SUMMARISING RUN PARAMETERS ========================== Input filename: /Users/strigg/Desktop/Salmo_Calig/16C_32psu_3_S3_L001_R1_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/16C_32psu_3_S3_L001_R1_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 468.61 s (34 us/read; 1.75 M reads/minute). === Summary === Total reads processed: 13,688,650 Reads with adapters: 11,692,195 (85.4%) Reads written (passing filters): 13,688,650 (100.0%) Total basepairs processed: 2,053,297,500 bp Quality-trimmed: 4,119,462 bp (0.2%) Total written (filtered): 1,465,023,732 bp (71.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11692195 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.2% C: 13.5% G: 21.8% T: 35.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 1153280 3422162.5 0 1153280 2 188115 855540.6 0 188115 3 111422 213885.2 0 111422 4 69723 53471.3 0 69723 5 62088 13367.8 0 62088 6 60662 3342.0 0 60662 7 51512 835.5 0 51512 8 64264 208.9 0 64264 9 63671 52.2 0 62836 835 10 60542 13.1 1 57278 3264 11 67613 3.3 1 62345 5268 12 65175 0.8 1 60838 4337 13 67473 0.2 1 62952 4521 14 68261 0.2 1 63487 4774 15 72178 0.2 1 67286 4892 16 70299 0.2 1 65086 5213 17 86060 0.2 1 78938 7122 18 74650 0.2 1 70063 4587 19 65040 0.2 1 60840 4200 20 78366 0.2 1 73149 5217 21 84846 0.2 1 78850 5996 22 74487 0.2 1 70107 4380 23 86083 0.2 1 80316 5767 24 80721 0.2 1 73972 6749 25 87753 0.2 1 81677 6076 26 80514 0.2 1 75647 4867 27 90438 0.2 1 83662 6776 28 90174 0.2 1 83716 6458 29 93389 0.2 1 85784 7605 30 100786 0.2 1 94960 5826 31 81881 0.2 1 76679 5202 32 98375 0.2 1 91951 6424 33 93955 0.2 1 87212 6743 34 99759 0.2 1 92551 7208 35 105302 0.2 1 98208 7094 36 99885 0.2 1 93387 6498 37 106334 0.2 1 98270 8064 38 113806 0.2 1 106308 7498 39 98325 0.2 1 92047 6278 40 111911 0.2 1 104331 7580 41 123334 0.2 1 114370 8964 42 99813 0.2 1 92381 7432 43 174315 0.2 1 165200 9115 44 51463 0.2 1 46797 4666 45 117571 0.2 1 110330 7241 46 111696 0.2 1 104449 7247 47 119263 0.2 1 111850 7413 48 117185 0.2 1 109504 7681 49 129249 0.2 1 119912 9337 50 113265 0.2 1 106460 6805 51 123578 0.2 1 115577 8001 52 126860 0.2 1 117703 9157 53 136778 0.2 1 128183 8595 54 111542 0.2 1 104628 6914 55 130509 0.2 1 122033 8476 56 160806 0.2 1 151398 9408 57 105238 0.2 1 97627 7611 58 136703 0.2 1 129347 7356 59 118654 0.2 1 110900 7754 60 133349 0.2 1 124657 8692 61 131151 0.2 1 123141 8010 62 146081 0.2 1 137646 8435 63 116527 0.2 1 108569 7958 64 131388 0.2 1 123568 7820 65 146211 0.2 1 137343 8868 66 153623 0.2 1 144098 9525 67 163622 0.2 1 150969 12653 68 316517 0.2 1 301519 14998 69 50118 0.2 1 45752 4366 70 19043 0.2 1 15441 3602 71 86203 0.2 1 80944 5259 72 120080 0.2 1 113140 6940 73 127657 0.2 1 119892 7765 74 126886 0.2 1 119284 7602 75 126438 0.2 1 118691 7747 76 124650 0.2 1 117103 7547 77 126032 0.2 1 118426 7606 78 119720 0.2 1 112423 7297 79 118994 0.2 1 111880 7114 80 116560 0.2 1 109502 7058 81 114889 0.2 1 107938 6951 82 112663 0.2 1 105830 6833 83 109839 0.2 1 103073 6766 84 105779 0.2 1 99490 6289 85 104543 0.2 1 98380 6163 86 100937 0.2 1 94813 6124 87 97367 0.2 1 91433 5934 88 96957 0.2 1 90929 6028 89 91739 0.2 1 86072 5667 90 91064 0.2 1 85580 5484 91 86291 0.2 1 80995 5296 92 83034 0.2 1 77959 5075 93 78558 0.2 1 73687 4871 94 75965 0.2 1 71248 4717 95 70608 0.2 1 66214 4394 96 66613 0.2 1 62491 4122 97 63167 0.2 1 59156 4011 98 59278 0.2 1 55535 3743 99 58315 0.2 1 54380 3935 100 52512 0.2 1 49178 3334 101 49162 0.2 1 45965 3197 102 45067 0.2 1 42105 2962 103 41984 0.2 1 39185 2799 104 39240 0.2 1 36628 2612 105 34957 0.2 1 32577 2380 106 31819 0.2 1 29724 2095 107 29159 0.2 1 27051 2108 108 27128 0.2 1 25184 1944 109 24322 0.2 1 22614 1708 110 21994 0.2 1 20354 1640 111 19565 0.2 1 18156 1409 112 17167 0.2 1 15854 1313 113 14819 0.2 1 13686 1133 114 13381 0.2 1 12379 1002 115 11437 0.2 1 10576 861 116 9792 0.2 1 9003 789 117 8262 0.2 1 7551 711 118 7359 0.2 1 6738 621 119 6022 0.2 1 5480 542 120 5103 0.2 1 4650 453 121 4422 0.2 1 4023 399 122 3603 0.2 1 3261 342 123 3138 0.2 1 2830 308 124 2526 0.2 1 2281 245 125 2064 0.2 1 1886 178 126 1770 0.2 1 1574 196 127 1476 0.2 1 1324 152 128 1074 0.2 1 953 121 129 984 0.2 1 870 114 130 708 0.2 1 638 70 131 577 0.2 1 522 55 132 547 0.2 1 477 70 133 519 0.2 1 468 51 134 567 0.2 1 518 49 135 307 0.2 1 275 32 136 217 0.2 1 195 22 137 172 0.2 1 148 24 138 111 0.2 1 95 16 139 77 0.2 1 67 10 140 52 0.2 1 47 5 141 43 0.2 1 38 5 142 44 0.2 1 33 11 143 50 0.2 1 44 6 144 49 0.2 1 46 3 145 55 0.2 1 44 11 146 89 0.2 1 78 11 147 261 0.2 1 233 28 148 216 0.2 1 199 17 149 67 0.2 1 64 3 150 763 0.2 1 633 130 RUN STATISTICS FOR INPUT FILE: /Users/strigg/Desktop/Salmo_Calig/16C_32psu_3_S3_L001_R1_001.fastq.gz ============================================= 13688650 sequences processed in total