SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/CTRL_8C_26psu_2_S18_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/CTRL_8C_26psu_2_S18_L002_R1_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 587.68 s (35 us/read; 1.73 M reads/minute). === Summary === Total reads processed: 16,972,486 Reads with adapters: 15,279,419 (90.0%) Reads written (passing filters): 16,972,486 (100.0%) Total basepairs processed: 2,545,872,900 bp Quality-trimmed: 5,170,443 bp (0.2%) Total written (filtered): 1,660,911,595 bp (65.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 15279419 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.1% C: 17.9% G: 21.2% T: 32.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 937714 4243121.5 0 937714 2 159877 1060780.4 0 159877 3 104645 265195.1 0 104645 4 64394 66298.8 0 64394 5 60206 16574.7 0 60206 6 60143 4143.7 0 60143 7 49779 1035.9 0 49779 8 63607 259.0 0 63607 9 63633 64.7 0 62858 775 10 59492 16.2 1 55609 3883 11 70292 4.0 1 63860 6432 12 65718 1.0 1 60580 5138 13 68404 0.3 1 63070 5334 14 69496 0.3 1 63637 5859 15 74672 0.3 1 68604 6068 16 72665 0.3 1 66207 6458 17 90074 0.3 1 81360 8714 18 80053 0.3 1 74306 5747 19 65594 0.3 1 60638 4956 20 83351 0.3 1 76880 6471 21 92562 0.3 1 85115 7447 22 78449 0.3 1 72991 5458 23 93136 0.3 1 85970 7166 24 87973 0.3 1 80003 7970 25 95468 0.3 1 87873 7595 26 87079 0.3 1 80742 6337 27 100093 0.3 1 91614 8479 28 99879 0.3 1 92166 7713 29 105478 0.3 1 95962 9516 30 116678 0.3 1 108856 7822 31 86678 0.3 1 80098 6580 32 107759 0.3 1 99613 8146 33 109432 0.3 1 99874 9558 34 138284 0.3 1 125790 12494 35 117450 0.3 1 109376 8074 36 91614 0.3 1 84735 6879 37 124777 0.3 1 114386 10391 38 138573 0.3 1 126348 12225 39 118413 0.3 1 109918 8495 40 138324 0.3 1 126104 12220 41 158476 0.3 1 144761 13715 42 109596 0.3 1 99995 9601 43 214148 0.3 1 200447 13701 44 58836 0.3 1 52468 6368 45 143215 0.3 1 132338 10877 46 142842 0.3 1 132071 10771 47 146328 0.3 1 136022 10306 48 147735 0.3 1 136182 11553 49 164993 0.3 1 151819 13174 50 138531 0.3 1 129039 9492 51 154359 0.3 1 142921 11438 52 163104 0.3 1 149477 13627 53 181208 0.3 1 168727 12481 54 135823 0.3 1 125879 9944 55 172933 0.3 1 159987 12946 56 212770 0.3 1 198564 14206 57 137905 0.3 1 126707 11198 58 179533 0.3 1 168232 11301 59 154787 0.3 1 143238 11549 60 178048 0.3 1 165291 12757 61 178798 0.3 1 166319 12479 62 194586 0.3 1 181612 12974 63 159546 0.3 1 147478 12068 64 175838 0.3 1 164219 11619 65 199150 0.3 1 185246 13904 66 207681 0.3 1 193071 14610 67 227820 0.3 1 208839 18981 68 430170 0.3 1 406697 23473 69 101761 0.3 1 93311 8450 70 37741 0.3 1 31764 5977 71 116561 0.3 1 108649 7912 72 170878 0.3 1 160245 10633 73 185808 0.3 1 173840 11968 74 185713 0.3 1 173236 12477 75 186685 0.3 1 173898 12787 76 187774 0.3 1 174524 13250 77 190253 0.3 1 177207 13046 78 180228 0.3 1 167656 12572 79 181970 0.3 1 169235 12735 80 180269 0.3 1 167504 12765 81 180129 0.3 1 167834 12295 82 176778 0.3 1 164262 12516 83 174648 0.3 1 162652 11996 84 170683 0.3 1 158618 12065 85 167207 0.3 1 155648 11559 86 165775 0.3 1 154402 11373 87 159710 0.3 1 148769 10941 88 161141 0.3 1 150001 11140 89 154725 0.3 1 143979 10746 90 156314 0.3 1 145746 10568 91 151370 0.3 1 140729 10641 92 145834 0.3 1 135746 10088 93 137534 0.3 1 127986 9548 94 136265 0.3 1 126825 9440 95 127646 0.3 1 118675 8971 96 123166 0.3 1 114494 8672 97 117318 0.3 1 109181 8137 98 111017 0.3 1 103130 7887 99 109081 0.3 1 101041 8040 100 101164 0.3 1 94080 7084 101 96193 0.3 1 89369 6824 102 90471 0.3 1 84087 6384 103 85738 0.3 1 79491 6247 104 80436 0.3 1 74816 5620 105 72717 0.3 1 67687 5030 106 67684 0.3 1 62759 4925 107 62704 0.3 1 58171 4533 108 59951 0.3 1 55617 4334 109 54357 0.3 1 50236 4121 110 50115 0.3 1 46382 3733 111 45371 0.3 1 41955 3416 112 40800 0.3 1 37574 3226 113 35447 0.3 1 32646 2801 114 32325 0.3 1 29802 2523 115 28709 0.3 1 26438 2271 116 25389 0.3 1 23337 2052 117 21950 0.3 1 20122 1828 118 19200 0.3 1 17593 1607 119 16278 0.3 1 14896 1382 120 14121 0.3 1 12882 1239 121 12963 0.3 1 11779 1184 122 10628 0.3 1 9652 976 123 9232 0.3 1 8435 797 124 7617 0.3 1 6893 724 125 6474 0.3 1 5870 604 126 5569 0.3 1 5024 545 127 4721 0.3 1 4238 483 128 3597 0.3 1 3214 383 129 3083 0.3 1 2780 303 130 2334 0.3 1 2063 271 131 2035 0.3 1 1816 219 132 1850 0.3 1 1686 164 133 2327 0.3 1 2083 244 134 4554 0.3 1 4279 275 135 1805 0.3 1 1652 153 136 606 0.3 1 541 65 137 448 0.3 1 385 63 138 325 0.3 1 262 63 139 199 0.3 1 170 29 140 136 0.3 1 115 21 141 92 0.3 1 70 22 142 61 0.3 1 44 17 143 68 0.3 1 60 8 144 63 0.3 1 59 4 145 123 0.3 1 108 15 146 160 0.3 1 140 20 147 706 0.3 1 621 85 148 490 0.3 1 450 40 149 296 0.3 1 261 35 150 3088 0.3 1 2616 472 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/CTRL_8C_26psu_2_S18_L002_R1_001.fastq.gz ============================================= 16972486 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 19505 (0.1%)