SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_26psu_1_S9_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_1_S9_L002_R2_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 779.38 s (43 us/read; 1.39 M reads/minute). === Summary === Total reads processed: 18,056,494 Reads with adapters: 13,833,491 (76.6%) Reads written (passing filters): 18,056,494 (100.0%) Total basepairs processed: 2,708,474,100 bp Quality-trimmed: 12,349,451 bp (0.5%) Total written (filtered): 2,141,212,582 bp (79.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 13833491 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.0% C: 12.5% G: 24.0% T: 34.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2568781 4514123.5 0 2568781 2 366057 1128530.9 0 366057 3 212077 282132.7 0 212077 4 115719 70533.2 0 115719 5 101735 17633.3 0 101735 6 89696 4408.3 0 89696 7 71264 1102.1 0 71264 8 102329 275.5 0 102329 9 81047 68.9 0 80732 315 10 86697 17.2 1 80878 5819 11 94697 4.3 1 87025 7672 12 93974 1.1 1 86609 7365 13 107111 0.3 1 98790 8321 14 98830 0.3 1 90363 8467 15 81863 0.3 1 75568 6295 16 116617 0.3 1 107560 9057 17 98434 0.3 1 90554 7880 18 88102 0.3 1 81367 6735 19 112551 0.3 1 103902 8649 20 106499 0.3 1 98559 7940 21 94529 0.3 1 87451 7078 22 105525 0.3 1 97752 7773 23 111250 0.3 1 102948 8302 24 110289 0.3 1 101801 8488 25 123454 0.3 1 115174 8280 26 102700 0.3 1 94614 8086 27 115670 0.3 1 106461 9209 28 103454 0.3 1 96996 6458 29 116676 0.3 1 108241 8435 30 110369 0.3 1 103124 7245 31 123948 0.3 1 115651 8297 32 105488 0.3 1 98700 6788 33 122972 0.3 1 114148 8824 34 158602 0.3 1 147860 10742 35 85176 0.3 1 79388 5788 36 121188 0.3 1 112686 8502 37 129603 0.3 1 120852 8751 38 121650 0.3 1 114412 7238 39 117499 0.3 1 110622 6877 40 132022 0.3 1 123436 8586 41 127439 0.3 1 119665 7774 42 130897 0.3 1 122691 8206 43 118466 0.3 1 111262 7204 44 136805 0.3 1 128115 8690 45 143267 0.3 1 134250 9017 46 105232 0.3 1 98689 6543 47 132632 0.3 1 125125 7507 48 128580 0.3 1 121138 7442 49 134590 0.3 1 126196 8394 50 129680 0.3 1 121594 8086 51 156936 0.3 1 147378 9558 52 115575 0.3 1 108787 6788 53 141220 0.3 1 133568 7652 54 104058 0.3 1 98240 5818 55 134625 0.3 1 127372 7253 56 138566 0.3 1 130360 8206 57 132925 0.3 1 126016 6909 58 127424 0.3 1 120849 6575 59 127371 0.3 1 120396 6975 60 132296 0.3 1 124969 7327 61 135056 0.3 1 127808 7248 62 146657 0.3 1 138388 8269 63 193947 0.3 1 184650 9297 64 155657 0.3 1 148867 6790 65 105922 0.3 1 100517 5405 66 114816 0.3 1 108826 5990 67 114246 0.3 1 108023 6223 68 115039 0.3 1 108957 6082 69 113573 0.3 1 107431 6142 70 118689 0.3 1 112276 6413 71 124010 0.3 1 117553 6457 72 118164 0.3 1 111917 6247 73 122662 0.3 1 116340 6322 74 113578 0.3 1 107524 6054 75 108812 0.3 1 102905 5907 76 105084 0.3 1 99284 5800 77 105545 0.3 1 99708 5837 78 100872 0.3 1 95568 5304 79 97026 0.3 1 91844 5182 80 95305 0.3 1 90356 4949 81 93857 0.3 1 89014 4843 82 90295 0.3 1 85582 4713 83 87301 0.3 1 82821 4480 84 85471 0.3 1 81218 4253 85 82978 0.3 1 78704 4274 86 82245 0.3 1 78140 4105 87 82525 0.3 1 78515 4010 88 80619 0.3 1 76785 3834 89 73370 0.3 1 69724 3646 90 70068 0.3 1 66584 3484 91 65835 0.3 1 62601 3234 92 61556 0.3 1 58566 2990 93 59482 0.3 1 56574 2908 94 57109 0.3 1 54269 2840 95 53973 0.3 1 51267 2706 96 51596 0.3 1 49048 2548 97 47434 0.3 1 45017 2417 98 44668 0.3 1 42540 2128 99 43184 0.3 1 41061 2123 100 40483 0.3 1 38511 1972 101 37015 0.3 1 35171 1844 102 34179 0.3 1 32525 1654 103 31254 0.3 1 29799 1455 104 30003 0.3 1 28488 1515 105 26714 0.3 1 25377 1337 106 24481 0.3 1 23332 1149 107 22254 0.3 1 21123 1131 108 20003 0.3 1 19023 980 109 18094 0.3 1 17150 944 110 16326 0.3 1 15479 847 111 15507 0.3 1 14783 724 112 13504 0.3 1 12807 697 113 11779 0.3 1 11204 575 114 10207 0.3 1 9684 523 115 8697 0.3 1 8286 411 116 7460 0.3 1 7104 356 117 6031 0.3 1 5703 328 118 5441 0.3 1 5182 259 119 4540 0.3 1 4315 225 120 3964 0.3 1 3742 222 121 3581 0.3 1 3393 188 122 2805 0.3 1 2657 148 123 2429 0.3 1 2278 151 124 2051 0.3 1 1954 97 125 1777 0.3 1 1683 94 126 1416 0.3 1 1338 78 127 1308 0.3 1 1214 94 128 919 0.3 1 855 64 129 823 0.3 1 781 42 130 653 0.3 1 614 39 131 581 0.3 1 548 33 132 573 0.3 1 541 32 133 789 0.3 1 754 35 134 1231 0.3 1 1179 52 135 458 0.3 1 447 11 136 175 0.3 1 164 11 137 112 0.3 1 103 9 138 94 0.3 1 84 10 139 57 0.3 1 53 4 140 65 0.3 1 58 7 141 32 0.3 1 29 3 142 35 0.3 1 31 4 143 17 0.3 1 15 2 144 11 0.3 1 9 2 145 30 0.3 1 28 2 146 19 0.3 1 19 147 64 0.3 1 61 3 148 47 0.3 1 44 3 149 34 0.3 1 32 2 150 415 0.3 1 377 38 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_26psu_1_S9_L002_R2_001.fastq.gz ============================================= 18056494 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 22077 (0.1%)