SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_26psu_3_S11_L002_R1_001.fastq.gz Trimming mode: single-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; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length before a sequence gets removed: 20 bp Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /Volumes/web/metacarcinus/Salmo_Calig/analyses/20190722/TRIM_adapt/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 /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_26psu_3_S11_L002_R1_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 637.91 s (37 us/read; 1.62 M reads/minute). === Summary === Total reads processed: 17,175,482 Reads with adapters: 14,848,929 (86.5%) Reads written (passing filters): 17,175,482 (100.0%) Total basepairs processed: 2,576,322,300 bp Quality-trimmed: 5,047,974 bp (0.2%) Total written (filtered): 1,818,633,191 bp (70.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14848929 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.8% C: 14.0% G: 22.1% T: 35.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 1338924 4293870.5 0 1338924 2 219387 1073467.6 0 219387 3 135027 268366.9 0 135027 4 85370 67091.7 0 85370 5 77474 16772.9 0 77474 6 77037 4193.2 0 77037 7 61988 1048.3 0 61988 8 79862 262.1 0 79862 9 79304 65.5 0 78415 889 10 74894 16.4 1 70380 4514 11 85385 4.1 1 78459 6926 12 81941 1.0 1 76091 5850 13 85904 0.3 1 79720 6184 14 83830 0.3 1 77435 6395 15 91251 0.3 1 84448 6803 16 87362 0.3 1 80132 7230 17 108027 0.3 1 98268 9759 18 97765 0.3 1 91194 6571 19 79668 0.3 1 74013 5655 20 98415 0.3 1 91325 7090 21 108861 0.3 1 100754 8107 22 92432 0.3 1 86497 5935 23 109093 0.3 1 101170 7923 24 102961 0.3 1 94241 8720 25 110529 0.3 1 102334 8195 26 102489 0.3 1 95783 6706 27 115669 0.3 1 106602 9067 28 113524 0.3 1 105254 8270 29 122345 0.3 1 111712 10633 30 129585 0.3 1 121424 8161 31 102733 0.3 1 95540 7193 32 124071 0.3 1 115107 8964 33 119235 0.3 1 110316 8919 34 135312 0.3 1 123053 12259 35 144848 0.3 1 135072 9776 36 111252 0.3 1 103350 7902 37 137690 0.3 1 126540 11150 38 183318 0.3 1 172054 11264 39 89425 0.3 1 80789 8636 40 143455 0.3 1 132529 10926 41 167032 0.3 1 153468 13564 42 121530 0.3 1 111758 9772 43 226339 0.3 1 213169 13170 44 63952 0.3 1 57726 6226 45 153236 0.3 1 142659 10577 46 145389 0.3 1 135235 10154 47 153266 0.3 1 143025 10241 48 152876 0.3 1 141831 11045 49 168461 0.3 1 156017 12444 50 143668 0.3 1 134304 9364 51 158306 0.3 1 147182 11124 52 165500 0.3 1 153119 12381 53 177823 0.3 1 165831 11992 54 142891 0.3 1 133186 9705 55 170342 0.3 1 158433 11909 56 212493 0.3 1 198685 13808 57 130099 0.3 1 120181 9918 58 177795 0.3 1 167072 10723 59 156878 0.3 1 145935 10943 60 169887 0.3 1 158157 11730 61 170084 0.3 1 159037 11047 62 189821 0.3 1 177611 12210 63 149110 0.3 1 138396 10714 64 169980 0.3 1 159400 10580 65 190750 0.3 1 178067 12683 66 196470 0.3 1 183447 13023 67 212313 0.3 1 195505 16808 68 400251 0.3 1 379902 20349 69 75488 0.3 1 68954 6534 70 29970 0.3 1 25043 4927 71 114346 0.3 1 107216 7130 72 155823 0.3 1 146728 9095 73 164934 0.3 1 154662 10272 74 163683 0.3 1 153217 10466 75 161985 0.3 1 151549 10436 76 161854 0.3 1 151132 10722 77 161503 0.3 1 151032 10471 78 154856 0.3 1 144180 10676 79 152863 0.3 1 142631 10232 80 150353 0.3 1 140171 10182 81 150454 0.3 1 140509 9945 82 145676 0.3 1 135805 9871 83 141824 0.3 1 132558 9266 84 137190 0.3 1 128021 9169 85 134663 0.3 1 125634 9029 86 130352 0.3 1 121592 8760 87 125876 0.3 1 117794 8082 88 125030 0.3 1 116803 8227 89 117792 0.3 1 109945 7847 90 117830 0.3 1 110051 7779 91 112910 0.3 1 105546 7364 92 106310 0.3 1 99476 6834 93 100338 0.3 1 93657 6681 94 97374 0.3 1 90887 6487 95 91711 0.3 1 85495 6216 96 86651 0.3 1 80705 5946 97 81512 0.3 1 76160 5352 98 75813 0.3 1 70557 5256 99 73615 0.3 1 68470 5145 100 67314 0.3 1 62734 4580 101 63335 0.3 1 58922 4413 102 58250 0.3 1 54144 4106 103 54120 0.3 1 50374 3746 104 50265 0.3 1 46857 3408 105 44626 0.3 1 41570 3056 106 40793 0.3 1 37936 2857 107 37321 0.3 1 34670 2651 108 34705 0.3 1 32091 2614 109 31002 0.3 1 28677 2325 110 27578 0.3 1 25574 2004 111 24603 0.3 1 22785 1818 112 21972 0.3 1 20247 1725 113 18720 0.3 1 17311 1409 114 16688 0.3 1 15435 1253 115 14432 0.3 1 13232 1200 116 12245 0.3 1 11232 1013 117 10552 0.3 1 9672 880 118 8984 0.3 1 8244 740 119 7381 0.3 1 6703 678 120 6463 0.3 1 5860 603 121 5515 0.3 1 4963 552 122 4409 0.3 1 4006 403 123 3731 0.3 1 3377 354 124 3097 0.3 1 2824 273 125 2558 0.3 1 2286 272 126 2102 0.3 1 1889 213 127 1729 0.3 1 1530 199 128 1388 0.3 1 1248 140 129 1146 0.3 1 1007 139 130 884 0.3 1 785 99 131 740 0.3 1 651 89 132 734 0.3 1 647 87 133 973 0.3 1 886 87 134 1537 0.3 1 1449 88 135 609 0.3 1 551 58 136 234 0.3 1 208 26 137 157 0.3 1 138 19 138 104 0.3 1 87 17 139 80 0.3 1 60 20 140 68 0.3 1 51 17 141 33 0.3 1 25 8 142 34 0.3 1 26 8 143 16 0.3 1 16 144 16 0.3 1 14 2 145 39 0.3 1 27 12 146 32 0.3 1 26 6 147 85 0.3 1 77 8 148 60 0.3 1 51 9 149 55 0.3 1 49 6 150 652 0.3 1 552 100 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_26psu_3_S11_L002_R1_001.fastq.gz ============================================= 17175482 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 6308 (0.0%)