SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_26psu_1_S9_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_1_S9_L002_R1_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 742.92 s (41 us/read; 1.46 M reads/minute). === Summary === Total reads processed: 18,056,494 Reads with adapters: 13,928,110 (77.1%) Reads written (passing filters): 18,056,494 (100.0%) Total basepairs processed: 2,708,474,100 bp Quality-trimmed: 5,741,117 bp (0.2%) Total written (filtered): 2,137,545,368 bp (78.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 13928110 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.7% C: 14.8% G: 20.2% T: 34.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2529563 4514123.5 0 2529563 2 355142 1128530.9 0 355142 3 202264 282132.7 0 202264 4 116958 70533.2 0 116958 5 97699 17633.3 0 97699 6 92485 4408.3 0 92485 7 72663 1102.1 0 72663 8 94383 275.5 0 94383 9 92644 68.9 0 91510 1134 10 86522 17.2 1 80894 5628 11 97786 4.3 1 89346 8440 12 93298 1.1 1 86415 6883 13 95771 0.3 1 88325 7446 14 95946 0.3 1 88058 7888 15 101399 0.3 1 93509 7890 16 98158 0.3 1 89606 8552 17 122597 0.3 1 111303 11294 18 101750 0.3 1 94436 7314 19 86831 0.3 1 80395 6436 20 105075 0.3 1 97137 7938 21 118601 0.3 1 108999 9602 22 97228 0.3 1 90470 6758 23 116927 0.3 1 107741 9186 24 105532 0.3 1 95756 9776 25 113828 0.3 1 105061 8767 26 103778 0.3 1 96608 7170 27 117560 0.3 1 107874 9686 28 114336 0.3 1 105504 8832 29 122580 0.3 1 111680 10900 30 130099 0.3 1 121451 8648 31 97669 0.3 1 90483 7186 32 124295 0.3 1 114657 9638 33 112476 0.3 1 103286 9190 34 140784 0.3 1 128812 11972 35 103370 0.3 1 96154 7216 36 134329 0.3 1 122737 11592 37 117550 0.3 1 108946 8604 38 133588 0.3 1 123334 10254 39 130482 0.3 1 119347 11135 40 122686 0.3 1 113961 8725 41 145432 0.3 1 132894 12538 42 118079 0.3 1 107701 10378 43 189764 0.3 1 177939 11825 44 65407 0.3 1 59230 6177 45 132188 0.3 1 122729 9459 46 127290 0.3 1 117848 9442 47 135499 0.3 1 126055 9444 48 126038 0.3 1 116373 9665 49 142407 0.3 1 130956 11451 50 121520 0.3 1 113382 8138 51 130837 0.3 1 121331 9506 52 138254 0.3 1 127263 10991 53 150154 0.3 1 140134 10020 54 113941 0.3 1 105808 8133 55 137202 0.3 1 127382 9820 56 163618 0.3 1 152691 10927 57 113941 0.3 1 104904 9037 58 135543 0.3 1 127222 8321 59 114833 0.3 1 106375 8458 60 134934 0.3 1 125495 9439 61 131069 0.3 1 122212 8857 62 140049 0.3 1 130678 9371 63 118477 0.3 1 109768 8709 64 123661 0.3 1 115672 7989 65 136910 0.3 1 127445 9465 66 142766 0.3 1 132932 9834 67 155161 0.3 1 142407 12754 68 281796 0.3 1 266464 15332 69 68541 0.3 1 62954 5587 70 25774 0.3 1 21904 3870 71 70954 0.3 1 66131 4823 72 107448 0.3 1 100862 6586 73 114621 0.3 1 107221 7400 74 114007 0.3 1 106477 7530 75 113035 0.3 1 105200 7835 76 110785 0.3 1 102896 7889 77 110971 0.3 1 103289 7682 78 105110 0.3 1 97785 7325 79 103881 0.3 1 96578 7303 80 100380 0.3 1 93184 7196 81 99197 0.3 1 92210 6987 82 96750 0.3 1 90051 6699 83 92818 0.3 1 86379 6439 84 91340 0.3 1 84942 6398 85 87669 0.3 1 81553 6116 86 83869 0.3 1 77984 5885 87 80883 0.3 1 75364 5519 88 79450 0.3 1 73820 5630 89 76461 0.3 1 71121 5340 90 75182 0.3 1 69973 5209 91 71175 0.3 1 66391 4784 92 67480 0.3 1 62890 4590 93 64001 0.3 1 59615 4386 94 61685 0.3 1 57457 4228 95 57220 0.3 1 53201 4019 96 54819 0.3 1 51015 3804 97 51023 0.3 1 47551 3472 98 47615 0.3 1 44173 3442 99 45999 0.3 1 42533 3466 100 42439 0.3 1 39454 2985 101 39032 0.3 1 36135 2897 102 36673 0.3 1 33901 2772 103 33569 0.3 1 31176 2393 104 31500 0.3 1 29209 2291 105 28075 0.3 1 26011 2064 106 25509 0.3 1 23615 1894 107 23441 0.3 1 21761 1680 108 21666 0.3 1 19921 1745 109 19354 0.3 1 17847 1507 110 17443 0.3 1 16060 1383 111 15864 0.3 1 14569 1295 112 13943 0.3 1 12833 1110 113 12164 0.3 1 11191 973 114 10656 0.3 1 9783 873 115 9192 0.3 1 8432 760 116 8137 0.3 1 7437 700 117 6646 0.3 1 6079 567 118 6028 0.3 1 5475 553 119 4941 0.3 1 4488 453 120 4276 0.3 1 3914 362 121 3804 0.3 1 3440 364 122 2994 0.3 1 2656 338 123 2568 0.3 1 2298 270 124 2204 0.3 1 2017 187 125 1837 0.3 1 1657 180 126 1524 0.3 1 1357 167 127 1388 0.3 1 1226 162 128 1017 0.3 1 890 127 129 886 0.3 1 773 113 130 713 0.3 1 646 67 131 614 0.3 1 547 67 132 610 0.3 1 554 56 133 738 0.3 1 662 76 134 1198 0.3 1 1126 72 135 479 0.3 1 433 46 136 180 0.3 1 151 29 137 120 0.3 1 102 18 138 100 0.3 1 79 21 139 54 0.3 1 43 11 140 63 0.3 1 49 14 141 34 0.3 1 27 7 142 36 0.3 1 27 9 143 19 0.3 1 17 2 144 13 0.3 1 11 2 145 29 0.3 1 22 7 146 21 0.3 1 18 3 147 72 0.3 1 61 11 148 53 0.3 1 46 7 149 48 0.3 1 42 6 150 601 0.3 1 530 71 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_26psu_1_S9_L002_R1_001.fastq.gz ============================================= 18056494 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 5143 (0.0%)