SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_32psu_1_S5_L001_R2_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_32psu_1_S5_L001_R2_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 499.63 s (36 us/read; 1.68 M reads/minute). === Summary === Total reads processed: 14,000,021 Reads with adapters: 12,482,400 (89.2%) Reads written (passing filters): 14,000,021 (100.0%) Total basepairs processed: 2,100,003,150 bp Quality-trimmed: 11,507,684 bp (0.5%) Total written (filtered): 1,389,836,957 bp (66.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 12482400 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 26.9% C: 13.5% G: 25.9% T: 33.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 842057 3500005.2 0 842057 2 142966 875001.3 0 142966 3 90255 218750.3 0 90255 4 55571 54687.6 0 55571 5 57545 13671.9 0 57545 6 49671 3418.0 0 49671 7 41298 854.5 0 41298 8 59001 213.6 0 59001 9 47476 53.4 0 47315 161 10 53026 13.4 1 50683 2343 11 55985 3.3 1 52789 3196 12 57070 0.8 1 53792 3278 13 64601 0.2 1 61294 3307 14 62201 0.2 1 58283 3918 15 50727 0.2 1 47889 2838 16 74265 0.2 1 70212 4053 17 60248 0.2 1 56657 3591 18 57873 0.2 1 54797 3076 19 74512 0.2 1 70251 4261 20 70260 0.2 1 66610 3650 21 62230 0.2 1 58933 3297 22 72026 0.2 1 68190 3836 23 75580 0.2 1 71483 4097 24 76103 0.2 1 71906 4197 25 87020 0.2 1 82705 4315 26 72653 0.2 1 68640 4013 27 81722 0.2 1 76658 5064 28 76893 0.2 1 73629 3264 29 84223 0.2 1 79742 4481 30 83568 0.2 1 79746 3822 31 92428 0.2 1 87765 4663 32 83785 0.2 1 79986 3799 33 94083 0.2 1 89299 4784 34 124234 0.2 1 117883 6351 35 70662 0.2 1 67495 3167 36 97571 0.2 1 92509 5062 37 105963 0.2 1 100553 5410 38 100112 0.2 1 95880 4232 39 98883 0.2 1 94704 4179 40 111592 0.2 1 106078 5514 41 108482 0.2 1 103543 4939 42 113048 0.2 1 108097 4951 43 104564 0.2 1 100168 4396 44 122044 0.2 1 116433 5611 45 132901 0.2 1 126882 6019 46 96495 0.2 1 92302 4193 47 123777 0.2 1 118653 5124 48 123419 0.2 1 118253 5166 49 130090 0.2 1 124494 5596 50 124769 0.2 1 119306 5463 51 159790 0.2 1 152747 7043 52 114726 0.2 1 110175 4551 53 140573 0.2 1 135310 5263 54 107631 0.2 1 103512 4119 55 142110 0.2 1 137013 5097 56 148511 0.2 1 142711 5800 57 141596 0.2 1 136449 5147 58 138299 0.2 1 133566 4733 59 142121 0.2 1 137002 5119 60 148830 0.2 1 143312 5518 61 154735 0.2 1 148878 5857 62 170128 0.2 1 163868 6260 63 234733 0.2 1 226789 7944 64 212296 0.2 1 206143 6153 65 126771 0.2 1 122389 4382 66 138120 0.2 1 133306 4814 67 139286 0.2 1 134193 5093 68 141731 0.2 1 136845 4886 69 141571 0.2 1 136513 5058 70 151101 0.2 1 145752 5349 71 165000 0.2 1 159543 5457 72 156137 0.2 1 150635 5502 73 168957 0.2 1 163425 5532 74 155346 0.2 1 150282 5064 75 149711 0.2 1 144684 5027 76 146688 0.2 1 141765 4923 77 148035 0.2 1 142983 5052 78 144141 0.2 1 139293 4848 79 140116 0.2 1 135357 4759 80 139815 0.2 1 135255 4560 81 140275 0.2 1 135701 4574 82 136237 0.2 1 131702 4535 83 133248 0.2 1 128960 4288 84 130802 0.2 1 126388 4414 85 131118 0.2 1 126640 4478 86 132538 0.2 1 128154 4384 87 134528 0.2 1 130166 4362 88 132145 0.2 1 127913 4232 89 119589 0.2 1 115716 3873 90 116381 0.2 1 112493 3888 91 109945 0.2 1 106186 3759 92 104899 0.2 1 101501 3398 93 102752 0.2 1 99467 3285 94 100398 0.2 1 97258 3140 95 96752 0.2 1 93687 3065 96 92474 0.2 1 89641 2833 97 85160 0.2 1 82565 2595 98 81057 0.2 1 78431 2626 99 79148 0.2 1 76636 2512 100 72036 0.2 1 69758 2278 101 69452 0.2 1 67404 2048 102 66047 0.2 1 64053 1994 103 62024 0.2 1 60217 1807 104 59709 0.2 1 57936 1773 105 53244 0.2 1 51636 1608 106 48557 0.2 1 47145 1412 107 44301 0.2 1 42956 1345 108 40672 0.2 1 39383 1289 109 36835 0.2 1 35717 1118 110 34356 0.2 1 33352 1004 111 32280 0.2 1 31328 952 112 28083 0.2 1 27306 777 113 24882 0.2 1 24139 743 114 22038 0.2 1 21386 652 115 18554 0.2 1 17942 612 116 16085 0.2 1 15523 562 117 13238 0.2 1 12820 418 118 11657 0.2 1 11269 388 119 10199 0.2 1 9853 346 120 8562 0.2 1 8250 312 121 7440 0.2 1 7187 253 122 5970 0.2 1 5758 212 123 5287 0.2 1 5099 188 124 4439 0.2 1 4276 163 125 3716 0.2 1 3583 133 126 2906 0.2 1 2772 134 127 2521 0.2 1 2432 89 128 1926 0.2 1 1855 71 129 1631 0.2 1 1564 67 130 1264 0.2 1 1221 43 131 1080 0.2 1 1044 36 132 1051 0.2 1 1017 34 133 1128 0.2 1 1088 40 134 1229 0.2 1 1204 25 135 567 0.2 1 545 22 136 312 0.2 1 296 16 137 233 0.2 1 225 8 138 145 0.2 1 135 10 139 105 0.2 1 99 6 140 127 0.2 1 124 3 141 54 0.2 1 50 4 142 42 0.2 1 36 6 143 34 0.2 1 31 3 144 35 0.2 1 32 3 145 45 0.2 1 43 2 146 40 0.2 1 38 2 147 105 0.2 1 96 9 148 62 0.2 1 59 3 149 54 0.2 1 50 4 150 462 0.2 1 437 25 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_32psu_1_S5_L001_R2_001.fastq.gz ============================================= 14000021 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 21943 (0.2%)