SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/analyses/20190806_TrimGalore/Sealice_F1_S20_L001_R2_001_val_2.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_R2_001_val_2.fq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 43396.28 s (383 us/read; 0.16 M reads/minute). === Summary === Total reads processed: 113,253,920 Reads with adapters: 34,655,811 (30.6%) Reads written (passing filters): 113,253,920 (100.0%) Total basepairs processed: 13,863,655,209 bp Quality-trimmed: 9,198,051 bp (0.1%) Total written (filtered): 13,807,908,392 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 34655811 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 49.8% C: 11.2% G: 12.6% T: 26.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 28202874 28313480.0 0 28202874 2 4517996 7078370.0 0 4517996 3 1382508 1769592.5 0 1382508 4 316842 442398.1 0 316842 5 10124 110599.5 0 10124 6 3888 27649.9 0 3888 7 950 6912.5 0 950 8 3434 1728.1 0 3434 9 2078 432.0 0 859 1219 10 7426 108.0 1 4140 3286 11 5381 27.0 1 1087 4294 12 9914 6.8 1 2122 7792 13 10263 1.7 1 0 10263 14 15009 1.7 1 0 15009 15 34126 1.7 1 0 34126 16 72970 1.7 1 0 72970 17 39934 1.7 1 0 39934 18 3972 1.7 1 0 3972 19 625 1.7 1 0 625 20 374 1.7 1 0 374 21 333 1.7 1 0 333 22 300 1.7 1 0 300 23 349 1.7 1 0 349 24 471 1.7 1 0 471 25 725 1.7 1 0 725 26 587 1.7 1 0 587 27 406 1.7 1 0 406 28 441 1.7 1 0 441 29 430 1.7 1 0 430 30 455 1.7 1 0 455 31 438 1.7 1 0 438 32 458 1.7 1 0 458 33 392 1.7 1 0 392 34 328 1.7 1 0 328 35 234 1.7 1 0 234 36 217 1.7 1 0 217 37 209 1.7 1 0 209 38 201 1.7 1 0 201 39 157 1.7 1 0 157 40 179 1.7 1 0 179 41 179 1.7 1 0 179 42 181 1.7 1 0 181 43 201 1.7 1 0 201 44 171 1.7 1 0 171 45 174 1.7 1 0 174 46 182 1.7 1 0 182 47 208 1.7 1 0 208 48 190 1.7 1 0 190 49 196 1.7 1 0 196 50 194 1.7 1 0 194 51 178 1.7 1 0 178 52 193 1.7 1 0 193 53 192 1.7 1 0 192 54 162 1.7 1 0 162 55 203 1.7 1 0 203 56 173 1.7 1 0 173 57 184 1.7 1 0 184 58 165 1.7 1 0 165 59 149 1.7 1 0 149 60 162 1.7 1 0 162 61 181 1.7 1 0 181 62 172 1.7 1 0 172 63 192 1.7 1 0 192 64 166 1.7 1 0 166 65 138 1.7 1 0 138 66 117 1.7 1 0 117 67 148 1.7 1 0 148 68 151 1.7 1 0 151 69 141 1.7 1 0 141 70 139 1.7 1 0 139 71 96 1.7 1 0 96 72 138 1.7 1 0 138 73 131 1.7 1 0 131 74 133 1.7 1 0 133 75 122 1.7 1 0 122 76 107 1.7 1 0 107 77 104 1.7 1 0 104 78 91 1.7 1 0 91 79 86 1.7 1 0 86 80 92 1.7 1 0 92 81 86 1.7 1 0 86 82 85 1.7 1 0 85 83 84 1.7 1 0 84 84 88 1.7 1 0 88 85 71 1.7 1 0 71 86 64 1.7 1 0 64 87 67 1.7 1 0 67 88 54 1.7 1 0 54 89 59 1.7 1 0 59 90 61 1.7 1 0 61 91 55 1.7 1 0 55 92 45 1.7 1 0 45 93 56 1.7 1 0 56 94 36 1.7 1 0 36 95 48 1.7 1 0 48 96 43 1.7 1 0 43 97 36 1.7 1 0 36 98 35 1.7 1 0 35 99 38 1.7 1 0 38 100 38 1.7 1 0 38 101 21 1.7 1 0 21 102 27 1.7 1 0 27 103 29 1.7 1 0 29 104 37 1.7 1 0 37 105 24 1.7 1 0 24 106 18 1.7 1 0 18 107 25 1.7 1 0 25 108 12 1.7 1 0 12 109 17 1.7 1 0 17 110 26 1.7 1 0 26 111 15 1.7 1 0 15 112 12 1.7 1 0 12 113 17 1.7 1 0 17 114 13 1.7 1 0 13 115 12 1.7 1 0 12 116 7 1.7 1 0 7 117 7 1.7 1 0 7 118 10 1.7 1 0 10 119 6 1.7 1 0 6 120 9 1.7 1 0 9 121 10 1.7 1 0 10 122 8 1.7 1 0 8 123 1 1.7 1 0 1 124 8 1.7 1 0 8 125 2 1.7 1 0 2 126 6 1.7 1 0 6 129 1 1.7 1 0 1 130 2 1.7 1 0 2 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/analyses/20190806_TrimGalore/Sealice_F1_S20_L001_R2_001_val_2.fq.gz ============================================= 113253920 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 113253920 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 454584 (0.40%)