SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_26psu_2_S10_L002_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_26psu_2_S10_L002_R2_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 772.54 s (42 us/read; 1.43 M reads/minute). === Summary === Total reads processed: 18,388,474 Reads with adapters: 14,677,085 (79.8%) Reads written (passing filters): 18,388,474 (100.0%) Total basepairs processed: 2,758,271,100 bp Quality-trimmed: 14,282,591 bp (0.5%) Total written (filtered): 2,101,274,280 bp (76.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14677085 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.7% C: 12.6% G: 24.2% T: 34.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2268778 4597118.5 0 2268778 2 320662 1149279.6 0 320662 3 193123 287319.9 0 193123 4 107505 71830.0 0 107505 5 98136 17957.5 0 98136 6 87605 4489.4 0 87605 7 69984 1122.3 0 69984 8 100736 280.6 0 100736 9 80882 70.1 0 80636 246 10 85130 17.5 1 79348 5782 11 93238 4.4 1 85689 7549 12 92545 1.1 1 85062 7483 13 106121 0.3 1 97648 8473 14 98586 0.3 1 90015 8571 15 79603 0.3 1 73456 6147 16 116674 0.3 1 107221 9453 17 98395 0.3 1 90346 8049 18 87513 0.3 1 80658 6855 19 114688 0.3 1 105582 9106 20 107373 0.3 1 99285 8088 21 94108 0.3 1 86828 7280 22 106536 0.3 1 98497 8039 23 113709 0.3 1 104976 8733 24 111940 0.3 1 103269 8671 25 127403 0.3 1 118648 8755 26 106762 0.3 1 98223 8539 27 118132 0.3 1 108645 9487 28 106930 0.3 1 99955 6975 29 120647 0.3 1 111606 9041 30 115537 0.3 1 107678 7859 31 127962 0.3 1 118733 9229 32 110371 0.3 1 102883 7488 33 128535 0.3 1 119135 9400 34 166074 0.3 1 154379 11695 35 88153 0.3 1 82039 6114 36 130243 0.3 1 120604 9639 37 137437 0.3 1 127611 9826 38 129360 0.3 1 121250 8110 39 122871 0.3 1 115373 7498 40 140913 0.3 1 131295 9618 41 137375 0.3 1 128487 8888 42 139853 0.3 1 130785 9068 43 126879 0.3 1 118647 8232 44 149301 0.3 1 139495 9806 45 151738 0.3 1 141722 10016 46 118782 0.3 1 111205 7577 47 144918 0.3 1 136263 8655 48 142402 0.3 1 133845 8557 49 148370 0.3 1 138956 9414 50 143101 0.3 1 133924 9177 51 175097 0.3 1 164092 11005 52 127562 0.3 1 119653 7909 53 156552 0.3 1 147706 8846 54 114039 0.3 1 107283 6756 55 151265 0.3 1 142708 8557 56 156754 0.3 1 146983 9771 57 149767 0.3 1 141656 8111 58 144481 0.3 1 136475 8006 59 145577 0.3 1 137588 7989 60 151210 0.3 1 142573 8637 61 154000 0.3 1 145457 8543 62 169208 0.3 1 159141 10067 63 223876 0.3 1 212453 11423 64 187828 0.3 1 179799 8029 65 121115 0.3 1 114588 6527 66 133231 0.3 1 126151 7080 67 130874 0.3 1 123245 7629 68 134376 0.3 1 127002 7374 69 132637 0.3 1 125114 7523 70 138657 0.3 1 130979 7678 71 148179 0.3 1 140033 8146 72 141424 0.3 1 133547 7877 73 147578 0.3 1 139587 7991 74 136704 0.3 1 129204 7500 75 129081 0.3 1 122024 7057 76 126400 0.3 1 119414 6986 77 125876 0.3 1 118871 7005 78 121079 0.3 1 114302 6777 79 116625 0.3 1 110208 6417 80 115718 0.3 1 109559 6159 81 115429 0.3 1 109090 6339 82 109791 0.3 1 103782 6009 83 107050 0.3 1 101360 5690 84 102872 0.3 1 97327 5545 85 102015 0.3 1 96553 5462 86 101949 0.3 1 96606 5343 87 102660 0.3 1 97419 5241 88 99584 0.3 1 94677 4907 89 90213 0.3 1 85644 4569 90 87335 0.3 1 82845 4490 91 81890 0.3 1 77745 4145 92 77363 0.3 1 73520 3843 93 73690 0.3 1 70013 3677 94 72610 0.3 1 68880 3730 95 68219 0.3 1 64684 3535 96 65235 0.3 1 61847 3388 97 59727 0.3 1 56753 2974 98 56047 0.3 1 53250 2797 99 53654 0.3 1 50884 2770 100 50544 0.3 1 48047 2497 101 46267 0.3 1 43991 2276 102 43012 0.3 1 40866 2146 103 39825 0.3 1 37849 1976 104 37894 0.3 1 35883 2011 105 33884 0.3 1 32215 1669 106 31153 0.3 1 29674 1479 107 28444 0.3 1 27053 1391 108 25994 0.3 1 24692 1302 109 23338 0.3 1 22212 1126 110 21606 0.3 1 20453 1153 111 20243 0.3 1 19234 1009 112 17922 0.3 1 16980 942 113 15507 0.3 1 14731 776 114 13757 0.3 1 13111 646 115 11617 0.3 1 11010 607 116 10230 0.3 1 9713 517 117 8353 0.3 1 7888 465 118 7422 0.3 1 7053 369 119 6284 0.3 1 5939 345 120 5303 0.3 1 5008 295 121 4751 0.3 1 4456 295 122 3933 0.3 1 3679 254 123 3312 0.3 1 3148 164 124 2831 0.3 1 2672 159 125 2374 0.3 1 2211 163 126 2009 0.3 1 1881 128 127 1689 0.3 1 1578 111 128 1328 0.3 1 1253 75 129 1073 0.3 1 1017 56 130 798 0.3 1 754 44 131 632 0.3 1 599 33 132 607 0.3 1 572 35 133 679 0.3 1 639 40 134 1080 0.3 1 1037 43 135 476 0.3 1 455 21 136 209 0.3 1 191 18 137 180 0.3 1 172 8 138 119 0.3 1 105 14 139 64 0.3 1 58 6 140 54 0.3 1 50 4 141 33 0.3 1 30 3 142 22 0.3 1 22 143 32 0.3 1 26 6 144 37 0.3 1 35 2 145 89 0.3 1 87 2 146 113 0.3 1 108 5 147 383 0.3 1 362 21 148 262 0.3 1 256 6 149 189 0.3 1 171 18 150 1406 0.3 1 1326 80 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_26psu_2_S10_L002_R2_001.fastq.gz ============================================= 18388474 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 27591 (0.2%)