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 will be GZIP compressed 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