq.gz<<< Started analysis of zr3644_14_R2_val_2.fq.gz Approx 5% complete for zr3644_14_R2_val_2.fq.gz Approx 10% complete for zr3644_14_R2_val_2.fq.gz Approx 15% complete for zr3644_14_R2_val_2.fq.gz Approx 20% complete for zr3644_14_R2_val_2.fq.gz Approx 25% complete for zr3644_14_R2_val_2.fq.gz Approx 30% complete for zr3644_14_R2_val_2.fq.gz Approx 35% complete for zr3644_14_R2_val_2.fq.gz Approx 40% complete for zr3644_14_R2_val_2.fq.gz Approx 45% complete for zr3644_14_R2_val_2.fq.gz Approx 50% complete for zr3644_14_R2_val_2.fq.gz Approx 55% complete for zr3644_14_R2_val_2.fq.gz Approx 60% complete for zr3644_14_R2_val_2.fq.gz Approx 65% complete for zr3644_14_R2_val_2.fq.gz Approx 70% complete for zr3644_14_R2_val_2.fq.gz Approx 75% complete for zr3644_14_R2_val_2.fq.gz Approx 80% complete for zr3644_14_R2_val_2.fq.gz Approx 85% complete for zr3644_14_R2_val_2.fq.gz Approx 90% complete for zr3644_14_R2_val_2.fq.gz Approx 95% complete for zr3644_14_R2_val_2.fq.gz Analysis complete for zr3644_14_R2_val_2.fq.gz Deleting both intermediate output files zr3644_14_R1_trimmed.fq.gz and zr3644_14_R2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_15_R1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_15_R1.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3644_15_R1_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_15_R1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_15_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1927.93 s (32 µs/read; 1.85 M reads/minute). === Summary === Total reads processed: 59,408,352 Reads with adapters: 25,824,093 (43.5%) Reads written (passing filters): 59,408,352 (100.0%) Total basepairs processed: 7,517,784,280 bp Quality-trimmed: 2,588,934 bp (0.0%) Total written (filtered): 7,484,679,145 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 25824093 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.1% C: 10.4% G: 6.3% T: 38.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 22938238 14852088.0 0 22938238 2 1912707 3713022.0 0 1912707 3 532313 928255.5 0 532313 4 327693 232063.9 0 327693 5 60219 58016.0 0 60219 6 15425 14504.0 0 15425 7 11062 3626.0 0 11062 8 8148 906.5 0 8148 9 2048 226.6 0 1595 453 10 14157 56.7 1 12921 1236 11 179 14.2 1 41 138 12 82 3.5 1 30 52 13 7 0.9 1 1 6 14 28 0.9 1 18 10 15 6 0.9 1 5 1 16 19 0.9 1 13 6 17 3 0.9 1 1 2 18 40 0.9 1 23 17 19 41 0.9 1 30 11 20 7 0.9 1 4 3 21 2 0.9 1 2 22 9 0.9 1 4 5 23 21 0.9 1 15 6 24 24 0.9 1 19 5 25 5 0.9 1 5 26 16 0.9 1 9 7 27 17 0.9 1 14 3 28 2 0.9 1 1 1 29 8 0.9 1 7 1 30 18 0.9 1 10 8 31 27 0.9 1 15 12 32 5 0.9 1 5 33 17 0.9 1 11 6 34 12 0.9 1 8 4 35 15 0.9 1 11 4 36 16 0.9 1 11 5 37 26 0.9 1 19 7 38 8 0.9 1 4 4 39 9 0.9 1 6 3 40 12 0.9 1 8 4 41 16 0.9 1 9 7 42 14 0.9 1 7 7 43 23 0.9 1 18 5 44 21 0.9 1 14 7 45 7 0.9 1 5 2 46 10 0.9 1 7 3 47 12 0.9 1 9 3 48 14 0.9 1 11 3 49 16 0.9 1 13 3 50 8 0.9 1 4 4 51 14 0.9 1 10 4 52 35 0.9 1 20 15 53 5 0.9 1 3 2 54 3 0.9 1 3 55 27 0.9 1 19 8 56 22 0.9 1 17 5 57 4 0.9 1 4 58 8 0.9 1 5 3 59 11 0.9 1 10 1 60 2 0.9 1 1 1 61 5 0.9 1 4 1 62 9 0.9 1 7 2 63 6 0.9 1 5 1 64 4 0.9 1 3 1 65 6 0.9 1 6 66 19 0.9 1 15 4 67 10 0.9 1 9 1 68 8 0.9 1 8 69 14 0.9 1 10 4 70 8 0.9 1 6 2 71 11 0.9 1 11 72 11 0.9 1 9 2 73 9 0.9 1 9 74 15 0.9 1 14 1 75 6 0.9 1 6 76 16 0.9 1 15 1 77 15 0.9 1 11 4 78 12 0.9 1 10 2 79 8 0.9 1 6 2 80 10 0.9 1 8 2 81 13 0.9 1 9 4 82 10 0.9 1 8 2 83 6 0.9 1 6 84 4 0.9 1 4 85 16 0.9 1 12 4 86 7 0.9 1 5 2 87 10 0.9 1 8 2 88 13 0.9 1 12 1 89 9 0.9 1 8 1 90 8 0.9 1 5 3 91 12 0.9 1 8 4 92 15 0.9 1 9 6 93 9 0.9 1 8 1 94 13 0.9 1 9 4 95 6 0.9 1 6 96 14 0.9 1 14 97 14 0.9 1 12 2 98 13 0.9 1 9 4 99 13 0.9 1 11 2 100 8 0.9 1 7 1 101 10 0.9 1 8 2 102 9 0.9 1 6 3 103 7 0.9 1 6 1 104 14 0.9 1 13 1 105 11 0.9 1 9 2 106 21 0.9 1 20 1 107 13 0.9 1 11 2 108 12 0.9 1 9 3 109 13 0.9 1 12 1 110 8 0.9 1 7 1 111 10 0.9 1 8 2 112 17 0.9 1 13 4 113 13 0.9 1 11 2 114 18 0.9 1 16 2 115 9 0.9 1 7 2 116 15 0.9 1 9 6 117 11 0.9 1 11 118 19 0.9 1 17 2 119 22 0.9 1 16 6 120 17 0.9 1 13 4 121 25 0.9 1 24 1 122 29 0.9 1 20 9 123 20 0.9 1 17 3 124 17 0.9 1 16 1 125 18 0.9 1 13 5 126 25 0.9 1 23 2 127 18 0.9 1 15 3 128 26 0.9 1 23 3 129 45 0.9 1 34 11 130 39 0.9 1 32 7 131 30 0.9 1 26 4 132 38 0.9 1 33 5 133 30 0.9 1 24 6 134 40 0.9 1 26 14 135 46 0.9 1 16 30 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_15_R1.fq.gz ============================================= 59408352 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_15_R2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_15_R2.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3644_15_R2_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_15_R2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_15_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1932.23 s (33 µs/read; 1.84 M reads/minute). === Summary === Total reads processed: 59,408,352 Reads with adapters: 25,648,945 (43.2%) Reads written (passing filters): 59,408,352 (100.0%) Total basepairs processed: 7,515,911,423 bp Quality-trimmed: 2,005,465 bp (0.0%) Total written (filtered): 7,483,739,706 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 25648945 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.6% C: 10.1% G: 6.2% T: 38.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 22912081 14852088.0 0 22912081 2 1772714 3713022.0 0 1772714 3 516812 928255.5 0 516812 4 333951 232063.9 0 333951 5 62195 58016.0 0 62195 6 15010 14504.0 0 15010 7 10651 3626.0 0 10651 8 7911 906.5 0 7911 9 2232 226.6 0 1710 522 10 13847 56.7 1 12684 1163 11 170 14.2 1 19 151 12 58 3.5 1 12 46 13 13 0.9 1 4 9 15 7 0.9 1 6 1 16 3 0.9 1 3 17 7 0.9 1 3 4 18 3 0.9 1 1 2 19 6 0.9 1 2 4 20 4 0.9 1 1 3 21 3 0.9 1 3 22 4 0.9 1 1 3 23 6 0.9 1 4 2 24 10 0.9 1 4 6 25 4 0.9 1 2 2 26 6 0.9 1 3 3 27 4 0.9 1 2 2 28 5 0.9 1 2 3 29 2 0.9 1 1 1 30 12 0.9 1 7 5 31 5 0.9 1 5 32 11 0.9 1 6 5 33 9 0.9 1 8 1 34 9 0.9 1 5 4 35 6 0.9 1 4 2 36 7 0.9 1 3 4 37 3 0.9 1 3 38 6 0.9 1 6 39 6 0.9 1 4 2 40 5 0.9 1 4 1 41 6 0.9 1 6 42 7 0.9 1 4 3 43 4 0.9 1 2 2 44 12 0.9 1 5 7 45 6 0.9 1 4 2 46 2 0.9 1 1 1 47 6 0.9 1 5 1 48 12 0.9 1 9 3 49 11 0.9 1 8 3 50 2 0.9 1 2 51 7 0.9 1 5 2 52 2 0.9 1 1 1 53 8 0.9 1 8 54 5 0.9 1 4 1 55 4 0.9 1 3 1 56 4 0.9 1 4 57 4 0.9 1 4 58 4 0.9 1 3 1 59 6 0.9 1 3 3 60 12 0.9 1 6 6 61 6 0.9 1 4 2 62 1 0.9 1 1 63 12 0.9 1 10 2 64 8 0.9 1 6 2 65 4 0.9 1 4 66 10 0.9 1 8 2 67 8 0.9 1 8 68 10 0.9 1 10 69 5 0.9 1 5 70 9 0.9 1 7 2 71 7 0.9 1 5 2 72 4 0.9 1 4 73 5 0.9 1 5 74 3 0.9 1 2 1 75 9 0.9 1 8 1 76 11 0.9 1 10 1 77 4 0.9 1 4 78 6 0.9 1 4 2 79 10 0.9 1 9 1 80 13 0.9 1 11 2 81 5 0.9 1 5 82 3 0.9 1 3 83 9 0.9 1 8 1 84 12 0.9 1 11 1 85 8 0.9 1 7 1 86 8 0.9 1 7 1 87 10 0.9 1 8 2 88 12 0.9 1 10 2 89 4 0.9 1 4 90 11 0.9 1 7 4 91 7 0.9 1 7 92 12 0.9 1 8 4 93 15 0.9 1 13 2 94 10 0.9 1 9 1 95 4 0.9 1 2 2 96 8 0.9 1 8 97 11 0.9 1 8 3 98 9 0.9 1 7 2 99 9 0.9 1 7 2 100 11 0.9 1 10 1 101 10 0.9 1 8 2 102 4 0.9 1 3 1 103 10 0.9 1 8 2 104 7 0.9 1 7 105 13 0.9 1 10 3 106 16 0.9 1 13 3 107 11 0.9 1 11 108 21 0.9 1 20 1 109 15 0.9 1 14 1 110 11 0.9 1 8 3 111 8 0.9 1 8 112 12 0.9 1 11 1 113 17 0.9 1 15 2 114 14 0.9 1 14 115 26 0.9 1 17 9 116 21 0.9 1 20 1 117 17 0.9 1 17 118 31 0.9 1 25 6 119 28 0.9 1 22 6 120 19 0.9 1 17 2 121 15 0.9 1 15 122 17 0.9 1 14 3 123 20 0.9 1 17 3 124 16 0.9 1 16 125 18 0.9 1 13 5 126 22 0.9 1 18 4 127 22 0.9 1 20 2 128 22 0.9 1 21 1 129 15 0.9 1 13 2 130 42 0.9 1 36 6 131 41 0.9 1 31 10 132 28 0.9 1 25 3 133 32 0.9 1 23 9 134 33 0.9 1 23 10 135 46 0.9 1 24 22 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_15_R2.fq.gz ============================================= 59408352 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_15_R1_trimmed.fq.gz and zr3644_15_R2_trimmed.fq.gz file_1: zr3644_15_R1_trimmed.fq.gz, file_2: zr3644_15_R2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_15_R1_trimmed.fq.gz and zr3644_15_R2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_15_R1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_15_R2_val_2.fq.gz Total number of sequences analysed: 59408352 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 270791 (0.46%) >>> Now running FastQC on the validated data zr3644_15_R1_val_1.fq.gz<<< Started analysis of zr3644_15_R1_val_1.fq.gz Approx 5% complete for zr3644_15_R1_val_1.fq.gz Approx 10% complete for zr3644_15_R1_val_1.fq.gz Approx 15% complete for zr3644_15_R1_val_1.fq.gz Approx 20% complete for zr3644_15_R1_val_1.fq.gz Approx 25% complete for zr3644_15_R1_val_1.fq.gz Approx 30% complete for zr3644_15_R1_val_1.fq.gz Approx 35% complete for zr3644_15_R1_val_1.fq.gz Approx 40% complete for zr3644_15_R1_val_1.fq.gz Approx 45% complete for zr3644_15_R1_val_1.fq.gz Approx 50% complete for zr3644_15_R1_val_1.fq.gz Approx 55% complete for zr3644_15_R1_val_1.fq.gz Approx 60% complete for zr3644_15_R1_val_1.fq.gz Approx 65% complete for zr3644_15_R1_val_1.fq.gz Approx 70% complete for zr3644_15_R1_val_1.fq.gz Approx 75% complete for zr3644_15_R1_val_1.fq.gz Approx 80% complete for zr3644_15_R1_val_1.fq.gz Approx 85% complete for zr3644_15_R1_val_1.fq.gz Approx 90% complete for zr3644_15_R1_val_1.fq.gz Approx 95% complete for zr3644_15_R1_val_1.fq.gz Analysis complete for zr3644_15_R1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_15_R2_val_2.fq.gz<<< Started analysis of zr3644_15_R2_val_2.fq.gz Approx 5% complete for zr3644_15_R2_val_2.fq.gz Approx 10% complete for zr3644_15_R2_val_2.fq.gz Approx 15% complete for zr3644_15_R2_val_2.fq.gz Approx 20% complete for zr3644_15_R2_val_2.fq.gz Approx 25% complete for zr3644_15_R2_val_2.fq.gz Approx 30% complete for zr3644_15_R2_val_2.fq.gz Approx 35% complete for zr3644_15_R2_val_2.fq.gz Approx 40% complete for zr3644_15_R2_val_2.fq.gz Approx 45% complete for zr3644_15_R2_val_2.fq.gz Approx 50% complete for zr3644_15_R2_val_2.fq.gz Approx 55% complete for zr3644_15_R2_val_2.fq.gz Approx 60% complete for zr3644_15_R2_val_2.fq.gz Approx 65% complete for zr3644_15_R2_val_2.fq.gz Approx 70% complete for zr3644_15_R2_val_2.fq.gz Approx 75% complete for zr3644_15_R2_val_2.fq.gz Approx 80% complete for zr3644_15_R2_val_2.fq.gz Approx 85% complete for zr3644_15_R2_val_2.fq.gz Approx 90% complete for zr3644_15_R2_val_2.fq.gz Approx 95% complete for zr3644_15_R2_val_2.fq.gz Analysis complete for zr3644_15_R2_val_2.fq.gz Deleting both intermediate output files zr3644_15_R1_trimmed.fq.gz and zr3644_15_R2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_16_R1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_16_R1.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3644_16_R1_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_16_R1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed slurmstepd: error: acct_gather_profile/influxdb _send_data: curl_easy_perform failed to send data (discarded). Reason: Couldn't connect to server This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_16_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 2310.82 s (45 µs/read; 1.35 M reads/minute). === Summary === Total reads processed: 51,910,846 Reads with adapters: 21,719,554 (41.8%) Reads written (passing filters): 51,910,846 (100.0%) Total basepairs processed: 6,471,217,372 bp Quality-trimmed: 2,317,730 bp (0.0%) Total written (filtered): 6,442,864,567 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 21719554 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 44.8% C: 10.3% G: 6.6% T: 38.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 19088005 12977711.5 0 19088005 2 1742115 3244427.9 0 1742115 3 463014 811107.0 0 463014 4 301783 202776.7 0 301783 5 65986 50694.2 0 65986 6 16831 12673.5 0 16831 7 12600 3168.4 0 12600 8 9587 792.1 0 9587 9 2503 198.0 0 2004 499 10 16022 49.5 1 14806 1216 11 172 12.4 1 26 146 12 50 3.1 1 11 39 13 4 0.8 1 0 4 14 3 0.8 1 2 1 15 1 0.8 1 0 1 16 5 0.8 1 2 3 17 3 0.8 1 2 1 18 12 0.8 1 6 6 19 6 0.8 1 3 3 20 2 0.8 1 0 2 21 3 0.8 1 0 3 22 1 0.8 1 0 1 23 3 0.8 1 3 24 2 0.8 1 2 25 1 0.8 1 0 1 26 1 0.8 1 1 27 4 0.8 1 3 1 28 4 0.8 1 3 1 29 5 0.8 1 5 31 2 0.8 1 1 1 33 1 0.8 1 1 34 1 0.8 1 0 1 35 7 0.8 1 3 4 36 2 0.8 1 1 1 37 2 0.8 1 0 2 38 3 0.8 1 2 1 39 5 0.8 1 2 3 40 3 0.8 1 2 1 42 4 0.8 1 1 3 43 2 0.8 1 1 1 44 4 0.8 1 4 45 3 0.8 1 2 1 46 5 0.8 1 3 2 48 7 0.8 1 4 3 49 3 0.8 1 1 2 50 1 0.8 1 1 51 5 0.8 1 3 2 52 3 0.8 1 1 2 53 1 0.8 1 1 54 5 0.8 1 2 3 55 2 0.8 1 1 1 56 1 0.8 1 1 57 2 0.8 1 0 2 58 4 0.8 1 4 59 9 0.8 1 9 60 5 0.8 1 3 2 61 7 0.8 1 3 4 62 6 0.8 1 3 3 63 2 0.8 1 1 1 64 1 0.8 1 0 1 65 6 0.8 1 6 66 6 0.8 1 3 3 67 3 0.8 1 3 68 7 0.8 1 7 69 10 0.8 1 8 2 70 5 0.8 1 4 1 71 6 0.8 1 5 1 72 10 0.8 1 7 3 73 7 0.8 1 6 1 74 5 0.8 1 3 2 75 4 0.8 1 4 76 4 0.8 1 4 77 2 0.8 1 1 1 78 3 0.8 1 2 1 79 5 0.8 1 4 1 80 2 0.8 1 2 81 2 0.8 1 2 82 9 0.8 1 7 2 83 5 0.8 1 5 84 9 0.8 1 7 2 85 3 0.8 1 2 1 86 8 0.8 1 7 1 87 1 0.8 1 1 88 6 0.8 1 5 1 89 4 0.8 1 3 1 90 7 0.8 1 6 1 91 9 0.8 1 8 1 92 8 0.8 1 4 4 93 4 0.8 1 3 1 94 10 0.8 1 9 1 95 7 0.8 1 6 1 96 8 0.8 1 6 2 97 10 0.8 1 8 2 98 16 0.8 1 10 6 99 4 0.8 1 2 2 100 5 0.8 1 4 1 101 9 0.8 1 7 2 102 8 0.8 1 5 3 103 8 0.8 1 8 104 5 0.8 1 4 1 105 4 0.8 1 4 106 10 0.8 1 6 4 107 4 0.8 1 3 1 108 18 0.8 1 12 6 109 15 0.8 1 15 110 14 0.8 1 14 111 15 0.8 1 14 1 112 12 0.8 1 11 1 113 12 0.8 1 12 114 10 0.8 1 8 2 115 6 0.8 1 5 1 116 16 0.8 1 11 5 117 19 0.8 1 17 2 118 9 0.8 1 7 2 119 5 0.8 1 3 2 120 7 0.8 1 6 1 121 15 0.8 1 13 2 122 11 0.8 1 10 1 123 12 0.8 1 10 2 124 12 0.8 1 10 2 125 12 0.8 1 11 1 126 30 0.8 1 27 3 127 14 0.8 1 14 128 14 0.8 1 14 129 17 0.8 1 17 130 15 0.8 1 13 2 131 26 0.8 1 21 5 132 28 0.8 1 23 5 133 25 0.8 1 19 6 134 25 0.8 1 19 6 135 36 0.8 1 14 22 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_16_R1.fq.gz ============================================= 51910846 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_16_R2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_16_R2.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3644_16_R2_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_16_R2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_16_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1684.20 s (32 µs/read; 1.85 M reads/minute). === Summary === Total reads processed: 51,910,846 Reads with adapters: 21,601,645 (41.6%) Reads written (passing filters): 51,910,846 (100.0%) Total basepairs processed: 6,469,595,542 bp Quality-trimmed: 2,140,341 bp (0.0%) Total written (filtered): 6,441,680,830 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 21601645 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.3% C: 10.1% G: 6.4% T: 38.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 19110675 12977711.5 0 19110675 2 1612493 3244427.9 0 1612493 3 445905 811107.0 0 445905 4 308602 202776.7 0 308602 5 66386 50694.2 0 66386 6 16416 12673.5 0 16416 7 12511 3168.4 0 12511 8 9358 792.1 0 9358 9 2445 198.0 0 2039 406 10 15613 49.5 1 14455 1158 11 193 12.4 1 35 158 12 47 3.1 1 7 40 13 2 0.8 1 0 2 14 10 0.8 1 3 7 15 3 0.8 1 1 2 16 7 0.8 1 1 6 17 2 0.8 1 1 1 18 6 0.8 1 2 4 19 17 0.8 1 8 9 20 1 0.8 1 1 21 2 0.8 1 0 2 22 6 0.8 1 4 2 23 8 0.8 1 6 2 24 6 0.8 1 3 3 25 2 0.8 1 0 2 26 2 0.8 1 2 27 3 0.8 1 1 2 28 7 0.8 1 4 3 29 1 0.8 1 0 1 30 1 0.8 1 0 1 31 1 0.8 1 1 32 7 0.8 1 3 4 33 1 0.8 1 1 34 5 0.8 1 5 35 5 0.8 1 3 2 36 6 0.8 1 6 37 5 0.8 1 4 1 38 3 0.8 1 1 2 39 9 0.8 1 5 4 40 3 0.8 1 3 41 1 0.8 1 1 42 4 0.8 1 2 2 43 2 0.8 1 1 1 44 5 0.8 1 2 3 45 2 0.8 1 1 1 46 6 0.8 1 4 2 47 7 0.8 1 5 2 48 2 0.8 1 0 2 49 3 0.8 1 1 2 50 3 0.8 1 1 2 51 6 0.8 1 5 1 52 3 0.8 1 3 53 6 0.8 1 5 1 54 9 0.8 1 5 4 55 8 0.8 1 6 2 56 3 0.8 1 2 1 57 8 0.8 1 8 58 5 0.8 1 4 1 59 5 0.8 1 5 60 4 0.8 1 2 2 61 3 0.8 1 2 1 62 8 0.8 1 5 3 63 10 0.8 1 8 2 64 5 0.8 1 3 2 65 10 0.8 1 9 1 66 2 0.8 1 1 1 67 4 0.8 1 3 1 68 5 0.8 1 3 2 69 5 0.8 1 4 1 70 1 0.8 1 1 71 10 0.8 1 9 1 72 2 0.8 1 1 1 73 4 0.8 1 3 1 74 8 0.8 1 5 3 75 10 0.8 1 9 1 76 3 0.8 1 2 1 77 6 0.8 1 6 78 7 0.8 1 7 79 11 0.8 1 8 3 80 7 0.8 1 6 1 81 6 0.8 1 4 2 82 9 0.8 1 5 4 83 11 0.8 1 9 2 84 8 0.8 1 7 1 85 3 0.8 1 3 86 2 0.8 1 1 1 87 5 0.8 1 5 88 5 0.8 1 3 2 89 4 0.8 1 3 1 90 8 0.8 1 8 91 11 0.8 1 9 2 92 1 0.8 1 1 93 7 0.8 1 3 4 94 8 0.8 1 7 1 95 8 0.8 1 5 3 96 5 0.8 1 4 1 97 5 0.8 1 4 1 98 4 0.8 1 3 1 99 13 0.8 1 10 3 100 15 0.8 1 11 4 101 3 0.8 1 3 102 10 0.8 1 10 103 8 0.8 1 5 3 104 14 0.8 1 10 4 105 3 0.8 1 3 106 6 0.8 1 6 107 14 0.8 1 13 1 108 6 0.8 1 6 109 7 0.8 1 6 1 110 12 0.8 1 9 3 111 13 0.8 1 10 3 112 8 0.8 1 7 1 113 13 0.8 1 11 2 114 10 0.8 1 8 2 115 10 0.8 1 9 1 116 13 0.8 1 11 2 117 8 0.8 1 6 2 118 14 0.8 1 12 2 119 17 0.8 1 16 1 120 22 0.8 1 19 3 121 6 0.8 1 5 1 122 13 0.8 1 12 1 123 14 0.8 1 13 1 124 11 0.8 1 8 3 125 10 0.8 1 9 1 126 15 0.8 1 14 1 127 18 0.8 1 16 2 128 22 0.8 1 20 2 129 23 0.8 1 17 6 130 24 0.8 1 21 3 131 28 0.8 1 25 3 132 29 0.8 1 25 4 133 29 0.8 1 20 9 134 31 0.8 1 21 10 135 35 0.8 1 12 23 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_16_R2.fq.gz ============================================= 51910846 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_16_R1_trimmed.fq.gz and zr3644_16_R2_trimmed.fq.gz file_1: zr3644_16_R1_trimmed.fq.gz, file_2: zr3644_16_R2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_16_R1_trimmed.fq.gz and zr3644_16_R2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_16_R1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_16_R2_val_2.fq.gz Total number of sequences analysed: 51910846 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 294893 (0.57%) >>> Now running FastQC on the validated data zr3644_16_R1_val_1.fq.gz<<< Started analysis of zr3644_16_R1_val_1.fq.gz Approx 5% complete for zr3644_16_R1_val_1.fq.gz Approx 10% complete for zr3644_16_R1_val_1.fq.gz Approx 15% complete for zr3644_16_R1_val_1.fq.gz Approx 20% complete for zr3644_16_R1_val_1.fq.gz Approx 25% complete for zr3644_16_R1_val_1.fq.gz Approx 30% complete for zr3644_16_R1_val_1.fq.gz Approx 35% complete for zr3644_16_R1_val_1.fq.gz Approx 40% complete for zr3644_16_R1_val_1.fq.gz Approx 45% complete for zr3644_16_R1_val_1.fq.gz Approx 50% complete for zr3644_16_R1_val_1.fq.gz Approx 55% complete for zr3644_16_R1_val_1.fq.gz Approx 60% complete for zr3644_16_R1_val_1.fq.gz Approx 65% complete for zr3644_16_R1_val_1.fq.gz Approx 70% complete for zr3644_16_R1_val_1.fq.gz Approx 75% complete for zr3644_16_R1_val_1.fq.gz Approx 80% complete for zr3644_16_R1_val_1.fq.gz Approx 85% complete for zr3644_16_R1_val_1.fq.gz Approx 90% complete for zr3644_16_R1_val_1.fq.gz Approx 95% complete for zr3644_16_R1_val_1.fq.gz Analysis complete for zr3644_16_R1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_16_R2_val_2.fq.gz<<< Started analysis of zr3644_16_R2_val_2.fq.gz Approx 5% complete for zr3644_16_R2_val_2.fq.gz Approx 10% complete for zr3644_16_R2_val_2.fq.gz Approx 15% complete for zr3644_16_R2_val_2.fq.gz Approx 20% complete for zr3644_16_R2_val_2.fq.gz Approx 25% complete for zr3644_16_R2_val_2.fq.gz Approx 30% complete for zr3644_16_R2_val_2.fq.gz Approx 35% complete for zr3644_16_R2_val_2.fq.gz Approx 40% complete for zr3644_16_R2_val_2.fq.gz Approx 45% complete for zr3644_16_R2_val_2.fq.gz Approx 50% complete for zr3644_16_R2_val_2.fq.gz Approx 55% complete for zr3644_16_R2_val_2.fq.gz Approx 60% complete for zr3644_16_R2_val_2.fq.gz Approx 65% complete for zr3644_16_R2_val_2.fq.gz Approx 70% complete for zr3644_16_R2_val_2.fq.gz Approx 75% complete for zr3644_16_R2_val_2.fq.gz Approx 80% complete for zr3644_16_R2_val_2.fq.gz Approx 85% complete for zr3644_16_R2_val_2.fq.gz Approx 90% complete for zr3644_16_R2_val_2.fq.gz Approx 95% complete for zr3644_16_R2_val_2.fq.gz Analysis complete for zr3644_16_R2_val_2.fq.gz Deleting both intermediate output files zr3644_16_R1_trimmed.fq.gz and zr3644_16_R2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_17_R1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_17_R1.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3644_17_R1_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_17_R1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_17_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1852.70 s (32 µs/read; 1.90 M reads/minute). === Summary === Total reads processed: 58,612,409 Reads with adapters: 25,043,792 (42.7%) Reads written (passing filters): 58,612,409 (100.0%) Total basepairs processed: 7,368,913,020 bp Quality-trimmed: 1,953,416 bp (0.0%) Total written (filtered): 7,337,218,337 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 25043792 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.1% C: 10.4% G: 6.5% T: 37.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 22152651 14653102.2 0 22152651 2 1919505 3663275.6 0 1919505 3 518513 915818.9 0 518513 4 329859 228954.7 0 329859 5 66332 57238.7 0 66332 6 16516 14309.7 0 16516 7 12191 3577.4 0 12191 8 9163 894.4 0 9163 9 2338 223.6 0 1847 491 10 14730 55.9 1 13538 1192 11 197 14.0 1 33 164 12 109 3.5 1 50 59 13 7 0.9 1 3 4 14 36 0.9 1 22 14 15 4 0.9 1 1 3 16 30 0.9 1 20 10 17 2 0.9 1 1 1 18 52 0.9 1 32 20 19 66 0.9 1 43 23 20 5 0.9 1 2 3 21 6 0.9 1 3 3 22 5 0.9 1 2 3 23 36 0.9 1 25 11 24 51 0.9 1 35 16 25 2 0.9 1 2 26 26 0.9 1 19 7 27 21 0.9 1 16 5 28 4 0.9 1 2 2 29 22 0.9 1 11 11 30 32 0.9 1 27 5 31 31 0.9 1 24 7 32 7 0.9 1 5 2 33 29 0.9 1 22 7 34 9 0.9 1 7 2 35 12 0.9 1 7 5 36 18 0.9 1 14 4 37 19 0.9 1 11 8 38 9 0.9 1 6 3 39 15 0.9 1 13 2 40 20 0.9 1 13 7 41 15 0.9 1 13 2 42 24 0.9 1 20 4 43 28 0.9 1 20 8 44 31 0.9 1 27 4 45 12 0.9 1 9 3 46 14 0.9 1 9 5 47 4 0.9 1 2 2 48 34 0.9 1 30 4 49 11 0.9 1 10 1 50 6 0.9 1 4 2 51 13 0.9 1 10 3 52 41 0.9 1 31 10 53 4 0.9 1 3 1 54 9 0.9 1 7 2 55 29 0.9 1 19 10 56 18 0.9 1 11 7 57 5 0.9 1 4 1 58 8 0.9 1 6 2 59 21 0.9 1 18 3 60 2 0.9 1 1 1 61 2 0.9 1 2 62 19 0.9 1 15 4 63 7 0.9 1 7 64 2 0.9 1 2 65 9 0.9 1 9 66 20 0.9 1 16 4 67 3 0.9 1 1 2 68 7 0.9 1 7 69 6 0.9 1 5 1 70 4 0.9 1 1 3 71 5 0.9 1 5 72 9 0.9 1 6 3 73 9 0.9 1 8 1 74 9 0.9 1 8 1 75 6 0.9 1 3 3 76 8 0.9 1 5 3 77 8 0.9 1 7 1 78 8 0.9 1 7 1 79 6 0.9 1 4 2 80 10 0.9 1 8 2 81 7 0.9 1 5 2 82 8 0.9 1 6 2 83 11 0.9 1 10 1 84 8 0.9 1 6 2 85 7 0.9 1 5 2 86 10 0.9 1 5 5 87 5 0.9 1 5 88 7 0.9 1 5 2 89 5 0.9 1 5 90 5 0.9 1 4 1 91 11 0.9 1 9 2 92 9 0.9 1 6 3 93 9 0.9 1 8 1 94 8 0.9 1 7 1 95 7 0.9 1 6 1 96 12 0.9 1 8 4 97 9 0.9 1 6 3 98 9 0.9 1 7 2 99 8 0.9 1 6 2 100 6 0.9 1 2 4 101 5 0.9 1 4 1 102 6 0.9 1 4 2 103 1 0.9 1 1 104 14 0.9 1 11 3 105 7 0.9 1 6 1 106 10 0.9 1 7 3 107 7 0.9 1 6 1 108 10 0.9 1 9 1 109 5 0.9 1 4 1 110 8 0.9 1 5 3 111 11 0.9 1 7 4 112 3 0.9 1 2 1 113 5 0.9 1 4 1 114 16 0.9 1 16 115 12 0.9 1 9 3 116 7 0.9 1 6 1 117 9 0.9 1 9 118 20 0.9 1 14 6 119 19 0.9 1 12 7 120 14 0.9 1 14 121 22 0.9 1 19 3 122 19 0.9 1 13 6 123 11 0.9 1 10 1 124 9 0.9 1 8 1 125 6 0.9 1 5 1 126 13 0.9 1 13 127 9 0.9 1 8 1 128 20 0.9 1 18 2 129 19 0.9 1 18 1 130 28 0.9 1 26 2 131 16 0.9 1 15 1 132 21 0.9 1 21 133 24 0.9 1 18 6 134 24 0.9 1 17 7 135 35 0.9 1 12 23 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_17_R1.fq.gz ============================================= 58612409 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_17_R2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_17_R2.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3644_17_R2_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_17_R2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_17_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1882.20 s (32 µs/read; 1.87 M reads/minute). === Summary === Total reads processed: 58,612,409 Reads with adapters: 24,942,134 (42.6%) Reads written (passing filters): 58,612,409 (100.0%) Total basepairs processed: 7,367,240,322 bp Quality-trimmed: 2,008,699 bp (0.0%) Total written (filtered): 7,335,778,634 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 24942134 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.4% C: 10.2% G: 6.4% T: 38.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 22192488 14653102.2 0 22192488 2 1784824 3663275.6 0 1784824 3 509781 915818.9 0 509781 4 336912 228954.7 0 336912 5 64715 57238.7 0 64715 6 15565 14309.7 0 15565 7 11496 3577.4 0 11496 8 8910 894.4 0 8910 9 2289 223.6 0 1884 405 10 14019 55.9 1 12878 1141 11 169 14.0 1 18 151 12 47 3.5 1 13 34 13 5 0.9 1 1 4 14 8 0.9 1 5 3 15 4 0.9 1 1 3 16 3 0.9 1 1 2 17 13 0.9 1 9 4 18 6 0.9 1 4 2 19 8 0.9 1 4 4 20 4 0.9 1 0 4 21 7 0.9 1 5 2 22 6 0.9 1 3 3 23 4 0.9 1 3 1 24 14 0.9 1 6 8 25 5 0.9 1 3 2 26 4 0.9 1 2 2 27 3 0.9 1 1 2 28 4 0.9 1 2 2 29 2 0.9 1 1 1 30 6 0.9 1 4 2 31 1 0.9 1 1 32 10 0.9 1 5 5 33 13 0.9 1 6 7 34 2 0.9 1 1 1 35 7 0.9 1 3 4 36 2 0.9 1 2 38 7 0.9 1 6 1 39 4 0.9 1 1 3 40 2 0.9 1 0 2 42 4 0.9 1 1 3 43 3 0.9 1 2 1 44 3 0.9 1 1 2 45 6 0.9 1 4 2 46 6 0.9 1 2 4 47 5 0.9 1 4 1 48 6 0.9 1 4 2 49 6 0.9 1 3 3 50 2 0.9 1 2 51 2 0.9 1 1 1 52 4 0.9 1 3 1 53 10 0.9 1 7 3 54 1 0.9 1 1 55 3 0.9 1 3 56 5 0.9 1 5 57 7 0.9 1 3 4 58 3 0.9 1 1 2 59 4 0.9 1 3 1 60 12 0.9 1 5 7 61 4 0.9 1 4 62 3 0.9 1 3 63 10 0.9 1 7 3 64 5 0.9 1 4 1 65 1 0.9 1 0 1 66 7 0.9 1 6 1 67 3 0.9 1 3 68 3 0.9 1 3 69 4 0.9 1 4 70 6 0.9 1 6 71 4 0.9 1 3 1 72 3 0.9 1 2 1 73 5 0.9 1 2 3 74 4 0.9 1 3 1 75 3 0.9 1 2 1 76 6 0.9 1 3 3 77 7 0.9 1 4 3 78 5 0.9 1 4 1 79 6 0.9 1 5 1 80 5 0.9 1 5 81 4 0.9 1 3 1 82 2 0.9 1 0 2 83 6 0.9 1 2 4 84 8 0.9 1 8 85 7 0.9 1 5 2 86 3 0.9 1 3 87 7 0.9 1 5 2 88 5 0.9 1 3 2 89 9 0.9 1 4 5 90 7 0.9 1 5 2 91 11 0.9 1 8 3 92 9 0.9 1 9 93 6 0.9 1 5 1 94 5 0.9 1 4 1 95 4 0.9 1 2 2 96 9 0.9 1 9 97 12 0.9 1 9 3 98 3 0.9 1 3 99 6 0.9 1 5 1 100 8 0.9 1 7 1 101 9 0.9 1 8 1 102 5 0.9 1 4 1 103 3 0.9 1 3 104 5 0.9 1 5 105 6 0.9 1 4 2 106 6 0.9 1 5 1 107 8 0.9 1 5 3 108 13 0.9 1 11 2 109 13 0.9 1 12 1 110 5 0.9 1 5 111 11 0.9 1 11 112 8 0.9 1 5 3 113 6 0.9 1 6 114 9 0.9 1 6 3 115 15 0.9 1 13 2 116 8 0.9 1 8 117 17 0.9 1 12 5 118 10 0.9 1 8 2 119 10 0.9 1 7 3 120 21 0.9 1 18 3 121 8 0.9 1 8 122 10 0.9 1 9 1 123 12 0.9 1 11 1 124 9 0.9 1 8 1 125 17 0.9 1 15 2 126 10 0.9 1 8 2 127 27 0.9 1 26 1 128 20 0.9 1 19 1 129 17 0.9 1 14 3 130 16 0.9 1 14 2 131 12 0.9 1 10 2 132 38 0.9 1 32 6 133 15 0.9 1 11 4 134 25 0.9 1 17 8 135 24 0.9 1 11 13 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_17_R2.fq.gz ============================================= 58612409 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_17_R1_trimmed.fq.gz and zr3644_17_R2_trimmed.fq.gz file_1: zr3644_17_R1_trimmed.fq.gz, file_2: zr3644_17_R2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_17_R1_trimmed.fq.gz and zr3644_17_R2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_17_R1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_17_R2_val_2.fq.gz Total number of sequences analysed: 58612409 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 304716 (0.52%) >>> Now running FastQC on the validated data zr3644_17_R1_val_1.fq.gz<<< Started analysis of zr3644_17_R1_val_1.fq.gz Approx 5% complete for zr3644_17_R1_val_1.fq.gz Approx 10% complete for zr3644_17_R1_val_1.fq.gz Approx 15% complete for zr3644_17_R1_val_1.fq.gz Approx 20% complete for zr3644_17_R1_val_1.fq.gz Approx 25% complete for zr3644_17_R1_val_1.fq.gz Approx 30% complete for zr3644_17_R1_val_1.fq.gz Approx 35% complete for zr3644_17_R1_val_1.fq.gz Approx 40% complete for zr3644_17_R1_val_1.fq.gz Approx 45% complete for zr3644_17_R1_val_1.fq.gz Approx 50% complete for zr3644_17_R1_val_1.fq.gz Approx 55% complete for zr3644_17_R1_val_1.fq.gz Approx 60% complete for zr3644_17_R1_val_1.fq.gz Approx 65% complete for zr3644_17_R1_val_1.fq.gz Approx 70% complete for zr3644_17_R1_val_1.fq.gz Approx 75% complete for zr3644_17_R1_val_1.fq.gz Approx 80% complete for zr3644_17_R1_val_1.fq.gz Approx 85% complete for zr3644_17_R1_val_1.fq.gz Approx 90% complete for zr3644_17_R1_val_1.fq.gz Approx 95% complete for zr3644_17_R1_val_1.fq.gz Analysis complete for zr3644_17_R1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_17_R2_val_2.fq.gz<<< Started analysis of zr3644_17_R2_val_2.fq.gz Approx 5% complete for zr3644_17_R2_val_2.fq.gz Approx 10% complete for zr3644_17_R2_val_2.fq.gz Approx 15% complete for zr3644_17_R2_val_2.fq.gz Approx 20% complete for zr3644_17_R2_val_2.fq.gz Approx 25% complete for zr3644_17_R2_val_2.fq.gz Approx 30% complete for zr3644_17_R2_val_2.fq.gz Approx 35% complete for zr3644_17_R2_val_2.fq.gz Approx 40% complete for zr3644_17_R2_val_2.fq.gz Approx 45% complete for zr3644_17_R2_val_2.fq.gz Approx 50% complete for zr3644_17_R2_val_2.fq.gz Approx 55% complete for zr3644_17_R2_val_2.fq.gz Approx 60% complete for zr3644_17_R2_val_2.fq.gz Approx 65% complete for zr3644_17_R2_val_2.fq.gz Approx 70% complete for zr3644_17_R2_val_2.fq.gz Approx 75% complete for zr3644_17_R2_val_2.fq.gz Approx 80% complete for zr3644_17_R2_val_2.fq.gz Approx 85% complete for zr3644_17_R2_val_2.fq.gz Approx 90% complete for zr3644_17_R2_val_2.fq.gz Approx 95% complete for zr3644_17_R2_val_2.fq.gz Analysis complete for zr3644_17_R2_val_2.fq.gz Deleting both intermediate output files zr3644_17_R1_trimmed.fq.gz and zr3644_17_R2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_18_R1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_18_R1.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3644_18_R1_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_18_R1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_18_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1650.50 s (32 µs/read; 1.89 M reads/minute). === Summary === Total reads processed: 51,977,624 Reads with adapters: 22,254,918 (42.8%) Reads written (passing filters): 51,977,624 (100.0%) Total basepairs processed: 6,538,749,697 bp Quality-trimmed: 1,953,148 bp (0.0%) Total written (filtered): 6,510,376,573 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 22254918 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.0% C: 10.4% G: 6.5% T: 38.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 19679963 12994406.0 0 19679963 2 1715586 3248601.5 0 1715586 3 462343 812150.4 0 462343 4 293120 203037.6 0 293120 5 55471 50759.4 0 55471 6 14322 12689.8 0 14322 7 10221 3172.5 0 10221 8 7505 793.1 0 7505 9 1871 198.3 0 1431 440 10 12785 49.6 1 11769 1016 11 155 12.4 1 38 117 12 86 3.1 1 37 49 13 7 0.8 1 0 7 14 32 0.8 1 25 7 15 3 0.8 1 3 16 31 0.8 1 25 6 17 1 0.8 1 0 1 18 38 0.8 1 25 13 19 50 0.8 1 34 16 20 9 0.8 1 7 2 21 1 0.8 1 1 22 5 0.8 1 2 3 23 13 0.8 1 5 8 24 51 0.8 1 39 12 25 4 0.8 1 4 26 21 0.8 1 15 6 27 14 0.8 1 10 4 28 5 0.8 1 5 29 13 0.8 1 7 6 30 26 0.8 1 22 4 31 24 0.8 1 14 10 32 4 0.8 1 2 2 33 25 0.8 1 19 6 34 9 0.8 1 6 3 35 11 0.8 1 6 5 36 20 0.8 1 15 5 37 17 0.8 1 12 5 38 13 0.8 1 11 2 39 6 0.8 1 3 3 40 11 0.8 1 3 8 41 19 0.8 1 15 4 42 18 0.8 1 11 7 43 18 0.8 1 15 3 44 18 0.8 1 14 4 45 7 0.8 1 6 1 46 9 0.8 1 9 47 3 0.8 1 2 1 48 22 0.8 1 13 9 49 14 0.8 1 12 2 50 8 0.8 1 7 1 51 12 0.8 1 6 6 52 17 0.8 1 15 2 53 9 0.8 1 8 1 54 3 0.8 1 1 2 55 30 0.8 1 22 8 56 20 0.8 1 17 3 57 3 0.8 1 3 58 6 0.8 1 4 2 59 11 0.8 1 10 1 60 6 0.8 1 5 1 61 6 0.8 1 4 2 62 15 0.8 1 10 5 63 3 0.8 1 2 1 64 2 0.8 1 1 1 65 3 0.8 1 1 2 66 15 0.8 1 11 4 67 12 0.8 1 11 1 68 4 0.8 1 2 2 69 3 0.8 1 1 2 70 4 0.8 1 4 71 5 0.8 1 4 1 72 7 0.8 1 6 1 73 5 0.8 1 4 1 74 10 0.8 1 7 3 75 5 0.8 1 1 4 76 6 0.8 1 5 1 77 5 0.8 1 5 78 7 0.8 1 4 3 79 5 0.8 1 5 80 9 0.8 1 8 1 81 8 0.8 1 5 3 82 6 0.8 1 4 2 83 9 0.8 1 8 1 84 5 0.8 1 3 2 85 7 0.8 1 5 2 86 5 0.8 1 3 2 87 6 0.8 1 5 1 88 8 0.8 1 7 1 89 10 0.8 1 8 2 90 9 0.8 1 9 91 6 0.8 1 6 92 8 0.8 1 6 2 93 2 0.8 1 2 94 8 0.8 1 7 1 95 8 0.8 1 7 1 96 12 0.8 1 10 2 97 9 0.8 1 8 1 98 4 0.8 1 4 99 8 0.8 1 6 2 100 9 0.8 1 7 2 101 3 0.8 1 2 1 102 14 0.8 1 12 2 103 10 0.8 1 7 3 104 11 0.8 1 9 2 105 3 0.8 1 3 106 11 0.8 1 7 4 107 10 0.8 1 6 4 108 7 0.8 1 7 109 7 0.8 1 7 110 8 0.8 1 5 3 111 6 0.8 1 6 112 9 0.8 1 8 1 113 13 0.8 1 9 4 114 17 0.8 1 15 2 115 15 0.8 1 13 2 116 12 0.8 1 11 1 117 9 0.8 1 5 4 118 17 0.8 1 15 2 119 23 0.8 1 18 5 120 11 0.8 1 9 2 121 10 0.8 1 10 122 22 0.8 1 17 5 123 10 0.8 1 10 124 10 0.8 1 9 1 125 14 0.8 1 14 126 19 0.8 1 16 3 127 18 0.8 1 18 128 27 0.8 1 22 5 129 16 0.8 1 15 1 130 19 0.8 1 16 3 131 19 0.8 1 14 5 132 17 0.8 1 17 133 22 0.8 1 20 2 134 26 0.8 1 19 7 135 30 0.8 1 14 16 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_18_R1.fq.gz ============================================= 51977624 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_18_R2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_18_R2.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3644_18_R2_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_18_R2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_18_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1671.85 s (32 µs/read; 1.87 M reads/minute). === Summary === Total reads processed: 51,977,624 Reads with adapters: 22,212,667 (42.7%) Reads written (passing filters): 51,977,624 (100.0%) Total basepairs processed: 6,536,857,225 bp Quality-trimmed: 1,957,739 bp (0.0%) Total written (filtered): 6,508,713,820 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 22212667 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.4% C: 10.2% G: 6.2% T: 38.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 19795170 12994406.0 0 19795170 2 1568340 3248601.5 0 1568340 3 450861 812150.4 0 450861 4 297135 203037.6 0 297135 5 55089 50759.4 0 55089 6 13240 12689.8 0 13240 7 9989 3172.5 0 9989 8 7650 793.1 0 7650 9 2021 198.3 0 1637 384 10 12013 49.6 1 11024 989 11 161 12.4 1 25 136 12 52 3.1 1 9 43 13 3 0.8 1 1 2 14 5 0.8 1 2 3 15 6 0.8 1 3 3 16 1 0.8 1 1 17 7 0.8 1 5 2 18 1 0.8 1 0 1 19 9 0.8 1 3 6 20 8 0.8 1 4 4 21 4 0.8 1 3 1 22 12 0.8 1 7 5 23 3 0.8 1 1 2 24 6 0.8 1 5 1 25 7 0.8 1 4 3 26 6 0.8 1 4 2 27 3 0.8 1 2 1 28 10 0.8 1 8 2 29 5 0.8 1 2 3 30 9 0.8 1 8 1 31 5 0.8 1 5 32 5 0.8 1 4 1 33 5 0.8 1 2 3 34 3 0.8 1 2 1 35 5 0.8 1 2 3 36 1 0.8 1 1 37 1 0.8 1 0 1 38 3 0.8 1 3 39 1 0.8 1 0 1 40 7 0.8 1 7 41 1 0.8 1 1 42 6 0.8 1 3 3 43 2 0.8 1 1 1 44 5 0.8 1 2 3 45 7 0.8 1 5 2 46 8 0.8 1 6 2 47 6 0.8 1 2 4 48 7 0.8 1 4 3 49 6 0.8 1 3 3 50 4 0.8 1 2 2 51 2 0.8 1 2 52 2 0.8 1 1 1 53 8 0.8 1 6 2 54 9 0.8 1 9 55 3 0.8 1 1 2 56 3 0.8 1 2 1 57 6 0.8 1 5 1 58 8 0.8 1 5 3 59 2 0.8 1 2 60 4 0.8 1 3 1 61 1 0.8 1 1 62 4 0.8 1 2 2 63 10 0.8 1 7 3 64 11 0.8 1 9 2 65 3 0.8 1 1 2 66 1 0.8 1 1 67 4 0.8 1 4 68 6 0.8 1 6 69 7 0.8 1 3 4 70 8 0.8 1 8 71 6 0.8 1 6 72 1 0.8 1 1 73 4 0.8 1 3 1 74 4 0.8 1 4 75 6 0.8 1 6 76 5 0.8 1 5 77 5 0.8 1 5 78 3 0.8 1 2 1 79 2 0.8 1 1 1 80 5 0.8 1 4 1 81 8 0.8 1 7 1 82 2 0.8 1 2 83 8 0.8 1 4 4 84 5 0.8 1 3 2 85 5 0.8 1 4 1 86 7 0.8 1 5 2 87 2 0.8 1 2 88 6 0.8 1 6 89 6 0.8 1 5 1 90 5 0.8 1 3 2 91 4 0.8 1 4 92 10 0.8 1 7 3 93 5 0.8 1 5 94 5 0.8 1 1 4 95 6 0.8 1 6 96 8 0.8 1 6 2 97 9 0.8 1 7 2 98 8 0.8 1 6 2 99 8 0.8 1 8 100 4 0.8 1 3 1 101 8 0.8 1 8 102 7 0.8 1 6 1 103 8 0.8 1 6 2 104 8 0.8 1 5 3 105 7 0.8 1 6 1 106 15 0.8 1 15 107 9 0.8 1 8 1 108 7 0.8 1 6 1 109 9 0.8 1 7 2 110 11 0.8 1 9 2 111 14 0.8 1 11 3 112 9 0.8 1 6 3 113 9 0.8 1 6 3 114 14 0.8 1 13 1 115 8 0.8 1 5 3 116 6 0.8 1 6 117 11 0.8 1 9 2 118 14 0.8 1 11 3 119 16 0.8 1 15 1 120 9 0.8 1 6 3 121 19 0.8 1 14 5 122 15 0.8 1 14 1 123 14 0.8 1 11 3 124 12 0.8 1 8 4 125 12 0.8 1 10 2 126 11 0.8 1 10 1 127 20 0.8 1 17 3 128 15 0.8 1 13 2 129 20 0.8 1 17 3 130 19 0.8 1 18 1 131 18 0.8 1 15 3 132 19 0.8 1 14 5 133 21 0.8 1 14 7 134 27 0.8 1 18 9 135 48 0.8 1 19 29 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_18_R2.fq.gz ============================================= 51977624 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_18_R1_trimmed.fq.gz and zr3644_18_R2_trimmed.fq.gz file_1: zr3644_18_R1_trimmed.fq.gz, file_2: zr3644_18_R2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_18_R1_trimmed.fq.gz and zr3644_18_R2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_18_R1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_18_R2_val_2.fq.gz Total number of sequences analysed: 51977624 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 264448 (0.51%) >>> Now running FastQC on the validated data zr3644_18_R1_val_1.fq.gz<<< Started analysis of zr3644_18_R1_val_1.fq.gz Approx 5% complete for zr3644_18_R1_val_1.fq.gz Approx 10% complete for zr3644_18_R1_val_1.fq.gz Approx 15% complete for zr3644_18_R1_val_1.fq.gz Approx 20% complete for zr3644_18_R1_val_1.fq.gz Approx 25% complete for zr3644_18_R1_val_1.fq.gz Approx 30% complete for zr3644_18_R1_val_1.fq.gz Approx 35% complete for zr3644_18_R1_val_1.fq.gz Approx 40% complete for zr3644_18_R1_val_1.fq.gz Approx 45% complete for zr3644_18_R1_val_1.fq.gz Approx 50% complete for zr3644_18_R1_val_1.fq.gz Approx 55% complete for zr3644_18_R1_val_1.fq.gz Approx 60% complete for zr3644_18_R1_val_1.fq.gz Approx 65% complete for zr3644_18_R1_val_1.fq.gz Approx 70% complete for zr3644_18_R1_val_1.fq.gz Approx 75% complete for zr3644_18_R1_val_1.fq.gz Approx 80% complete for zr3644_18_R1_val_1.fq.gz Approx 85% complete for zr3644_18_R1_val_1.fq.gz Approx 90% complete for zr3644_18_R1_val_1.fq.gz Approx 95% complete for zr3644_18_R1_val_1.fq.gz Analysis complete for zr3644_18_R1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_18_R2_val_2.fq.gz<<< Started analysis of zr3644_18_R2_val_2.fq.gz Approx 5% complete for zr3644_18_R2_val_2.fq.gz Approx 10% complete for zr3644_18_R2_val_2.fq.gz Approx 15% complete for zr3644_18_R2_val_2.fq.gz Approx 20% complete for zr3644_18_R2_val_2.fq.gz Approx 25% complete for zr3644_18_R2_val_2.fq.gz Approx 30% complete for zr3644_18_R2_val_2.fq.gz Approx 35% complete for zr3644_18_R2_val_2.fq.gz Approx 40% complete for zr3644_18_R2_val_2.fq.gz Approx 45% complete for zr3644_18_R2_val_2.fq.gz Approx 50% complete for zr3644_18_R2_val_2.fq.gz Approx 55% complete for zr3644_18_R2_val_2.fq.gz Approx 60% complete for zr3644_18_R2_val_2.fq.gz Approx 65% complete for zr3644_18_R2_val_2.fq.gz Approx 70% complete for zr3644_18_R2_val_2.fq.gz Approx 75% complete for zr3644_18_R2_val_2.fq.gz Approx 80% complete for zr3644_18_R2_val_2.fq.gz Approx 85% complete for zr3644_18_R2_val_2.fq.gz Approx 90% complete for zr3644_18_R2_val_2.fq.gz Approx 95% complete for zr3644_18_R2_val_2.fq.gz Analysis complete for zr3644_18_R2_val_2.fq.gz Deleting both intermediate output files zr3644_18_R1_trimmed.fq.gz and zr3644_18_R2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_19_R1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_19_R1.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3644_19_R1_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_19_R1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_19_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1896.57 s (38 µs/read; 1.57 M reads/minute). === Summary === Total reads processed: 49,611,452 Reads with adapters: 21,362,959 (43.1%) Reads written (passing filters): 49,611,452 (100.0%) Total basepairs processed: 6,252,863,959 bp Quality-trimmed: 1,776,907 bp (0.0%) Total written (filtered): 6,225,809,904 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 21362959 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.2% C: 10.4% G: 6.4% T: 38.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 18933491 12402863.0 0 18933491 2 1613051 3100715.8 0 1613051 3 445071 775178.9 0 445071 4 275236 193794.7 0 275236 5 51936 48448.7 0 51936 6 13128 12112.2 0 13128 7 9175 3028.0 0 9175 8 6901 757.0 0 6901 9 1821 189.3 0 1428 393 10 11758 47.3 1 10773 985 11 162 11.8 1 27 135 12 60 3.0 1 22 38 13 7 0.7 1 2 5 14 23 0.7 1 13 10 15 5 0.7 1 3 2 16 20 0.7 1 17 3 18 40 0.7 1 24 16 19 30 0.7 1 19 11 20 2 0.7 1 1 1 21 1 0.7 1 1 22 1 0.7 1 1 23 24 0.7 1 14 10 24 20 0.7 1 15 5 25 3 0.7 1 2 1 26 8 0.7 1 5 3 27 5 0.7 1 5 28 1 0.7 1 0 1 29 8 0.7 1 4 4 30 15 0.7 1 10 5 31 21 0.7 1 15 6 32 4 0.7 1 3 1 33 15 0.7 1 10 5 34 7 0.7 1 1 6 35 10 0.7 1 6 4 36 10 0.7 1 7 3 37 9 0.7 1 5 4 38 19 0.7 1 9 10 39 16 0.7 1 10 6 40 5 0.7 1 4 1 41 14 0.7 1 9 5 42 9 0.7 1 7 2 43 10 0.7 1 5 5 44 18 0.7 1 13 5 45 3 0.7 1 3 46 11 0.7 1 8 3 47 5 0.7 1 5 48 21 0.7 1 16 5 49 13 0.7 1 6 7 50 13 0.7 1 6 7 51 11 0.7 1 6 5 52 16 0.7 1 14 2 53 5 0.7 1 5 54 5 0.7 1 5 55 20 0.7 1 13 7 56 10 0.7 1 8 2 57 1 0.7 1 1 58 5 0.7 1 4 1 59 9 0.7 1 6 3 60 1 0.7 1 1 61 2 0.7 1 2 62 11 0.7 1 7 4 63 2 0.7 1 2 64 7 0.7 1 5 2 65 3 0.7 1 0 3 66 10 0.7 1 8 2 67 5 0.7 1 4 1 68 8 0.7 1 6 2 69 7 0.7 1 6 1 70 3 0.7 1 3 71 4 0.7 1 1 3 72 4 0.7 1 3 1 73 6 0.7 1 2 4 74 2 0.7 1 2 75 3 0.7 1 2 1 76 7 0.7 1 5 2 77 13 0.7 1 9 4 78 7 0.7 1 6 1 79 6 0.7 1 3 3 80 8 0.7 1 6 2 81 7 0.7 1 7 82 2 0.7 1 1 1 83 6 0.7 1 4 2 84 1 0.7 1 0 1 85 11 0.7 1 11 86 10 0.7 1 5 5 87 4 0.7 1 4 88 9 0.7 1 6 3 89 7 0.7 1 7 90 6 0.7 1 4 2 91 7 0.7 1 5 2 92 2 0.7 1 2 93 5 0.7 1 5 94 1 0.7 1 1 95 4 0.7 1 4 96 7 0.7 1 7 97 3 0.7 1 2 1 98 8 0.7 1 8 99 10 0.7 1 9 1 100 5 0.7 1 4 1 101 4 0.7 1 3 1 102 7 0.7 1 7 103 5 0.7 1 3 2 104 7 0.7 1 6 1 105 8 0.7 1 5 3 106 8 0.7 1 5 3 107 7 0.7 1 5 2 108 4 0.7 1 3 1 109 4 0.7 1 3 1 110 5 0.7 1 3 2 111 10 0.7 1 10 112 5 0.7 1 4 1 113 5 0.7 1 5 114 6 0.7 1 6 115 7 0.7 1 6 1 116 7 0.7 1 5 2 117 13 0.7 1 12 1 118 19 0.7 1 16 3 119 12 0.7 1 11 1 120 8 0.7 1 8 121 13 0.7 1 12 1 122 13 0.7 1 10 3 123 13 0.7 1 13 124 12 0.7 1 12 125 20 0.7 1 13 7 126 11 0.7 1 5 6 127 10 0.7 1 8 2 128 18 0.7 1 18 129 14 0.7 1 10 4 130 15 0.7 1 13 2 131 23 0.7 1 19 4 132 22 0.7 1 17 5 133 17 0.7 1 13 4 134 24 0.7 1 14 10 135 31 0.7 1 11 20 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_19_R1.fq.gz ============================================= 49611452 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_19_R2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_19_R2.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3644_19_R2_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_19_R2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_19_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1655.35 s (33 µs/read; 1.80 M reads/minute). === Summary === Total reads processed: 49,611,452 Reads with adapters: 21,264,708 (42.9%) Reads written (passing filters): 49,611,452 (100.0%) Total basepairs processed: 6,250,440,107 bp Quality-trimmed: 1,909,058 bp (0.0%) Total written (filtered): 6,223,480,605 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 21264708 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.4% C: 10.2% G: 6.3% T: 38.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 18951183 12402863.0 0 18951183 2 1500520 3100715.8 0 1500520 3 436592 775178.9 0 436592 4 282984 193794.7 0 282984 5 51132 48448.7 0 51132 6 12327 12112.2 0 12327 7 8936 3028.0 0 8936 8 6950 757.0 0 6950 9 1871 189.3 0 1439 432 10 11241 47.3 1 10289 952 11 133 11.8 1 19 114 12 32 3.0 1 6 26 13 5 0.7 1 1 4 14 2 0.7 1 2 15 4 0.7 1 2 2 16 5 0.7 1 3 2 17 6 0.7 1 2 4 19 5 0.7 1 3 2 21 1 0.7 1 1 22 6 0.7 1 4 2 23 4 0.7 1 0 4 24 3 0.7 1 1 2 25 4 0.7 1 1 3 26 3 0.7 1 2 1 27 5 0.7 1 3 2 28 7 0.7 1 3 4 29 4 0.7 1 2 2 31 3 0.7 1 2 1 32 6 0.7 1 4 2 33 3 0.7 1 1 2 34 5 0.7 1 4 1 35 6 0.7 1 4 2 36 3 0.7 1 3 37 2 0.7 1 1 1 38 3 0.7 1 1 2 39 2 0.7 1 2 40 1 0.7 1 0 1 41 1 0.7 1 1 42 3 0.7 1 3 43 7 0.7 1 5 2 44 4 0.7 1 3 1 45 6 0.7 1 4 2 46 4 0.7 1 2 2 47 2 0.7 1 0 2 49 2 0.7 1 2 50 2 0.7 1 2 52 1 0.7 1 0 1 53 6 0.7 1 3 3 54 3 0.7 1 2 1 55 1 0.7 1 1 56 4 0.7 1 1 3 57 6 0.7 1 6 58 8 0.7 1 5 3 59 2 0.7 1 2 60 3 0.7 1 0 3 61 3 0.7 1 3 62 4 0.7 1 3 1 63 2 0.7 1 1 1 64 2 0.7 1 1 1 65 5 0.7 1 5 66 4 0.7 1 2 2 67 5 0.7 1 4 1 68 6 0.7 1 6 69 1 0.7 1 0 1 70 3 0.7 1 3 71 4 0.7 1 3 1 72 2 0.7 1 2 73 3 0.7 1 3 74 2 0.7 1 2 75 5 0.7 1 5 76 3 0.7 1 3 77 7 0.7 1 4 3 78 3 0.7 1 3 79 3 0.7 1 3 80 5 0.7 1 3 2 81 5 0.7 1 4 1 82 4 0.7 1 3 1 83 2 0.7 1 2 84 1 0.7 1 1 85 3 0.7 1 2 1 86 4 0.7 1 4 87 4 0.7 1 4 88 7 0.7 1 5 2 89 7 0.7 1 5 2 90 8 0.7 1 6 2 91 4 0.7 1 3 1 92 5 0.7 1 5 93 5 0.7 1 4 1 94 4 0.7 1 3 1 95 3 0.7 1 3 96 7 0.7 1 7 97 9 0.7 1 5 4 98 5 0.7 1 3 2 99 11 0.7 1 8 3 100 11 0.7 1 10 1 101 9 0.7 1 4 5 102 15 0.7 1 12 3 103 1 0.7 1 1 104 4 0.7 1 3 1 105 5 0.7 1 4 1 106 7 0.7 1 6 1 107 3 0.7 1 3 108 10 0.7 1 9 1 109 16 0.7 1 12 4 110 12 0.7 1 11 1 111 9 0.7 1 8 1 112 11 0.7 1 11 113 10 0.7 1 7 3 114 9 0.7 1 6 3 115 7 0.7 1 5 2 116 9 0.7 1 8 1 117 9 0.7 1 7 2 118 11 0.7 1 10 1 119 20 0.7 1 17 3 120 7 0.7 1 6 1 121 12 0.7 1 11 1 122 13 0.7 1 12 1 123 12 0.7 1 9 3 124 13 0.7 1 12 1 125 20 0.7 1 16 4 126 14 0.7 1 12 2 127 11 0.7 1 11 128 16 0.7 1 15 1 129 17 0.7 1 15 2 130 17 0.7 1 14 3 131 21 0.7 1 18 3 132 15 0.7 1 11 4 133 23 0.7 1 18 5 134 33 0.7 1 19 14 135 42 0.7 1 19 23 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_19_R2.fq.gz ============================================= 49611452 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_19_R1_trimmed.fq.gz and zr3644_19_R2_trimmed.fq.gz file_1: zr3644_19_R1_trimmed.fq.gz, file_2: zr3644_19_R2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_19_R1_trimmed.fq.gz and zr3644_19_R2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_19_R1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_19_R2_val_2.fq.gz Total number of sequences analysed: 49611452 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 248048 (0.50%) >>> Now running FastQC on the validated data zr3644_19_R1_val_1.fq.gz<<< Started analysis of zr3644_19_R1_val_1.fq.gz Approx 5% complete for zr3644_19_R1_val_1.fq.gz Approx 10% complete for zr3644_19_R1_val_1.fq.gz Approx 15% complete for zr3644_19_R1_val_1.fq.gz Approx 20% complete for zr3644_19_R1_val_1.fq.gz Approx 25% complete for zr3644_19_R1_val_1.fq.gz Approx 30% complete for zr3644_19_R1_val_1.fq.gz Approx 35% complete for zr3644_19_R1_val_1.fq.gz Approx 40% complete for zr3644_19_R1_val_1.fq.gz Approx 45% complete for zr3644_19_R1_val_1.fq.gz Approx 50% complete for zr3644_19_R1_val_1.fq.gz Approx 55% complete for zr3644_19_R1_val_1.fq.gz Approx 60% complete for zr3644_19_R1_val_1.fq.gz Approx 65% complete for zr3644_19_R1_val_1.fq.gz Approx 70% complete for zr3644_19_R1_val_1.fq.gz Approx 75% complete for zr3644_19_R1_val_1.fq.gz Approx 80% complete for zr3644_19_R1_val_1.fq.gz Approx 85% complete for zr3644_19_R1_val_1.fq.gz Approx 90% complete for zr3644_19_R1_val_1.fq.gz Approx 95% complete for zr3644_19_R1_val_1.fq.gz Analysis complete for zr3644_19_R1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_19_R2_val_2.fq.gz<<< Started analysis of zr3644_19_R2_val_2.fq.gz Approx 5% complete for zr3644_19_R2_val_2.fq.gz Approx 10% complete for zr3644_19_R2_val_2.fq.gz Approx 15% complete for zr3644_19_R2_val_2.fq.gz Approx 20% complete for zr3644_19_R2_val_2.fq.gz Approx 25% complete for zr3644_19_R2_val_2.fq.gz Approx 30% complete for zr3644_19_R2_val_2.fq.gz Approx 35% complete for zr3644_19_R2_val_2.fq.gz Approx 40% complete for zr3644_19_R2_val_2.fq.gz Approx 45% complete for zr3644_19_R2_val_2.fq.gz Approx 50% complete for zr3644_19_R2_val_2.fq.gz Approx 55% complete for zr3644_19_R2_val_2.fq.gz Approx 60% complete for zr3644_19_R2_val_2.fq.gz Approx 65% complete for zr3644_19_R2_val_2.fq.gz Approx 70% complete for zr3644_19_R2_val_2.fq.gz Approx 75% complete for zr3644_19_R2_val_2.fq.gz Approx 80% complete for zr3644_19_R2_val_2.fq.gz Approx 85% complete for zr3644_19_R2_val_2.fq.gz Approx 90% complete for zr3644_19_R2_val_2.fq.gz Approx 95% complete for zr3644_19_R2_val_2.fq.gz Analysis complete for zr3644_19_R2_val_2.fq.gz Deleting both intermediate output files zr3644_19_R1_trimmed.fq.gz and zr3644_19_R2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_20_R1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_20_R1.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3644_20_R1_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_20_R1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_20_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 2108.84 s (39 µs/read; 1.55 M reads/minute). === Summary === Total reads processed: 54,311,933 Reads with adapters: 24,163,085 (44.5%) Reads written (passing filters): 54,311,933 (100.0%) Total basepairs processed: 6,898,362,841 bp Quality-trimmed: 4,325,943 bp (0.1%) Total written (filtered): 6,865,728,474 bp (99.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 24163085 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 44.2% C: 11.4% G: 6.4% T: 37.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 21536201 13577983.2 0 21536201 2 1743756 3394495.8 0 1743756 3 527423 848624.0 0 527423 4 276862 212156.0 0 276862 5 40127 53039.0 0 40127 6 11848 13259.7 0 11848 7 8239 3314.9 0 8239 8 5344 828.7 0 5344 9 1714 207.2 0 1298 416 10 10370 51.8 1 9078 1292 11 145 12.9 1 18 127 12 38 3.2 1 3 35 13 12 0.8 1 1 11 15 1 0.8 1 0 1 16 2 0.8 1 0 2 17 3 0.8 1 1 2 18 8 0.8 1 4 4 19 5 0.8 1 2 3 20 3 0.8 1 2 1 21 3 0.8 1 1 2 22 7 0.8 1 4 3 23 2 0.8 1 1 1 24 2 0.8 1 2 25 1 0.8 1 1 26 3 0.8 1 0 3 27 3 0.8 1 2 1 28 4 0.8 1 0 4 29 2 0.8 1 1 1 30 3 0.8 1 2 1 31 3 0.8 1 1 2 32 5 0.8 1 2 3 33 2 0.8 1 2 34 3 0.8 1 2 1 35 2 0.8 1 2 36 2 0.8 1 2 37 1 0.8 1 0 1 38 2 0.8 1 1 1 39 3 0.8 1 3 40 2 0.8 1 2 41 6 0.8 1 5 1 42 4 0.8 1 2 2 43 5 0.8 1 3 2 44 3 0.8 1 3 45 4 0.8 1 3 1 46 2 0.8 1 1 1 47 4 0.8 1 1 3 48 2 0.8 1 2 49 1 0.8 1 0 1 50 8 0.8 1 8 51 4 0.8 1 4 52 4 0.8 1 4 53 5 0.8 1 4 1 54 4 0.8 1 3 1 55 3 0.8 1 3 56 2 0.8 1 2 57 4 0.8 1 2 2 58 3 0.8 1 1 2 59 1 0.8 1 0 1 60 5 0.8 1 2 3 61 4 0.8 1 2 2 62 5 0.8 1 4 1 63 6 0.8 1 6 64 6 0.8 1 5 1 65 2 0.8 1 0 2 66 4 0.8 1 2 2 67 2 0.8 1 2 68 1 0.8 1 1 69 7 0.8 1 5 2 70 1 0.8 1 0 1 71 3 0.8 1 3 72 6 0.8 1 5 1 73 3 0.8 1 1 2 74 7 0.8 1 6 1 75 2 0.8 1 1 1 76 8 0.8 1 7 1 77 3 0.8 1 1 2 78 3 0.8 1 3 79 11 0.8 1 8 3 80 3 0.8 1 3 81 8 0.8 1 7 1 82 2 0.8 1 1 1 83 10 0.8 1 5 5 84 13 0.8 1 13 85 5 0.8 1 2 3 86 3 0.8 1 1 2 87 5 0.8 1 2 3 88 8 0.8 1 5 3 89 13 0.8 1 13 90 9 0.8 1 8 1 91 7 0.8 1 5 2 92 6 0.8 1 5 1 93 4 0.8 1 2 2 94 3 0.8 1 2 1 95 6 0.8 1 6 96 7 0.8 1 5 2 97 6 0.8 1 6 98 7 0.8 1 7 99 5 0.8 1 1 4 100 12 0.8 1 11 1 101 8 0.8 1 7 1 102 10 0.8 1 7 3 103 12 0.8 1 10 2 104 8 0.8 1 7 1 105 10 0.8 1 8 2 106 10 0.8 1 9 1 107 4 0.8 1 4 108 8 0.8 1 6 2 109 9 0.8 1 9 110 6 0.8 1 5 1 111 21 0.8 1 12 9 112 15 0.8 1 14 1 113 14 0.8 1 13 1 114 11 0.8 1 10 1 115 14 0.8 1 12 2 116 9 0.8 1 9 117 13 0.8 1 11 2 118 20 0.8 1 15 5 119 22 0.8 1 21 1 120 18 0.8 1 17 1 121 17 0.8 1 12 5 122 15 0.8 1 10 5 123 19 0.8 1 17 2 124 25 0.8 1 18 7 125 20 0.8 1 14 6 126 22 0.8 1 19 3 127 24 0.8 1 20 4 128 27 0.8 1 23 4 129 28 0.8 1 24 4 130 19 0.8 1 16 3 131 30 0.8 1 20 10 132 32 0.8 1 27 5 133 40 0.8 1 34 6 134 29 0.8 1 20 9 135 40 0.8 1 18 22 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_20_R1.fq.gz ============================================= 54311933 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_20_R2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_20_R2.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3644_20_R2_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_20_R2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_20_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1737.72 s (32 µs/read; 1.88 M reads/minute). === Summary === Total reads processed: 54,311,933 Reads with adapters: 23,519,270 (43.3%) Reads written (passing filters): 54,311,933 (100.0%) Total basepairs processed: 6,895,076,635 bp Quality-trimmed: 1,433,956 bp (0.0%) Total written (filtered): 6,866,031,990 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 23519270 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.3% C: 9.9% G: 6.2% T: 38.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 20991923 13577983.2 0 20991923 2 1654391 3394495.8 0 1654391 3 474601 848624.0 0 474601 4 306931 212156.0 0 306931 5 48854 53039.0 0 48854 6 12498 13259.7 0 12498 7 8779 3314.9 0 8779 8 6824 828.7 0 6824 9 1898 207.2 0 1449 449 10 11483 51.8 1 10532 951 11 146 12.9 1 20 126 12 49 3.2 1 14 35 13 11 0.8 1 3 8 14 3 0.8 1 1 2 15 5 0.8 1 4 1 16 2 0.8 1 0 2 17 6 0.8 1 4 2 18 4 0.8 1 4 19 3 0.8 1 1 2 20 1 0.8 1 0 1 21 1 0.8 1 1 22 5 0.8 1 2 3 23 2 0.8 1 1 1 24 4 0.8 1 2 2 25 1 0.8 1 1 26 2 0.8 1 1 1 27 5 0.8 1 3 2 28 1 0.8 1 1 29 3 0.8 1 2 1 31 1 0.8 1 1 32 5 0.8 1 4 1 33 4 0.8 1 1 3 34 2 0.8 1 1 1 35 4 0.8 1 3 1 36 3 0.8 1 2 1 37 4 0.8 1 4 38 1 0.8 1 1 39 6 0.8 1 6 40 3 0.8 1 2 1 41 6 0.8 1 5 1 42 1 0.8 1 0 1 44 2 0.8 1 1 1 45 3 0.8 1 3 46 1 0.8 1 1 47 6 0.8 1 5 1 48 2 0.8 1 2 49 2 0.8 1 0 2 50 2 0.8 1 1 1 51 1 0.8 1 1 52 1 0.8 1 1 53 7 0.8 1 4 3 54 1 0.8 1 0 1 55 5 0.8 1 2 3 56 4 0.8 1 1 3 57 2 0.8 1 2 58 2 0.8 1 2 59 2 0.8 1 2 60 3 0.8 1 3 61 1 0.8 1 0 1 62 3 0.8 1 3 64 7 0.8 1 5 2 65 1 0.8 1 1 66 2 0.8 1 2 67 2 0.8 1 1 1 68 1 0.8 1 1 69 3 0.8 1 3 70 7 0.8 1 5 2 71 6 0.8 1 6 72 9 0.8 1 8 1 73 4 0.8 1 2 2 74 3 0.8 1 3 75 2 0.8 1 2 76 6 0.8 1 5 1 77 8 0.8 1 5 3 78 6 0.8 1 2 4 79 2 0.8 1 1 1 80 5 0.8 1 5 81 4 0.8 1 4 82 5 0.8 1 5 83 1 0.8 1 1 84 4 0.8 1 4 85 9 0.8 1 7 2 86 8 0.8 1 6 2 87 5 0.8 1 5 88 5 0.8 1 4 1 89 5 0.8 1 3 2 90 5 0.8 1 4 1 91 7 0.8 1 6 1 92 8 0.8 1 8 93 4 0.8 1 4 94 2 0.8 1 2 95 8 0.8 1 7 1 96 8 0.8 1 5 3 97 15 0.8 1 11 4 98 6 0.8 1 6 99 6 0.8 1 6 100 5 0.8 1 4 1 101 9 0.8 1 8 1 102 11 0.8 1 11 103 3 0.8 1 2 1 104 10 0.8 1 8 2 105 4 0.8 1 3 1 106 6 0.8 1 6 107 9 0.8 1 8 1 108 14 0.8 1 10 4 109 12 0.8 1 12 110 15 0.8 1 14 1 111 9 0.8 1 6 3 112 6 0.8 1 4 2 113 12 0.8 1 11 1 114 15 0.8 1 15 115 8 0.8 1 5 3 116 10 0.8 1 9 1 117 11 0.8 1 10 1 118 13 0.8 1 12 1 119 16 0.8 1 14 2 120 18 0.8 1 16 2 121 12 0.8 1 10 2 122 25 0.8 1 21 4 123 2 0.8 1 2 124 17 0.8 1 16 1 125 13 0.8 1 12 1 126 17 0.8 1 14 3 127 31 0.8 1 29 2 128 25 0.8 1 21 4 129 20 0.8 1 18 2 130 20 0.8 1 17 3 131 27 0.8 1 21 6 132 22 0.8 1 20 2 133 33 0.8 1 26 7 134 29 0.8 1 24 5 135 46 0.8 1 14 32 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_20_R2.fq.gz ============================================= 54311933 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_20_R1_trimmed.fq.gz and zr3644_20_R2_trimmed.fq.gz file_1: zr3644_20_R1_trimmed.fq.gz, file_2: zr3644_20_R2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_20_R1_trimmed.fq.gz and zr3644_20_R2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_20_R1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_20_R2_val_2.fq.gz Total number of sequences analysed: 54311933 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 227036 (0.42%) >>> Now running FastQC on the validated data zr3644_20_R1_val_1.fq.gz<<< Started analysis of zr3644_20_R1_val_1.fq.gz Approx 5% complete for zr3644_20_R1_val_1.fq.gz Approx 10% complete for zr3644_20_R1_val_1.fq.gz Approx 15% complete for zr3644_20_R1_val_1.fq.gz Approx 20% complete for zr3644_20_R1_val_1.fq.gz Approx 25% complete for zr3644_20_R1_val_1.fq.gz Approx 30% complete for zr3644_20_R1_val_1.fq.gz Approx 35% complete for zr3644_20_R1_val_1.fq.gz Approx 40% complete for zr3644_20_R1_val_1.fq.gz Approx 45% complete for zr3644_20_R1_val_1.fq.gz Approx 50% complete for zr3644_20_R1_val_1.fq.gz Approx 55% complete for zr3644_20_R1_val_1.fq.gz Approx 60% complete for zr3644_20_R1_val_1.fq.gz Approx 65% complete for zr3644_20_R1_val_1.fq.gz Approx 70% complete for zr3644_20_R1_val_1.fq.gz Approx 75% complete for zr3644_20_R1_val_1.fq.gz Approx 80% complete for zr3644_20_R1_val_1.fq.gz Approx 85% complete for zr3644_20_R1_val_1.fq.gz Approx 90% complete for zr3644_20_R1_val_1.fq.gz Approx 95% complete for zr3644_20_R1_val_1.fq.gz Analysis complete for zr3644_20_R1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_20_R2_val_2.fq.gz<<< Started analysis of zr3644_20_R2_val_2.fq.gz Approx 5% complete for zr3644_20_R2_val_2.fq.gz Approx 10% complete for zr3644_20_R2_val_2.fq.gz Approx 15% complete for zr3644_20_R2_val_2.fq.gz Approx 20% complete for zr3644_20_R2_val_2.fq.gz Approx 25% complete for zr3644_20_R2_val_2.fq.gz Approx 30% complete for zr3644_20_R2_val_2.fq.gz Approx 35% complete for zr3644_20_R2_val_2.fq.gz Approx 40% complete for zr3644_20_R2_val_2.fq.gz Approx 45% complete for zr3644_20_R2_val_2.fq.gz Approx 50% complete for zr3644_20_R2_val_2.fq.gz Approx 55% complete for zr3644_20_R2_val_2.fq.gz Approx 60% complete for zr3644_20_R2_val_2.fq.gz Approx 65% complete for zr3644_20_R2_val_2.fq.gz Approx 70% complete for zr3644_20_R2_val_2.fq.gz Approx 75% complete for zr3644_20_R2_val_2.fq.gz Approx 80% complete for zr3644_20_R2_val_2.fq.gz Approx 85% complete for zr3644_20_R2_val_2.fq.gz Approx 90% complete for zr3644_20_R2_val_2.fq.gz Approx 95% complete for zr3644_20_R2_val_2.fq.gz Analysis complete for zr3644_20_R2_val_2.fq.gz Deleting both intermediate output files zr3644_20_R1_trimmed.fq.gz and zr3644_20_R2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_21_R1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_21_R1.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3644_21_R1_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_21_R1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_21_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1734.86 s (34 µs/read; 1.78 M reads/minute). === Summary === Total reads processed: 51,337,098 Reads with adapters: 22,468,074 (43.8%) Reads written (passing filters): 51,337,098 (100.0%) Total basepairs processed: 6,504,759,787 bp Quality-trimmed: 2,335,656 bp (0.0%) Total written (filtered): 6,475,942,942 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 22468074 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.0% C: 10.6% G: 6.3% T: 38.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 19979505 12834274.5 0 19979505 2 1650411 3208568.6 0 1650411 3 470020 802142.2 0 470020 4 279846 200535.5 0 279846 5 46716 50133.9 0 46716 6 12187 12533.5 0 12187 7 8532 3133.4 0 8532 8 5998 783.3 0 5998 9 1655 195.8 0 1276 379 10 10922 49.0 1 9939 983 11 175 12.2 1 38 137 12 114 3.1 1 48 66 13 13 0.8 1 5 8 14 35 0.8 1 26 9 15 5 0.8 1 3 2 16 40 0.8 1 28 12 17 3 0.8 1 3 18 59 0.8 1 45 14 19 107 0.8 1 73 34 20 4 0.8 1 3 1 21 1 0.8 1 1 22 8 0.8 1 3 5 23 49 0.8 1 36 13 24 56 0.8 1 48 8 25 3 0.8 1 1 2 26 28 0.8 1 23 5 27 20 0.8 1 19 1 28 1 0.8 1 1 29 24 0.8 1 14 10 30 33 0.8 1 21 12 31 48 0.8 1 37 11 32 12 0.8 1 7 5 33 43 0.8 1 32 11 34 16 0.8 1 11 5 35 16 0.8 1 10 6 36 43 0.8 1 33 10 37 26 0.8 1 14 12 38 9 0.8 1 8 1 39 10 0.8 1 6 4 40 21 0.8 1 15 6 41 10 0.8 1 8 2 42 37 0.8 1 28 9 43 25 0.8 1 19 6 44 30 0.8 1 24 6 45 9 0.8 1 8 1 46 19 0.8 1 17 2 47 5 0.8 1 4 1 48 36 0.8 1 26 10 49 24 0.8 1 15 9 50 26 0.8 1 20 6 51 18 0.8 1 16 2 52 51 0.8 1 41 10 53 11 0.8 1 10 1 54 4 0.8 1 3 1 55 35 0.8 1 31 4 56 29 0.8 1 25 4 57 7 0.8 1 4 3 58 8 0.8 1 6 2 59 21 0.8 1 17 4 60 5 0.8 1 5 61 9 0.8 1 6 3 62 25 0.8 1 21 4 63 4 0.8 1 3 1 64 9 0.8 1 5 4 65 12 0.8 1 12 66 21 0.8 1 17 4 67 10 0.8 1 9 1 68 7 0.8 1 7 69 3 0.8 1 3 70 2 0.8 1 1 1 71 3 0.8 1 2 1 72 3 0.8 1 3 73 5 0.8 1 4 1 74 6 0.8 1 3 3 75 4 0.8 1 4 76 6 0.8 1 6 77 11 0.8 1 10 1 78 12 0.8 1 11 1 79 7 0.8 1 7 80 10 0.8 1 8 2 81 5 0.8 1 4 1 82 11 0.8 1 6 5 83 8 0.8 1 8 84 8 0.8 1 7 1 85 10 0.8 1 9 1 86 6 0.8 1 5 1 87 7 0.8 1 5 2 88 6 0.8 1 6 89 8 0.8 1 7 1 90 8 0.8 1 7 1 91 6 0.8 1 4 2 92 5 0.8 1 4 1 93 6 0.8 1 6 94 6 0.8 1 6 95 6 0.8 1 6 96 9 0.8 1 9 97 8 0.8 1 5 3 98 10 0.8 1 9 1 99 16 0.8 1 14 2 100 8 0.8 1 7 1 101 4 0.8 1 4 102 6 0.8 1 4 2 103 8 0.8 1 8 104 6 0.8 1 4 2 105 9 0.8 1 9 106 2 0.8 1 2 107 9 0.8 1 8 1 108 6 0.8 1 4 2 109 11 0.8 1 10 1 110 8 0.8 1 7 1 111 7 0.8 1 6 1 112 12 0.8 1 10 2 113 9 0.8 1 8 1 114 10 0.8 1 9 1 115 7 0.8 1 4 3 116 15 0.8 1 14 1 117 19 0.8 1 17 2 118 21 0.8 1 19 2 119 16 0.8 1 15 1 120 13 0.8 1 11 2 121 18 0.8 1 13 5 122 15 0.8 1 12 3 123 12 0.8 1 8 4 124 14 0.8 1 12 2 125 15 0.8 1 12 3 126 25 0.8 1 21 4 127 21 0.8 1 18 3 128 17 0.8 1 14 3 129 17 0.8 1 13 4 130 29 0.8 1 23 6 131 21 0.8 1 17 4 132 29 0.8 1 28 1 133 27 0.8 1 18 9 134 25 0.8 1 20 5 135 41 0.8 1 20 21 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_21_R1.fq.gz ============================================= 51337098 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_21_R2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_21_R2.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3644_21_R2_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_21_R2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_21_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1655.18 s (32 µs/read; 1.86 M reads/minute). === Summary === Total reads processed: 51,337,098 Reads with adapters: 22,250,143 (43.3%) Reads written (passing filters): 51,337,098 (100.0%) Total basepairs processed: 6,502,868,062 bp Quality-trimmed: 1,736,389 bp (0.0%) Total written (filtered): 6,475,103,537 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 22250143 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.7% C: 10.2% G: 6.0% T: 38.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 19934151 12834274.5 0 19934151 2 1505115 3208568.6 0 1505115 3 442293 802142.2 0 442293 4 281742 200535.5 0 281742 5 47399 50133.9 0 47399 6 11600 12533.5 0 11600 7 8370 3133.4 0 8370 8 6041 783.3 0 6041 9 1708 195.8 0 1349 359 10 10424 49.0 1 9483 941 11 127 12.2 1 27 100 12 48 3.1 1 15 33 13 9 0.8 1 2 7 14 12 0.8 1 6 6 15 7 0.8 1 5 2 16 4 0.8 1 3 1 17 11 0.8 1 6 5 18 1 0.8 1 1 19 17 0.8 1 8 9 20 7 0.8 1 6 1 21 3 0.8 1 1 2 22 5 0.8 1 5 23 8 0.8 1 3 5 24 20 0.8 1 9 11 25 7 0.8 1 5 2 26 7 0.8 1 5 2 27 3 0.8 1 3 28 9 0.8 1 4 5 29 6 0.8 1 4 2 30 8 0.8 1 0 8 31 5 0.8 1 4 1 32 10 0.8 1 3 7 33 8 0.8 1 7 1 34 3 0.8 1 3 35 7 0.8 1 6 1 36 4 0.8 1 4 37 5 0.8 1 4 1 38 6 0.8 1 3 3 39 14 0.8 1 8 6 40 10 0.8 1 4 6 41 4 0.8 1 2 2 42 14 0.8 1 11 3 43 6 0.8 1 5 1 44 6 0.8 1 4 2 45 9 0.8 1 7 2 46 5 0.8 1 4 1 47 10 0.8 1 5 5 48 9 0.8 1 5 4 49 15 0.8 1 12 3 50 5 0.8 1 4 1 51 8 0.8 1 6 2 52 10 0.8 1 8 2 53 8 0.8 1 6 2 54 6 0.8 1 4 2 55 7 0.8 1 6 1 56 4 0.8 1 2 2 57 6 0.8 1 4 2 58 6 0.8 1 4 2 60 10 0.8 1 6 4 61 2 0.8 1 2 62 8 0.8 1 6 2 63 12 0.8 1 8 4 64 7 0.8 1 6 1 65 6 0.8 1 5 1 66 12 0.8 1 10 2 67 5 0.8 1 3 2 68 2 0.8 1 2 69 9 0.8 1 9 70 6 0.8 1 4 2 71 5 0.8 1 3 2 72 2 0.8 1 2 73 10 0.8 1 10 74 4 0.8 1 3 1 75 6 0.8 1 4 2 76 5 0.8 1 3 2 77 7 0.8 1 5 2 78 6 0.8 1 6 79 11 0.8 1 8 3 80 6 0.8 1 4 2 81 6 0.8 1 4 2 82 7 0.8 1 4 3 83 7 0.8 1 7 84 6 0.8 1 5 1 85 10 0.8 1 7 3 86 9 0.8 1 7 2 87 3 0.8 1 1 2 88 12 0.8 1 11 1 89 2 0.8 1 1 1 90 9 0.8 1 5 4 91 8 0.8 1 8 92 3 0.8 1 1 2 93 2 0.8 1 2 94 1 0.8 1 0 1 95 8 0.8 1 4 4 96 8 0.8 1 6 2 97 5 0.8 1 5 98 11 0.8 1 10 1 99 5 0.8 1 3 2 100 12 0.8 1 9 3 101 6 0.8 1 5 1 102 9 0.8 1 8 1 103 10 0.8 1 7 3 104 5 0.8 1 5 105 10 0.8 1 8 2 106 9 0.8 1 7 2 107 12 0.8 1 11 1 108 10 0.8 1 8 2 109 9 0.8 1 9 110 10 0.8 1 9 1 111 9 0.8 1 6 3 112 8 0.8 1 8 113 6 0.8 1 6 114 10 0.8 1 9 1 115 16 0.8 1 14 2 116 10 0.8 1 9 1 117 13 0.8 1 12 1 118 18 0.8 1 12 6 119 8 0.8 1 4 4 120 15 0.8 1 14 1 121 15 0.8 1 13 2 122 11 0.8 1 8 3 123 19 0.8 1 15 4 124 16 0.8 1 16 125 12 0.8 1 10 2 126 16 0.8 1 15 1 127 16 0.8 1 15 1 128 26 0.8 1 25 1 129 19 0.8 1 16 3 130 16 0.8 1 13 3 131 33 0.8 1 27 6 132 14 0.8 1 11 3 133 24 0.8 1 22 2 134 25 0.8 1 19 6 135 31 0.8 1 13 18 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_21_R2.fq.gz ============================================= 51337098 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_21_R1_trimmed.fq.gz and zr3644_21_R2_trimmed.fq.gz file_1: zr3644_21_R1_trimmed.fq.gz, file_2: zr3644_21_R2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_21_R1_trimmed.fq.gz and zr3644_21_R2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_21_R1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_21_R2_val_2.fq.gz Total number of sequences analysed: 51337098 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 224543 (0.44%) >>> Now running FastQC on the validated data zr3644_21_R1_val_1.fq.gz<<< Started analysis of zr3644_21_R1_val_1.fq.gz Approx 5% complete for zr3644_21_R1_val_1.fq.gz Approx 10% complete for zr3644_21_R1_val_1.fq.gz Approx 15% complete for zr3644_21_R1_val_1.fq.gz Approx 20% complete for zr3644_21_R1_val_1.fq.gz Approx 25% complete for zr3644_21_R1_val_1.fq.gz Approx 30% complete for zr3644_21_R1_val_1.fq.gz Approx 35% complete for zr3644_21_R1_val_1.fq.gz Approx 40% complete for zr3644_21_R1_val_1.fq.gz Approx 45% complete for zr3644_21_R1_val_1.fq.gz Approx 50% complete for zr3644_21_R1_val_1.fq.gz Approx 55% complete for zr3644_21_R1_val_1.fq.gz Approx 60% complete for zr3644_21_R1_val_1.fq.gz Approx 65% complete for zr3644_21_R1_val_1.fq.gz Approx 70% complete for zr3644_21_R1_val_1.fq.gz Approx 75% complete for zr3644_21_R1_val_1.fq.gz Approx 80% complete for zr3644_21_R1_val_1.fq.gz Approx 85% complete for zr3644_21_R1_val_1.fq.gz Approx 90% complete for zr3644_21_R1_val_1.fq.gz Approx 95% complete for zr3644_21_R1_val_1.fq.gz Analysis complete for zr3644_21_R1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_21_R2_val_2.fq.gz<<< Started analysis of zr3644_21_R2_val_2.fq.gz Approx 5% complete for zr3644_21_R2_val_2.fq.gz Approx 10% complete for zr3644_21_R2_val_2.fq.gz Approx 15% complete for zr3644_21_R2_val_2.fq.gz Approx 20% complete for zr3644_21_R2_val_2.fq.gz Approx 25% complete for zr3644_21_R2_val_2.fq.gz Approx 30% complete for zr3644_21_R2_val_2.fq.gz Approx 35% complete for zr3644_21_R2_val_2.fq.gz Approx 40% complete for zr3644_21_R2_val_2.fq.gz Approx 45% complete for zr3644_21_R2_val_2.fq.gz Approx 50% complete for zr3644_21_R2_val_2.fq.gz Approx 55% complete for zr3644_21_R2_val_2.fq.gz Approx 60% complete for zr3644_21_R2_val_2.fq.gz Approx 65% complete for zr3644_21_R2_val_2.fq.gz Approx 70% complete for zr3644_21_R2_val_2.fq.gz Approx 75% complete for zr3644_21_R2_val_2.fq.gz Approx 80% complete for zr3644_21_R2_val_2.fq.gz Approx 85% complete for zr3644_21_R2_val_2.fq.gz Approx 90% complete for zr3644_21_R2_val_2.fq.gz Approx 95% complete for zr3644_21_R2_val_2.fq.gz Analysis complete for zr3644_21_R2_val_2.fq.gz Deleting both intermediate output files zr3644_21_R1_trimmed.fq.gz and zr3644_21_R2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_22_R1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_22_R1.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3644_22_R1_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_22_R1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_22_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1627.27 s (34 µs/read; 1.77 M reads/minute). === Summary === Total reads processed: 47,948,800 Reads with adapters: 20,718,810 (43.2%) Reads written (passing filters): 47,948,800 (100.0%) Total basepairs processed: 6,055,877,417 bp Quality-trimmed: 1,943,004 bp (0.0%) Total written (filtered): 6,029,422,572 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 20718810 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.1% C: 10.4% G: 6.4% T: 38.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 18375993 11987200.0 0 18375993 2 1552544 2996800.0 0 1552544 3 429835 749200.0 0 429835 4 267870 187300.0 0 267870 5 49252 46825.0 0 49252 6 12776 11706.2 0 12776 7 9104 2926.6 0 9104 8 6650 731.6 0 6650 9 1753 182.9 0 1370 383 10 11436 45.7 1 10502 934 11 156 11.4 1 30 126 12 70 2.9 1 31 39 13 10 0.7 1 3 7 14 20 0.7 1 15 5 15 2 0.7 1 1 1 16 32 0.7 1 24 8 17 5 0.7 1 4 1 18 41 0.7 1 20 21 19 44 0.7 1 33 11 20 2 0.7 1 1 1 21 1 0.7 1 0 1 22 6 0.7 1 2 4 23 23 0.7 1 16 7 24 35 0.7 1 21 14 25 1 0.7 1 1 26 14 0.7 1 11 3 27 15 0.7 1 8 7 28 6 0.7 1 2 4 29 10 0.7 1 8 2 30 23 0.7 1 13 10 31 28 0.7 1 20 8 32 9 0.7 1 6 3 33 30 0.7 1 25 5 34 9 0.7 1 8 1 35 9 0.7 1 7 2 36 20 0.7 1 16 4 37 9 0.7 1 9 38 14 0.7 1 10 4 39 9 0.7 1 6 3 40 10 0.7 1 8 2 41 24 0.7 1 18 6 42 12 0.7 1 9 3 43 16 0.7 1 14 2 44 24 0.7 1 19 5 45 3 0.7 1 1 2 46 6 0.7 1 5 1 47 5 0.7 1 2 3 48 20 0.7 1 17 3 49 13 0.7 1 10 3 50 10 0.7 1 9 1 51 4 0.7 1 3 1 52 26 0.7 1 22 4 53 3 0.7 1 3 54 1 0.7 1 1 55 20 0.7 1 17 3 56 24 0.7 1 20 4 57 5 0.7 1 4 1 58 3 0.7 1 3 59 16 0.7 1 14 2 60 1 0.7 1 1 61 4 0.7 1 3 1 62 16 0.7 1 14 2 63 2 0.7 1 2 64 7 0.7 1 5 2 65 6 0.7 1 4 2 66 18 0.7 1 12 6 67 9 0.7 1 4 5 68 7 0.7 1 6 1 69 4 0.7 1 2 2 70 6 0.7 1 6 71 3 0.7 1 3 72 2 0.7 1 2 73 7 0.7 1 5 2 74 4 0.7 1 4 75 9 0.7 1 7 2 76 5 0.7 1 5 77 3 0.7 1 3 78 5 0.7 1 5 79 5 0.7 1 5 80 7 0.7 1 5 2 81 6 0.7 1 3 3 82 5 0.7 1 5 83 10 0.7 1 9 1 85 7 0.7 1 7 86 4 0.7 1 4 87 7 0.7 1 6 1 88 9 0.7 1 7 2 89 9 0.7 1 4 5 90 5 0.7 1 5 91 5 0.7 1 5 92 7 0.7 1 4 3 93 5 0.7 1 4 1 94 5 0.7 1 2 3 95 7 0.7 1 6 1 96 5 0.7 1 1 4 97 10 0.7 1 6 4 98 2 0.7 1 1 1 99 5 0.7 1 4 1 100 4 0.7 1 4 101 10 0.7 1 10 102 9 0.7 1 8 1 103 10 0.7 1 8 2 104 8 0.7 1 8 105 9 0.7 1 6 3 106 3 0.7 1 1 2 107 11 0.7 1 9 2 108 12 0.7 1 12 109 9 0.7 1 8 1 110 7 0.7 1 6 1 111 9 0.7 1 9 112 6 0.7 1 2 4 113 11 0.7 1 8 3 114 4 0.7 1 2 2 115 14 0.7 1 13 1 116 9 0.7 1 8 1 117 11 0.7 1 8 3 118 15 0.7 1 13 2 119 16 0.7 1 15 1 120 17 0.7 1 13 4 121 17 0.7 1 16 1 122 9 0.7 1 6 3 123 6 0.7 1 4 2 124 16 0.7 1 14 2 125 12 0.7 1 9 3 126 20 0.7 1 15 5 127 10 0.7 1 9 1 128 17 0.7 1 17 129 14 0.7 1 12 2 130 18 0.7 1 16 2 131 17 0.7 1 16 1 132 16 0.7 1 14 2 133 23 0.7 1 19 4 134 30 0.7 1 19 11 135 27 0.7 1 10 17 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_22_R1.fq.gz ============================================= 47948800 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_22_R2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_22_R2.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3644_22_R2_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_22_R2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_22_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1915.16 s (40 µs/read; 1.50 M reads/minute). === Summary === Total reads processed: 47,948,800 Reads with adapters: 20,603,226 (43.0%) Reads written (passing filters): 47,948,800 (100.0%) Total basepairs processed: 6,053,610,438 bp Quality-trimmed: 2,087,826 bp (0.0%) Total written (filtered): 6,027,275,695 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 20603226 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.3% C: 10.3% G: 6.3% T: 38.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 18375358 11987200.0 0 18375358 2 1443882 2996800.0 0 1443882 3 420748 749200.0 0 420748 4 272111 187300.0 0 272111 5 49381 46825.0 0 49381 6 12266 11706.2 0 12266 7 9063 2926.6 0 9063 8 6684 731.6 0 6684 9 1756 182.9 0 1408 348 10 11040 45.7 1 10119 921 11 126 11.4 1 15 111 12 46 2.9 1 9 37 13 10 0.7 1 3 7 14 6 0.7 1 1 5 15 7 0.7 1 3 4 16 2 0.7 1 2 17 4 0.7 1 3 1 18 1 0.7 1 1 19 3 0.7 1 2 1 20 3 0.7 1 3 21 2 0.7 1 2 22 2 0.7 1 1 1 23 5 0.7 1 2 3 24 7 0.7 1 3 4 25 5 0.7 1 2 3 26 2 0.7 1 0 2 27 5 0.7 1 2 3 28 4 0.7 1 3 1 29 3 0.7 1 2 1 30 3 0.7 1 3 31 3 0.7 1 2 1 32 8 0.7 1 3 5 33 4 0.7 1 2 2 34 7 0.7 1 6 1 35 2 0.7 1 1 1 36 7 0.7 1 3 4 37 7 0.7 1 4 3 38 3 0.7 1 1 2 39 7 0.7 1 4 3 40 5 0.7 1 3 2 41 4 0.7 1 2 2 42 2 0.7 1 1 1 43 3 0.7 1 2 1 44 7 0.7 1 4 3 45 7 0.7 1 5 2 46 3 0.7 1 2 1 47 2 0.7 1 1 1 48 9 0.7 1 6 3 49 7 0.7 1 6 1 50 3 0.7 1 1 2 51 5 0.7 1 4 1 52 2 0.7 1 2 53 5 0.7 1 2 3 54 3 0.7 1 3 55 2 0.7 1 1 1 56 3 0.7 1 3 57 7 0.7 1 4 3 58 3 0.7 1 0 3 59 4 0.7 1 1 3 60 9 0.7 1 7 2 61 7 0.7 1 5 2 62 3 0.7 1 3 63 5 0.7 1 3 2 64 8 0.7 1 6 2 65 2 0.7 1 2 66 6 0.7 1 1 5 67 3 0.7 1 2 1 68 5 0.7 1 4 1 69 6 0.7 1 5 1 70 8 0.7 1 6 2 71 3 0.7 1 2 1 72 2 0.7 1 2 73 5 0.7 1 4 1 75 3 0.7 1 3 76 3 0.7 1 2 1 77 3 0.7 1 3 78 2 0.7 1 0 2 79 5 0.7 1 4 1 80 4 0.7 1 4 81 7 0.7 1 4 3 82 1 0.7 1 1 83 3 0.7 1 0 3 84 2 0.7 1 1 1 85 6 0.7 1 3 3 86 4 0.7 1 3 1 87 4 0.7 1 4 88 11 0.7 1 8 3 89 3 0.7 1 3 90 6 0.7 1 5 1 91 3 0.7 1 3 92 3 0.7 1 3 93 9 0.7 1 9 94 5 0.7 1 4 1 95 3 0.7 1 2 1 96 5 0.7 1 5 97 3 0.7 1 3 98 10 0.7 1 6 4 99 5 0.7 1 4 1 100 11 0.7 1 9 2 101 5 0.7 1 4 1 102 4 0.7 1 4 103 2 0.7 1 2 104 6 0.7 1 6 105 8 0.7 1 7 1 106 6 0.7 1 4 2 107 5 0.7 1 5 108 5 0.7 1 2 3 109 5 0.7 1 5 110 8 0.7 1 8 111 7 0.7 1 7 112 6 0.7 1 5 1 113 10 0.7 1 8 2 114 8 0.7 1 6 2 115 5 0.7 1 5 116 5 0.7 1 5 117 5 0.7 1 1 4 118 9 0.7 1 8 1 119 10 0.7 1 8 2 120 15 0.7 1 13 2 121 11 0.7 1 10 1 122 12 0.7 1 11 1 123 9 0.7 1 6 3 124 11 0.7 1 11 125 14 0.7 1 11 3 126 15 0.7 1 12 3 127 8 0.7 1 7 1 128 16 0.7 1 11 5 129 21 0.7 1 21 130 13 0.7 1 13 131 20 0.7 1 18 2 132 18 0.7 1 17 1 133 20 0.7 1 16 4 134 10 0.7 1 6 4 135 29 0.7 1 8 21 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_22_R2.fq.gz ============================================= 47948800 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_22_R1_trimmed.fq.gz and zr3644_22_R2_trimmed.fq.gz file_1: zr3644_22_R1_trimmed.fq.gz, file_2: zr3644_22_R2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_22_R1_trimmed.fq.gz and zr3644_22_R2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_22_R1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_22_R2_val_2.fq.gz Total number of sequences analysed: 47948800 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 223618 (0.47%) >>> Now running FastQC on the validated data zr3644_22_R1_val_1.fq.gz<<< Started analysis of zr3644_22_R1_val_1.fq.gz Approx 5% complete for zr3644_22_R1_val_1.fq.gz Approx 10% complete for zr3644_22_R1_val_1.fq.gz Approx 15% complete for zr3644_22_R1_val_1.fq.gz Approx 20% complete for zr3644_22_R1_val_1.fq.gz Approx 25% complete for zr3644_22_R1_val_1.fq.gz Approx 30% complete for zr3644_22_R1_val_1.fq.gz Approx 35% complete for zr3644_22_R1_val_1.fq.gz Approx 40% complete for zr3644_22_R1_val_1.fq.gz Approx 45% complete for zr3644_22_R1_val_1.fq.gz Approx 50% complete for zr3644_22_R1_val_1.fq.gz Approx 55% complete for zr3644_22_R1_val_1.fq.gz Approx 60% complete for zr3644_22_R1_val_1.fq.gz Approx 65% complete for zr3644_22_R1_val_1.fq.gz Approx 70% complete for zr3644_22_R1_val_1.fq.gz Approx 75% complete for zr3644_22_R1_val_1.fq.gz Approx 80% complete for zr3644_22_R1_val_1.fq.gz Approx 85% complete for zr3644_22_R1_val_1.fq.gz Approx 90% complete for zr3644_22_R1_val_1.fq.gz Approx 95% complete for zr3644_22_R1_val_1.fq.gz Analysis complete for zr3644_22_R1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_22_R2_val_2.fq.gz<<< Started analysis of zr3644_22_R2_val_2.fq.gz Approx 5% complete for zr3644_22_R2_val_2.fq.gz Approx 10% complete for zr3644_22_R2_val_2.fq.gz Approx 15% complete for zr3644_22_R2_val_2.fq.gz Approx 20% complete for zr3644_22_R2_val_2.fq.gz Approx 25% complete for zr3644_22_R2_val_2.fq.gz Approx 30% complete for zr3644_22_R2_val_2.fq.gz Approx 35% complete for zr3644_22_R2_val_2.fq.gz Approx 40% complete for zr3644_22_R2_val_2.fq.gz Approx 45% complete for zr3644_22_R2_val_2.fq.gz Approx 50% complete for zr3644_22_R2_val_2.fq.gz Approx 55% complete for zr3644_22_R2_val_2.fq.gz Approx 60% complete for zr3644_22_R2_val_2.fq.gz Approx 65% complete for zr3644_22_R2_val_2.fq.gz Approx 70% complete for zr3644_22_R2_val_2.fq.gz Approx 75% complete for zr3644_22_R2_val_2.fq.gz Approx 80% complete for zr3644_22_R2_val_2.fq.gz Approx 85% complete for zr3644_22_R2_val_2.fq.gz Approx 90% complete for zr3644_22_R2_val_2.fq.gz Approx 95% complete for zr3644_22_R2_val_2.fq.gz Analysis complete for zr3644_22_R2_val_2.fq.gz Deleting both intermediate output files zr3644_22_R1_trimmed.fq.gz and zr3644_22_R2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_23_R1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_23_R1.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3644_23_R1_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_23_R1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_23_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1279.27 s (31 µs/read; 1.91 M reads/minute). === Summary === Total reads processed: 40,743,756 Reads with adapters: 17,444,950 (42.8%) Reads written (passing filters): 40,743,756 (100.0%) Total basepairs processed: 5,122,390,542 bp Quality-trimmed: 1,745,274 bp (0.0%) Total written (filtered): 5,099,945,615 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 17444950 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.0% C: 10.4% G: 6.4% T: 38.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 15432601 10185939.0 0 15432601 2 1339323 2546484.8 0 1339323 3 361842 636621.2 0 361842 4 229699 159155.3 0 229699 5 43790 39788.8 0 43790 6 11029 9947.2 0 11029 7 8042 2486.8 0 8042 8 5919 621.7 0 5919 9 1553 155.4 0 1177 376 10 10046 38.9 1 9143 903 11 134 9.7 1 21 113 12 41 2.4 1 18 23 13 6 0.6 1 0 6 14 11 0.6 1 5 6 15 2 0.6 1 2 16 9 0.6 1 7 2 17 3 0.6 1 2 1 18 18 0.6 1 11 7 19 14 0.6 1 9 5 20 4 0.6 1 2 2 21 2 0.6 1 1 1 22 3 0.6 1 2 1 23 14 0.6 1 8 6 24 11 0.6 1 5 6 25 3 0.6 1 3 26 3 0.6 1 3 27 4 0.6 1 3 1 28 3 0.6 1 1 2 29 5 0.6 1 4 1 30 6 0.6 1 1 5 31 11 0.6 1 8 3 32 2 0.6 1 2 33 12 0.6 1 8 4 34 4 0.6 1 2 2 35 8 0.6 1 8 36 16 0.6 1 13 3 37 4 0.6 1 3 1 38 2 0.6 1 2 39 5 0.6 1 5 40 2 0.6 1 1 1 41 6 0.6 1 5 1 42 6 0.6 1 5 1 43 12 0.6 1 7 5 44 3 0.6 1 3 45 5 0.6 1 4 1 46 6 0.6 1 4 2 47 6 0.6 1 4 2 48 10 0.6 1 9 1 49 3 0.6 1 1 2 50 8 0.6 1 6 2 51 5 0.6 1 3 2 52 8 0.6 1 5 3 53 5 0.6 1 5 54 2 0.6 1 2 55 6 0.6 1 4 2 56 5 0.6 1 1 4 57 5 0.6 1 5 58 4 0.6 1 4 59 4 0.6 1 2 2 60 3 0.6 1 2 1 61 1 0.6 1 1 62 2 0.6 1 2 63 2 0.6 1 1 1 64 4 0.6 1 4 65 3 0.6 1 3 66 10 0.6 1 9 1 67 6 0.6 1 5 1 68 2 0.6 1 2 69 10 0.6 1 8 2 70 2 0.6 1 2 71 2 0.6 1 0 2 72 5 0.6 1 4 1 73 10 0.6 1 8 2 74 6 0.6 1 2 4 75 2 0.6 1 0 2 76 7 0.6 1 2 5 77 7 0.6 1 4 3 78 7 0.6 1 6 1 79 4 0.6 1 4 80 5 0.6 1 4 1 81 8 0.6 1 5 3 82 5 0.6 1 4 1 83 4 0.6 1 3 1 84 8 0.6 1 7 1 85 2 0.6 1 2 86 7 0.6 1 6 1 87 4 0.6 1 2 2 88 6 0.6 1 5 1 89 2 0.6 1 2 90 7 0.6 1 7 91 5 0.6 1 5 92 7 0.6 1 6 1 93 4 0.6 1 4 94 1 0.6 1 1 95 8 0.6 1 7 1 96 4 0.6 1 2 2 97 5 0.6 1 4 1 98 5 0.6 1 3 2 99 9 0.6 1 8 1 100 1 0.6 1 1 101 5 0.6 1 4 1 102 6 0.6 1 5 1 103 8 0.6 1 5 3 104 9 0.6 1 7 2 105 6 0.6 1 6 106 11 0.6 1 8 3 107 5 0.6 1 5 108 10 0.6 1 8 2 109 8 0.6 1 8 110 8 0.6 1 6 2 111 11 0.6 1 8 3 112 6 0.6 1 6 113 19 0.6 1 18 1 114 10 0.6 1 6 4 115 12 0.6 1 10 2 116 9 0.6 1 8 1 117 10 0.6 1 9 1 118 13 0.6 1 9 4 119 12 0.6 1 11 1 120 23 0.6 1 18 5 121 15 0.6 1 14 1 122 8 0.6 1 8 123 16 0.6 1 15 1 124 8 0.6 1 6 2 125 15 0.6 1 13 2 126 11 0.6 1 11 127 12 0.6 1 10 2 128 11 0.6 1 11 129 25 0.6 1 22 3 130 20 0.6 1 19 1 131 15 0.6 1 15 132 10 0.6 1 8 2 133 16 0.6 1 14 2 134 25 0.6 1 18 7 135 25 0.6 1 13 12 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_23_R1.fq.gz ============================================= 40743756 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_23_R2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_23_R2.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3644_23_R2_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_23_R2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_23_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1318.67 s (32 µs/read; 1.85 M reads/minute). === Summary === Total reads processed: 40,743,756 Reads with adapters: 17,351,768 (42.6%) Reads written (passing filters): 40,743,756 (100.0%) Total basepairs processed: 5,120,592,948 bp Quality-trimmed: 1,710,015 bp (0.0%) Total written (filtered): 5,098,406,294 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 17351768 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.4% C: 10.2% G: 6.3% T: 38.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 15448638 10185939.0 0 15448638 2 1237821 2546484.8 0 1237821 3 352171 636621.2 0 352171 4 234395 159155.3 0 234395 5 42680 39788.8 0 42680 6 10437 9947.2 0 10437 7 7966 2486.8 0 7966 8 5733 621.7 0 5733 9 1586 155.4 0 1253 333 10 9480 38.9 1 8647 833 11 83 9.7 1 10 73 12 28 2.4 1 6 22 13 3 0.6 1 1 2 14 5 0.6 1 1 4 15 2 0.6 1 1 1 16 3 0.6 1 1 2 17 4 0.6 1 1 3 19 2 0.6 1 0 2 20 4 0.6 1 2 2 21 3 0.6 1 3 22 5 0.6 1 5 23 5 0.6 1 2 3 24 5 0.6 1 0 5 25 2 0.6 1 2 27 3 0.6 1 2 1 28 4 0.6 1 3 1 29 4 0.6 1 3 1 30 5 0.6 1 5 31 4 0.6 1 2 2 32 2 0.6 1 2 33 2 0.6 1 1 1 34 3 0.6 1 1 2 35 5 0.6 1 4 1 38 2 0.6 1 2 39 3 0.6 1 1 2 40 4 0.6 1 3 1 41 4 0.6 1 4 42 3 0.6 1 3 43 5 0.6 1 4 1 44 5 0.6 1 2 3 45 5 0.6 1 2 3 46 6 0.6 1 3 3 47 5 0.6 1 3 2 48 2 0.6 1 2 49 5 0.6 1 4 1 50 3 0.6 1 3 51 4 0.6 1 3 1 52 1 0.6 1 1 53 4 0.6 1 2 2 54 1 0.6 1 0 1 55 7 0.6 1 5 2 56 3 0.6 1 2 1 57 5 0.6 1 1 4 58 7 0.6 1 4 3 59 5 0.6 1 5 60 4 0.6 1 3 1 61 4 0.6 1 4 62 4 0.6 1 2 2 63 2 0.6 1 1 1 64 2 0.6 1 2 65 9 0.6 1 8 1 66 4 0.6 1 0 4 67 1 0.6 1 1 68 5 0.6 1 4 1 69 4 0.6 1 3 1 70 6 0.6 1 5 1 71 6 0.6 1 3 3 72 3 0.6 1 2 1 73 6 0.6 1 4 2 74 3 0.6 1 2 1 75 2 0.6 1 2 76 2 0.6 1 1 1 77 3 0.6 1 2 1 78 3 0.6 1 2 1 79 5 0.6 1 4 1 80 3 0.6 1 3 81 6 0.6 1 4 2 82 7 0.6 1 7 83 6 0.6 1 4 2 84 1 0.6 1 1 85 3 0.6 1 2 1 86 5 0.6 1 3 2 87 3 0.6 1 3 88 5 0.6 1 4 1 89 5 0.6 1 4 1 90 5 0.6 1 4 1 91 2 0.6 1 1 1 92 3 0.6 1 3 93 1 0.6 1 1 94 3 0.6 1 2 1 95 2 0.6 1 1 1 96 4 0.6 1 3 1 97 10 0.6 1 6 4 98 12 0.6 1 11 1 99 12 0.6 1 11 1 100 11 0.6 1 7 4 101 7 0.6 1 6 1 102 9 0.6 1 8 1 103 4 0.6 1 1 3 104 6 0.6 1 3 3 105 4 0.6 1 2 2 106 4 0.6 1 3 1 107 6 0.6 1 3 3 108 3 0.6 1 3 109 5 0.6 1 4 1 110 7 0.6 1 6 1 111 7 0.6 1 6 1 112 10 0.6 1 9 1 113 4 0.6 1 3 1 114 10 0.6 1 10 115 9 0.6 1 5 4 116 12 0.6 1 9 3 117 15 0.6 1 12 3 118 12 0.6 1 12 119 9 0.6 1 7 2 120 19 0.6 1 17 2 121 13 0.6 1 12 1 122 17 0.6 1 15 2 123 9 0.6 1 9 124 20 0.6 1 19 1 125 8 0.6 1 8 126 14 0.6 1 11 3 127 14 0.6 1 9 5 128 12 0.6 1 11 1 129 20 0.6 1 15 5 130 21 0.6 1 18 3 131 14 0.6 1 12 2 132 16 0.6 1 15 1 133 19 0.6 1 17 2 134 17 0.6 1 11 6 135 23 0.6 1 10 13 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_23_R2.fq.gz ============================================= 40743756 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_23_R1_trimmed.fq.gz and zr3644_23_R2_trimmed.fq.gz file_1: zr3644_23_R1_trimmed.fq.gz, file_2: zr3644_23_R2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_23_R1_trimmed.fq.gz and zr3644_23_R2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_23_R1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_23_R2_val_2.fq.gz Total number of sequences analysed: 40743756 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 204735 (0.50%) >>> Now running FastQC on the validated data zr3644_23_R1_val_1.fq.gz<<< Started analysis of zr3644_23_R1_val_1.fq.gz Approx 5% complete for zr3644_23_R1_val_1.fq.gz Approx 10% complete for zr3644_23_R1_val_1.fq.gz Approx 15% complete for zr3644_23_R1_val_1.fq.gz Approx 20% complete for zr3644_23_R1_val_1.fq.gz Approx 25% complete for zr3644_23_R1_val_1.fq.gz Approx 30% complete for zr3644_23_R1_val_1.fq.gz Approx 35% complete for zr3644_23_R1_val_1.fq.gz Approx 40% complete for zr3644_23_R1_val_1.fq.gz Approx 45% complete for zr3644_23_R1_val_1.fq.gz Approx 50% complete for zr3644_23_R1_val_1.fq.gz Approx 55% complete for zr3644_23_R1_val_1.fq.gz Approx 60% complete for zr3644_23_R1_val_1.fq.gz Approx 65% complete for zr3644_23_R1_val_1.fq.gz Approx 70% complete for zr3644_23_R1_val_1.fq.gz Approx 75% complete for zr3644_23_R1_val_1.fq.gz Approx 80% complete for zr3644_23_R1_val_1.fq.gz Approx 85% complete for zr3644_23_R1_val_1.fq.gz Approx 90% complete for zr3644_23_R1_val_1.fq.gz Approx 95% complete for zr3644_23_R1_val_1.fq.gz Analysis complete for zr3644_23_R1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_23_R2_val_2.fq.gz<<< Started analysis of zr3644_23_R2_val_2.fq.gz Approx 5% complete for zr3644_23_R2_val_2.fq.gz Approx 10% complete for zr3644_23_R2_val_2.fq.gz Approx 15% complete for zr3644_23_R2_val_2.fq.gz Approx 20% complete for zr3644_23_R2_val_2.fq.gz Approx 25% complete for zr3644_23_R2_val_2.fq.gz Approx 30% complete for zr3644_23_R2_val_2.fq.gz Approx 35% complete for zr3644_23_R2_val_2.fq.gz Approx 40% complete for zr3644_23_R2_val_2.fq.gz Approx 45% complete for zr3644_23_R2_val_2.fq.gz Approx 50% complete for zr3644_23_R2_val_2.fq.gz Approx 55% complete for zr3644_23_R2_val_2.fq.gz Approx 60% complete for zr3644_23_R2_val_2.fq.gz Approx 65% complete for zr3644_23_R2_val_2.fq.gz Approx 70% complete for zr3644_23_R2_val_2.fq.gz Approx 75% complete for zr3644_23_R2_val_2.fq.gz Approx 80% complete for zr3644_23_R2_val_2.fq.gz Approx 85% complete for zr3644_23_R2_val_2.fq.gz Approx 90% complete for zr3644_23_R2_val_2.fq.gz Approx 95% complete for zr3644_23_R2_val_2.fq.gz Approx 100% complete for zr3644_23_R2_val_2.fq.gz Analysis complete for zr3644_23_R2_val_2.fq.gz Deleting both intermediate output files zr3644_23_R1_trimmed.fq.gz and zr3644_23_R2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_24_R1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_24_R1.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3644_24_R1_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_24_R1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_24_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1728.47 s (33 µs/read; 1.85 M reads/minute). === Summary === Total reads processed: 53,154,280 Reads with adapters: 23,096,436 (43.5%) Reads written (passing filters): 53,154,280 (100.0%) Total basepairs processed: 6,723,235,587 bp Quality-trimmed: 2,278,769 bp (0.0%) Total written (filtered): 6,693,671,857 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 23096436 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.1% C: 10.5% G: 6.4% T: 38.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 20502045 13288570.0 0 20502045 2 1722172 3322142.5 0 1722172 3 475946 830535.6 0 475946 4 293396 207633.9 0 293396 5 54450 51908.5 0 54450 6 14073 12977.1 0 14073 7 10189 3244.3 0 10189 8 7696 811.1 0 7696 9 2014 202.8 0 1595 419 10 13015 50.7 1 11941 1074 11 181 12.7 1 26 155 12 66 3.2 1 19 47 13 6 0.8 1 1 5 14 24 0.8 1 17 7 15 4 0.8 1 3 1 16 14 0.8 1 8 6 17 2 0.8 1 1 1 18 21 0.8 1 8 13 19 26 0.8 1 11 15 20 2 0.8 1 2 21 1 0.8 1 1 22 8 0.8 1 5 3 23 19 0.8 1 10 9 24 22 0.8 1 16 6 25 4 0.8 1 2 2 26 13 0.8 1 9 4 27 9 0.8 1 9 29 7 0.8 1 3 4 30 13 0.8 1 7 6 31 12 0.8 1 9 3 32 4 0.8 1 2 2 33 18 0.8 1 9 9 34 2 0.8 1 1 1 35 6 0.8 1 5 1 36 9 0.8 1 7 2 37 17 0.8 1 10 7 38 6 0.8 1 5 1 39 7 0.8 1 6 1 40 11 0.8 1 8 3 41 11 0.8 1 6 5 42 9 0.8 1 7 2 43 9 0.8 1 6 3 44 11 0.8 1 7 4 45 3 0.8 1 1 2 46 10 0.8 1 5 5 47 4 0.8 1 2 2 48 17 0.8 1 12 5 49 11 0.8 1 4 7 50 6 0.8 1 3 3 51 5 0.8 1 3 2 52 11 0.8 1 11 53 5 0.8 1 5 54 6 0.8 1 6 55 12 0.8 1 7 5 56 10 0.8 1 8 2 57 5 0.8 1 5 58 2 0.8 1 2 59 10 0.8 1 9 1 60 4 0.8 1 3 1 61 3 0.8 1 2 1 62 12 0.8 1 8 4 63 1 0.8 1 1 64 3 0.8 1 1 2 66 13 0.8 1 11 2 67 8 0.8 1 7 1 68 9 0.8 1 8 1 69 5 0.8 1 2 3 70 5 0.8 1 5 71 10 0.8 1 6 4 72 7 0.8 1 5 2 73 5 0.8 1 4 1 74 2 0.8 1 2 75 8 0.8 1 7 1 76 2 0.8 1 1 1 77 9 0.8 1 7 2 78 8 0.8 1 6 2 79 1 0.8 1 0 1 80 5 0.8 1 4 1 81 6 0.8 1 4 2 82 7 0.8 1 5 2 83 2 0.8 1 1 1 84 4 0.8 1 4 85 7 0.8 1 7 86 6 0.8 1 5 1 87 10 0.8 1 9 1 88 5 0.8 1 4 1 89 11 0.8 1 9 2 90 8 0.8 1 7 1 91 6 0.8 1 5 1 92 8 0.8 1 6 2 93 4 0.8 1 4 94 3 0.8 1 3 95 4 0.8 1 4 96 6 0.8 1 6 97 4 0.8 1 4 98 7 0.8 1 7 99 4 0.8 1 4 100 6 0.8 1 4 2 101 7 0.8 1 7 102 4 0.8 1 1 3 103 6 0.8 1 6 104 5 0.8 1 4 1 105 7 0.8 1 7 106 8 0.8 1 7 1 107 16 0.8 1 11 5 108 17 0.8 1 12 5 109 15 0.8 1 10 5 110 6 0.8 1 5 1 111 5 0.8 1 4 1 112 11 0.8 1 11 113 13 0.8 1 10 3 114 11 0.8 1 9 2 115 8 0.8 1 5 3 116 5 0.8 1 5 117 8 0.8 1 6 2 118 10 0.8 1 7 3 119 12 0.8 1 10 2 120 15 0.8 1 14 1 121 26 0.8 1 22 4 122 26 0.8 1 21 5 123 9 0.8 1 6 3 124 19 0.8 1 16 3 125 19 0.8 1 13 6 126 15 0.8 1 15 127 13 0.8 1 12 1 128 29 0.8 1 26 3 129 32 0.8 1 29 3 130 12 0.8 1 10 2 131 22 0.8 1 20 2 132 31 0.8 1 26 5 133 22 0.8 1 18 4 134 16 0.8 1 12 4 135 31 0.8 1 15 16 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_24_R1.fq.gz ============================================= 53154280 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_24_R2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_24_R2.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3644_24_R2_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_24_R2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_24_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1767.65 s (33 µs/read; 1.80 M reads/minute). === Summary === Total reads processed: 53,154,280 Reads with adapters: 22,971,054 (43.2%) Reads written (passing filters): 53,154,280 (100.0%) Total basepairs processed: 6,721,606,596 bp Quality-trimmed: 2,105,426 bp (0.0%) Total written (filtered): 6,692,511,074 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 22971054 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.4% C: 10.3% G: 6.2% T: 38.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 20528839 13288570.0 0 20528839 2 1576070 3322142.5 0 1576070 3 464029 830535.6 0 464029 4 301169 207633.9 0 301169 5 54394 51908.5 0 54394 6 13620 12977.1 0 13620 7 10129 3244.3 0 10129 8 7521 811.1 0 7521 9 2045 202.8 0 1651 394 10 12162 50.7 1 11158 1004 11 139 12.7 1 19 120 12 37 3.2 1 7 30 13 10 0.8 1 1 9 14 3 0.8 1 2 1 15 2 0.8 1 0 2 16 1 0.8 1 1 17 4 0.8 1 2 2 18 3 0.8 1 2 1 19 6 0.8 1 2 4 20 4 0.8 1 2 2 22 3 0.8 1 2 1 24 4 0.8 1 0 4 25 7 0.8 1 3 4 26 3 0.8 1 0 3 27 2 0.8 1 2 28 5 0.8 1 2 3 29 1 0.8 1 0 1 30 5 0.8 1 3 2 31 2 0.8 1 2 32 6 0.8 1 4 2 33 3 0.8 1 0 3 34 6 0.8 1 5 1 35 1 0.8 1 1 36 6 0.8 1 3 3 37 1 0.8 1 1 38 6 0.8 1 4 2 39 3 0.8 1 1 2 40 12 0.8 1 6 6 41 1 0.8 1 1 42 6 0.8 1 5 1 43 2 0.8 1 0 2 44 3 0.8 1 1 2 45 6 0.8 1 5 1 46 2 0.8 1 1 1 47 5 0.8 1 4 1 48 4 0.8 1 2 2 49 4 0.8 1 4 50 1 0.8 1 0 1 51 7 0.8 1 4 3 52 2 0.8 1 1 1 53 3 0.8 1 2 1 54 3 0.8 1 2 1 55 2 0.8 1 2 56 5 0.8 1 2 3 57 4 0.8 1 4 58 4 0.8 1 1 3 59 1 0.8 1 1 60 7 0.8 1 4 3 61 2 0.8 1 1 1 62 3 0.8 1 3 63 3 0.8 1 2 1 64 3 0.8 1 2 1 65 5 0.8 1 3 2 66 6 0.8 1 3 3 67 6 0.8 1 3 3 68 2 0.8 1 0 2 69 5 0.8 1 4 1 70 2 0.8 1 2 71 2 0.8 1 0 2 72 4 0.8 1 4 73 3 0.8 1 1 2 74 9 0.8 1 6 3 76 7 0.8 1 6 1 77 5 0.8 1 3 2 78 9 0.8 1 9 79 5 0.8 1 5 80 7 0.8 1 7 81 7 0.8 1 4 3 82 4 0.8 1 2 2 83 3 0.8 1 2 1 84 8 0.8 1 5 3 85 8 0.8 1 7 1 86 8 0.8 1 7 1 87 6 0.8 1 4 2 88 6 0.8 1 3 3 90 7 0.8 1 5 2 91 3 0.8 1 3 92 8 0.8 1 8 93 9 0.8 1 6 3 94 8 0.8 1 5 3 95 3 0.8 1 2 1 96 7 0.8 1 4 3 97 6 0.8 1 5 1 98 10 0.8 1 8 2 99 11 0.8 1 11 100 10 0.8 1 6 4 101 18 0.8 1 16 2 102 9 0.8 1 7 2 103 9 0.8 1 9 104 3 0.8 1 2 1 105 9 0.8 1 9 106 10 0.8 1 9 1 107 6 0.8 1 4 2 108 14 0.8 1 12 2 109 8 0.8 1 7 1 110 13 0.8 1 10 3 111 10 0.8 1 8 2 112 7 0.8 1 5 2 113 11 0.8 1 9 2 114 12 0.8 1 10 2 115 9 0.8 1 7 2 116 13 0.8 1 11 2 117 12 0.8 1 11 1 118 16 0.8 1 14 2 119 8 0.8 1 8 120 12 0.8 1 10 2 121 16 0.8 1 13 3 122 16 0.8 1 15 1 123 11 0.8 1 8 3 124 14 0.8 1 13 1 125 17 0.8 1 15 2 126 13 0.8 1 13 127 22 0.8 1 21 1 128 16 0.8 1 13 3 129 20 0.8 1 19 1 130 20 0.8 1 16 4 131 29 0.8 1 27 2 132 25 0.8 1 20 5 133 18 0.8 1 13 5 134 24 0.8 1 14 10 135 29 0.8 1 13 16 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_24_R2.fq.gz ============================================= 53154280 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_24_R1_trimmed.fq.gz and zr3644_24_R2_trimmed.fq.gz file_1: zr3644_24_R1_trimmed.fq.gz, file_2: zr3644_24_R2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_24_R1_trimmed.fq.gz and zr3644_24_R2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_24_R1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_24_R2_val_2.fq.gz Total number of sequences analysed: 53154280 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 231736 (0.44%) >>> Now running FastQC on the validated data zr3644_24_R1_val_1.fq.gz<<< Started analysis of zr3644_24_R1_val_1.fq.gz Approx 5% complete for zr3644_24_R1_val_1.fq.gz Approx 10% complete for zr3644_24_R1_val_1.fq.gz Approx 15% complete for zr3644_24_R1_val_1.fq.gz Approx 20% complete for zr3644_24_R1_val_1.fq.gz Approx 25% complete for zr3644_24_R1_val_1.fq.gz Approx 30% complete for zr3644_24_R1_val_1.fq.gz Approx 35% complete for zr3644_24_R1_val_1.fq.gz Approx 40% complete for zr3644_24_R1_val_1.fq.gz Approx 45% complete for zr3644_24_R1_val_1.fq.gz Approx 50% complete for zr3644_24_R1_val_1.fq.gz Approx 55% complete for zr3644_24_R1_val_1.fq.gz Approx 60% complete for zr3644_24_R1_val_1.fq.gz Approx 65% complete for zr3644_24_R1_val_1.fq.gz Approx 70% complete for zr3644_24_R1_val_1.fq.gz Approx 75% complete for zr3644_24_R1_val_1.fq.gz Approx 80% complete for zr3644_24_R1_val_1.fq.gz Approx 85% complete for zr3644_24_R1_val_1.fq.gz Approx 90% complete for zr3644_24_R1_val_1.fq.gz Approx 95% complete for zr3644_24_R1_val_1.fq.gz Analysis complete for zr3644_24_R1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_24_R2_val_2.fq.gz<<< Started analysis of zr3644_24_R2_val_2.fq.gz Approx 5% complete for zr3644_24_R2_val_2.fq.gz Approx 10% complete for zr3644_24_R2_val_2.fq.gz Approx 15% complete for zr3644_24_R2_val_2.fq.gz Approx 20% complete for zr3644_24_R2_val_2.fq.gz Approx 25% complete for zr3644_24_R2_val_2.fq.gz Approx 30% complete for zr3644_24_R2_val_2.fq.gz Approx 35% complete for zr3644_24_R2_val_2.fq.gz Approx 40% complete for zr3644_24_R2_val_2.fq.gz Approx 45% complete for zr3644_24_R2_val_2.fq.gz Approx 50% complete for zr3644_24_R2_val_2.fq.gz Approx 55% complete for zr3644_24_R2_val_2.fq.gz Approx 60% complete for zr3644_24_R2_val_2.fq.gz Approx 65% complete for zr3644_24_R2_val_2.fq.gz Approx 70% complete for zr3644_24_R2_val_2.fq.gz Approx 75% complete for zr3644_24_R2_val_2.fq.gz Approx 80% complete for zr3644_24_R2_val_2.fq.gz Approx 85% complete for zr3644_24_R2_val_2.fq.gz Approx 90% complete for zr3644_24_R2_val_2.fq.gz Approx 95% complete for zr3644_24_R2_val_2.fq.gz Analysis complete for zr3644_24_R2_val_2.fq.gz Deleting both intermediate output files zr3644_24_R1_trimmed.fq.gz and zr3644_24_R2_trimmed.fq.gz ==================================================================================================== [INFO ] multiqc : This is MultiQC v1.8 [INFO ] multiqc : Template : default [INFO ] multiqc : Searching : /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore [INFO ] cutadapt : Found 48 reports [INFO ] fastqc : Found 48 reports [INFO ] multiqc : Compressing plot data [WARNING] multiqc : Previous MultiQC output found! Adjusting filenames.. [WARNING] multiqc : Use -f or --force to overwrite existing reports instead [INFO ] multiqc : Report : multiqc_report_1.html [INFO ] multiqc : Data : multiqc_data_1 [INFO ] multiqc : MultiQC complete