SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/analyses/20190806_TrimGalore/Sealice_F1_S20_L001_R1_001_val_1.fq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection)) 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 7 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 7 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 7 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 7 bp from their 3' end to avoid poor qualities or biases Output file will be GZIP compressed This is cutadapt 1.16 with Python 3.6.8 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /Volumes/web/metacarcinus/Salmo_Calig/analyses/20190806_TrimGalore/Sealice_F1_S20_L001_R1_001_val_1.fq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 14125.09 s (125 us/read; 0.48 M reads/minute). === Summary === Total reads processed: 113,253,920 Reads with adapters: 32,901,059 (29.1%) Reads written (passing filters): 113,253,920 (100.0%) Total basepairs processed: 13,839,041,941 bp Quality-trimmed: 4,233,820 bp (0.0%) Total written (filtered): 13,791,013,279 bp (99.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 32901059 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 46.9% C: 10.9% G: 14.0% T: 28.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 27249332 28313480.0 0 27249332 2 3756099 7078370.0 0 3756099 3 1353389 1769592.5 0 1353389 4 339506 442398.1 0 339506 5 10944 110599.5 0 10944 6 3619 27649.9 0 3619 7 756 6912.5 0 756 8 2137 1728.1 0 2137 9 1436 432.0 0 600 836 10 5243 108.0 1 3042 2201 11 3617 27.0 1 690 2927 12 6645 6.8 1 1430 5215 13 9003 1.7 1 0 9003 14 11117 1.7 1 0 11117 15 22931 1.7 1 0 22931 16 57394 1.7 1 0 57394 17 43251 1.7 1 0 43251 18 3691 1.7 1 0 3691 19 640 1.7 1 0 640 20 422 1.7 1 0 422 21 457 1.7 1 0 457 22 442 1.7 1 0 442 23 456 1.7 1 0 456 24 517 1.7 1 0 517 25 639 1.7 1 0 639 26 712 1.7 1 0 712 27 481 1.7 1 0 481 28 504 1.7 1 0 504 29 474 1.7 1 0 474 30 541 1.7 1 0 541 31 595 1.7 1 0 595 32 522 1.7 1 0 522 33 468 1.7 1 0 468 34 409 1.7 1 0 409 35 312 1.7 1 0 312 36 282 1.7 1 0 282 37 289 1.7 1 0 289 38 259 1.7 1 0 259 39 280 1.7 1 0 280 40 258 1.7 1 0 258 41 286 1.7 1 0 286 42 272 1.7 1 0 272 43 247 1.7 1 0 247 44 287 1.7 1 0 287 45 268 1.7 1 0 268 46 299 1.7 1 0 299 47 264 1.7 1 0 264 48 256 1.7 1 0 256 49 304 1.7 1 0 304 50 251 1.7 1 0 251 51 278 1.7 1 0 278 52 224 1.7 1 0 224 53 238 1.7 1 0 238 54 252 1.7 1 0 252 55 250 1.7 1 0 250 56 277 1.7 1 0 277 57 224 1.7 1 0 224 58 236 1.7 1 0 236 59 231 1.7 1 0 231 60 242 1.7 1 0 242 61 229 1.7 1 0 229 62 240 1.7 1 0 240 63 212 1.7 1 0 212 64 224 1.7 1 0 224 65 189 1.7 1 0 189 66 185 1.7 1 0 185 67 230 1.7 1 0 230 68 214 1.7 1 0 214 69 198 1.7 1 0 198 70 201 1.7 1 0 201 71 186 1.7 1 0 186 72 191 1.7 1 0 191 73 162 1.7 1 0 162 74 165 1.7 1 0 165 75 169 1.7 1 0 169 76 168 1.7 1 0 168 77 151 1.7 1 0 151 78 154 1.7 1 0 154 79 117 1.7 1 0 117 80 141 1.7 1 0 141 81 106 1.7 1 0 106 82 109 1.7 1 0 109 83 108 1.7 1 0 108 84 102 1.7 1 0 102 85 114 1.7 1 0 114 86 102 1.7 1 0 102 87 109 1.7 1 0 109 88 105 1.7 1 0 105 89 105 1.7 1 0 105 90 81 1.7 1 0 81 91 82 1.7 1 0 82 92 82 1.7 1 0 82 93 52 1.7 1 0 52 94 63 1.7 1 0 63 95 46 1.7 1 0 46 96 53 1.7 1 0 53 97 56 1.7 1 0 56 98 56 1.7 1 0 56 99 48 1.7 1 0 48 100 44 1.7 1 0 44 101 53 1.7 1 0 53 102 38 1.7 1 0 38 103 48 1.7 1 0 48 104 27 1.7 1 0 27 105 38 1.7 1 0 38 106 29 1.7 1 0 29 107 29 1.7 1 0 29 108 22 1.7 1 0 22 109 18 1.7 1 0 18 110 17 1.7 1 0 17 111 8 1.7 1 0 8 112 12 1.7 1 0 12 113 11 1.7 1 0 11 114 15 1.7 1 0 15 115 8 1.7 1 0 8 116 18 1.7 1 0 18 117 9 1.7 1 0 9 118 14 1.7 1 0 14 119 11 1.7 1 0 11 120 5 1.7 1 0 5 121 4 1.7 1 0 4 122 3 1.7 1 0 3 123 4 1.7 1 0 4 124 4 1.7 1 0 4 125 2 1.7 1 0 2 126 2 1.7 1 0 2 127 3 1.7 1 0 3 128 1 1.7 1 0 1 130 1 1.7 1 0 1 131 1 1.7 1 0 1 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/analyses/20190806_TrimGalore/Sealice_F1_S20_L001_R1_001_val_1.fq.gz ============================================= 113253920 sequences processed in total