SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_32psu_3_S3_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/16C_32psu_3_S3_L001_R2_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 535.60 s (39 us/read; 1.53 M reads/minute). === Summary === Total reads processed: 13,688,650 Reads with adapters: 11,592,048 (84.7%) Reads written (passing filters): 13,688,650 (100.0%) Total basepairs processed: 2,053,297,500 bp Quality-trimmed: 12,031,923 bp (0.6%) Total written (filtered): 1,469,819,891 bp (71.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11592048 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.6% C: 12.3% G: 24.9% T: 34.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 1214265 3422162.5 0 1214265 2 193972 855540.6 0 193972 3 118499 213885.2 0 118499 4 69716 53471.3 0 69716 5 68874 13367.8 0 68874 6 59538 3342.0 0 59538 7 48194 835.5 0 48194 8 70200 208.9 0 70200 9 54828 52.2 0 54657 171 10 61679 13.1 1 58439 3240 11 64699 3.3 1 60413 4286 12 66050 0.8 1 61625 4425 13 73701 0.2 1 69161 4540 14 72487 0.2 1 67153 5334 15 56503 0.2 1 52652 3851 16 83460 0.2 1 77990 5470 17 68575 0.2 1 63675 4900 18 63646 0.2 1 59572 4074 19 84575 0.2 1 78822 5753 20 78107 0.2 1 73276 4831 21 67477 0.2 1 63200 4277 22 79410 0.2 1 74414 4996 23 81981 0.2 1 76795 5186 24 83330 0.2 1 77735 5595 25 95526 0.2 1 89714 5812 26 78503 0.2 1 73254 5249 27 85319 0.2 1 79062 6257 28 83102 0.2 1 78541 4561 29 88168 0.2 1 82573 5595 30 89538 0.2 1 84298 5240 31 96658 0.2 1 90668 5990 32 88293 0.2 1 83312 4981 33 97915 0.2 1 91746 6169 34 124838 0.2 1 117069 7769 35 74005 0.2 1 69745 4260 36 101096 0.2 1 94692 6404 37 106262 0.2 1 99713 6549 38 101787 0.2 1 96374 5413 39 98728 0.2 1 93495 5233 40 111334 0.2 1 104562 6772 41 108250 0.2 1 102276 5974 42 114250 0.2 1 107889 6361 43 101869 0.2 1 96202 5667 44 119468 0.2 1 112651 6817 45 134184 0.2 1 126701 7483 46 88069 0.2 1 83261 4808 47 117053 0.2 1 110868 6185 48 117366 0.2 1 111327 6039 49 124438 0.2 1 117817 6621 50 117444 0.2 1 111059 6385 51 154247 0.2 1 146044 8203 52 106291 0.2 1 100997 5294 53 129680 0.2 1 123785 5895 54 97816 0.2 1 92887 4929 55 130824 0.2 1 124577 6247 56 135217 0.2 1 128490 6727 57 127931 0.2 1 122024 5907 58 124239 0.2 1 118784 5455 59 127293 0.2 1 121311 5982 60 131981 0.2 1 125772 6209 61 137697 0.2 1 130983 6714 62 152253 0.2 1 144774 7479 63 201898 0.2 1 193113 8785 64 172675 0.2 1 166389 6286 65 108874 0.2 1 104021 4853 66 119610 0.2 1 114446 5164 67 118964 0.2 1 113321 5643 68 119680 0.2 1 114293 5387 69 119889 0.2 1 114293 5596 70 125777 0.2 1 120013 5764 71 132876 0.2 1 127109 5767 72 127787 0.2 1 121904 5883 73 134940 0.2 1 129055 5885 74 125685 0.2 1 120224 5461 75 120939 0.2 1 115502 5437 76 116878 0.2 1 111806 5072 77 119317 0.2 1 114031 5286 78 114912 0.2 1 109837 5075 79 111961 0.2 1 107098 4863 80 111439 0.2 1 106611 4828 81 110252 0.2 1 105525 4727 82 104612 0.2 1 100154 4458 83 103450 0.2 1 99126 4324 84 97944 0.2 1 93515 4429 85 99039 0.2 1 94552 4487 86 98012 0.2 1 93716 4296 87 99549 0.2 1 95300 4249 88 97562 0.2 1 93249 4313 89 87175 0.2 1 83280 3895 90 83950 0.2 1 80287 3663 91 78836 0.2 1 75281 3555 92 74886 0.2 1 71664 3222 93 72687 0.2 1 69632 3055 94 70208 0.2 1 67258 2950 95 66190 0.2 1 63387 2803 96 63977 0.2 1 61304 2673 97 60139 0.2 1 57625 2514 98 58153 0.2 1 55728 2425 99 56999 0.2 1 54663 2336 100 49226 0.2 1 47327 1899 101 45428 0.2 1 43567 1861 102 41140 0.2 1 39441 1699 103 38223 0.2 1 36634 1589 104 36626 0.2 1 35088 1538 105 32982 0.2 1 31676 1306 106 30175 0.2 1 28923 1252 107 27378 0.2 1 26210 1168 108 24859 0.2 1 23806 1053 109 22755 0.2 1 21778 977 110 20637 0.2 1 19770 867 111 19236 0.2 1 18439 797 112 16601 0.2 1 15906 695 113 14600 0.2 1 13964 636 114 12946 0.2 1 12440 506 115 10705 0.2 1 10194 511 116 9020 0.2 1 8602 418 117 7442 0.2 1 7107 335 118 6690 0.2 1 6379 311 119 5516 0.2 1 5293 223 120 4632 0.2 1 4427 205 121 4146 0.2 1 3939 207 122 3352 0.2 1 3190 162 123 2944 0.2 1 2813 131 124 2397 0.2 1 2279 118 125 1984 0.2 1 1898 86 126 1679 0.2 1 1593 86 127 1365 0.2 1 1295 70 128 964 0.2 1 919 45 129 925 0.2 1 886 39 130 667 0.2 1 644 23 131 533 0.2 1 504 29 132 511 0.2 1 485 26 133 492 0.2 1 476 16 134 547 0.2 1 526 21 135 276 0.2 1 266 10 136 213 0.2 1 198 15 137 138 0.2 1 130 8 138 104 0.2 1 100 4 139 66 0.2 1 61 5 140 52 0.2 1 48 4 141 37 0.2 1 34 3 142 40 0.2 1 40 143 44 0.2 1 40 4 144 45 0.2 1 42 3 145 50 0.2 1 48 2 146 86 0.2 1 82 4 147 237 0.2 1 232 5 148 198 0.2 1 192 6 149 62 0.2 1 55 7 150 658 0.2 1 640 18 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_32psu_3_S3_L001_R2_001.fastq.gz ============================================= 13688650 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 23444 (0.2%)