SUMMARISING RUN PARAMETERS ========================== Input filename: /Users/strigg/Desktop/Salmo_Calig/8C_26psu_2_S10_L001_R2_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.6.0 Cutadapt version: 2.4 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; auto-detected) 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 5 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 5 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /Users/strigg/Desktop/Salmo_Calig/TRIM/FASTQC Output file will be GZIP compressed This is cutadapt 2.4 with Python 3.6.8 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /Users/strigg/Desktop/Salmo_Calig/8C_26psu_2_S10_L001_R2_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 708.77 s (38 us/read; 1.56 M reads/minute). === Summary === Total reads processed: 18,482,577 Reads with adapters: 14,753,598 (79.8%) Reads written (passing filters): 18,482,577 (100.0%) Total basepairs processed: 2,772,386,550 bp Quality-trimmed: 14,899,580 bp (0.5%) Total written (filtered): 2,113,888,686 bp (76.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14753598 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.7% C: 12.5% G: 24.2% T: 34.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2286581 4620644.2 0 2286581 2 330310 1155161.1 0 330310 3 190033 288790.3 0 190033 4 111417 72197.6 0 111417 5 101556 18049.4 0 101556 6 87150 4512.3 0 87150 7 71559 1128.1 0 71559 8 101450 282.0 0 101450 9 81706 70.5 0 81446 260 10 88967 17.6 1 84555 4412 11 93801 4.4 1 88117 5684 12 95662 1.1 1 89704 5958 13 105924 0.3 1 99758 6166 14 100634 0.3 1 93826 6808 15 81502 0.3 1 76286 5216 16 118419 0.3 1 111030 7389 17 95042 0.3 1 88712 6330 18 90615 0.3 1 85225 5390 19 115837 0.3 1 108486 7351 20 108535 0.3 1 102151 6384 21 96158 0.3 1 90241 5917 22 109681 0.3 1 102998 6683 23 113064 0.3 1 106255 6809 24 112402 0.3 1 105369 7033 25 127609 0.3 1 120247 7362 26 106198 0.3 1 99534 6664 27 117379 0.3 1 109394 7985 28 111310 0.3 1 105607 5703 29 119257 0.3 1 111876 7381 30 117422 0.3 1 111230 6192 31 127799 0.3 1 120363 7436 32 115547 0.3 1 109515 6032 33 127479 0.3 1 119672 7807 34 163653 0.3 1 154089 9564 35 93410 0.3 1 88452 4958 36 129603 0.3 1 121811 7792 37 138172 0.3 1 130055 8117 38 129571 0.3 1 123089 6482 39 126899 0.3 1 120584 6315 40 141131 0.3 1 133007 8124 41 136856 0.3 1 129602 7254 42 140475 0.3 1 133264 7211 43 128682 0.3 1 121911 6771 44 148231 0.3 1 140352 7879 45 152393 0.3 1 144497 7896 46 120446 0.3 1 114128 6318 47 146135 0.3 1 138949 7186 48 143271 0.3 1 136268 7003 49 150045 0.3 1 142543 7502 50 141618 0.3 1 134295 7323 51 177184 0.3 1 168273 8911 52 127868 0.3 1 121986 5882 53 154234 0.3 1 147269 6965 54 117590 0.3 1 112052 5538 55 152743 0.3 1 146054 6689 56 157680 0.3 1 150094 7586 57 149551 0.3 1 143020 6531 58 143483 0.3 1 137470 6013 59 145998 0.3 1 139352 6646 60 151232 0.3 1 144310 6922 61 157550 0.3 1 150162 7388 62 169489 0.3 1 161516 7973 63 228128 0.3 1 218668 9460 64 191978 0.3 1 184960 7018 65 121739 0.3 1 116395 5344 66 132352 0.3 1 126524 5828 67 131028 0.3 1 125146 5882 68 132829 0.3 1 127004 5825 69 131726 0.3 1 125866 5860 70 137789 0.3 1 131635 6154 71 147946 0.3 1 141769 6177 72 139415 0.3 1 133242 6173 73 148725 0.3 1 142498 6227 74 135207 0.3 1 129643 5564 75 128520 0.3 1 123034 5486 76 126065 0.3 1 120765 5300 77 126228 0.3 1 120717 5511 78 120120 0.3 1 114978 5142 79 115495 0.3 1 110595 4900 80 116213 0.3 1 111348 4865 81 114795 0.3 1 109987 4808 82 110451 0.3 1 105814 4637 83 106907 0.3 1 102515 4392 84 102431 0.3 1 98006 4425 85 101678 0.3 1 97283 4395 86 102018 0.3 1 97662 4356 87 102379 0.3 1 98265 4114 88 100269 0.3 1 95923 4346 89 89766 0.3 1 85935 3831 90 86353 0.3 1 82825 3528 91 80857 0.3 1 77356 3501 92 76306 0.3 1 73107 3199 93 73595 0.3 1 70492 3103 94 71587 0.3 1 68546 3041 95 68110 0.3 1 65320 2790 96 64867 0.3 1 62264 2603 97 59245 0.3 1 56835 2410 98 55305 0.3 1 52942 2363 99 53891 0.3 1 51732 2159 100 50005 0.3 1 47952 2053 101 45894 0.3 1 44011 1883 102 43298 0.3 1 41576 1722 103 39322 0.3 1 37781 1541 104 38059 0.3 1 36523 1536 105 33918 0.3 1 32538 1380 106 31438 0.3 1 30241 1197 107 28204 0.3 1 27113 1091 108 26258 0.3 1 25170 1088 109 23534 0.3 1 22556 978 110 21525 0.3 1 20673 852 111 20335 0.3 1 19508 827 112 17540 0.3 1 16818 722 113 15580 0.3 1 14966 614 114 13626 0.3 1 13076 550 115 11545 0.3 1 11044 501 116 9893 0.3 1 9487 406 117 8220 0.3 1 7857 363 118 7416 0.3 1 7106 310 119 6364 0.3 1 6067 297 120 5214 0.3 1 4965 249 121 4800 0.3 1 4601 199 122 3856 0.3 1 3683 173 123 3424 0.3 1 3271 153 124 2951 0.3 1 2795 156 125 2462 0.3 1 2355 107 126 2026 0.3 1 1922 104 127 1586 0.3 1 1509 77 128 1233 0.3 1 1162 71 129 1142 0.3 1 1091 51 130 841 0.3 1 788 53 131 705 0.3 1 671 34 132 609 0.3 1 572 37 133 673 0.3 1 638 35 134 1003 0.3 1 960 43 135 407 0.3 1 396 11 136 221 0.3 1 202 19 137 162 0.3 1 156 6 138 117 0.3 1 109 8 139 71 0.3 1 63 8 140 67 0.3 1 63 4 141 48 0.3 1 47 1 142 50 0.3 1 49 1 143 41 0.3 1 37 4 144 23 0.3 1 20 3 145 62 0.3 1 59 3 146 126 0.3 1 123 3 147 381 0.3 1 366 15 148 234 0.3 1 226 8 149 166 0.3 1 155 11 150 1412 0.3 1 1344 68 RUN STATISTICS FOR INPUT FILE: /Users/strigg/Desktop/Salmo_Calig/8C_26psu_2_S10_L001_R2_001.fastq.gz ============================================= 18482577 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 18482577 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 43255 (0.23%)