SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_32psu_1_S5_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_32psu_1_S5_L002_R1_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 485.81 s (35 us/read; 1.73 M reads/minute). === Summary === Total reads processed: 13,980,098 Reads with adapters: 12,547,273 (89.8%) Reads written (passing filters): 13,980,098 (100.0%) Total basepairs processed: 2,097,014,700 bp Quality-trimmed: 3,995,329 bp (0.2%) Total written (filtered): 1,381,322,734 bp (65.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 12547273 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.6% C: 15.4% G: 21.7% T: 34.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 797770 3495024.5 0 797770 2 136013 873756.1 0 136013 3 88578 218439.0 0 88578 4 54507 54609.8 0 54507 5 51433 13652.4 0 51433 6 50368 3413.1 0 50368 7 41781 853.3 0 41781 8 52923 213.3 0 52923 9 54051 53.3 0 53431 620 10 50288 13.3 1 47174 3114 11 58137 3.3 1 53328 4809 12 55530 0.8 1 51625 3905 13 56413 0.2 1 52378 4035 14 59004 0.2 1 54278 4726 15 60957 0.2 1 56359 4598 16 62617 0.2 1 57287 5330 17 77034 0.2 1 70041 6993 18 64851 0.2 1 60415 4436 19 55636 0.2 1 51675 3961 20 69068 0.2 1 64118 4950 21 78331 0.2 1 72354 5977 22 65036 0.2 1 60845 4191 23 77471 0.2 1 71757 5714 24 73017 0.2 1 66655 6362 25 80097 0.2 1 74072 6025 26 72725 0.2 1 67966 4759 27 83104 0.2 1 76594 6510 28 81931 0.2 1 75845 6086 29 90548 0.2 1 82404 8144 30 97688 0.2 1 91724 5964 31 71240 0.2 1 66196 5044 32 92668 0.2 1 85724 6944 33 88978 0.2 1 82032 6946 34 98712 0.2 1 91302 7410 35 92968 0.2 1 85787 7181 36 107083 0.2 1 98683 8400 37 102524 0.2 1 93933 8591 38 103053 0.2 1 96018 7035 39 106015 0.2 1 98258 7757 40 105210 0.2 1 97541 7669 41 121909 0.2 1 112224 9685 42 102833 0.2 1 93869 8964 43 167631 0.2 1 157548 10083 44 59347 0.2 1 53867 5480 45 119124 0.2 1 111193 7931 46 115006 0.2 1 106994 8012 47 123238 0.2 1 114804 8434 48 121882 0.2 1 113175 8707 49 136657 0.2 1 126388 10269 50 117352 0.2 1 109816 7536 51 128981 0.2 1 119944 9037 52 136441 0.2 1 126118 10323 53 146650 0.2 1 137000 9650 54 118855 0.2 1 110740 8115 55 142441 0.2 1 132669 9772 56 173419 0.2 1 162260 11159 57 115395 0.2 1 106550 8845 58 148737 0.2 1 140083 8654 59 131828 0.2 1 122332 9496 60 148604 0.2 1 138387 10217 61 147891 0.2 1 138429 9462 62 164090 0.2 1 153607 10483 63 134153 0.2 1 124429 9724 64 146788 0.2 1 137613 9175 65 167405 0.2 1 156219 11186 66 175152 0.2 1 163306 11846 67 193973 0.2 1 178444 15529 68 355893 0.2 1 337623 18270 69 77628 0.2 1 71288 6340 70 32194 0.2 1 27237 4957 71 98744 0.2 1 92367 6377 72 142722 0.2 1 134109 8613 73 153911 0.2 1 144323 9588 74 152982 0.2 1 143267 9715 75 155312 0.2 1 145139 10173 76 154296 0.2 1 143821 10475 77 156257 0.2 1 146141 10116 78 149276 0.2 1 139442 9834 79 150468 0.2 1 140290 10178 80 147626 0.2 1 137573 10053 81 147629 0.2 1 137952 9677 82 146000 0.2 1 136195 9805 83 142550 0.2 1 133188 9362 84 139878 0.2 1 130510 9368 85 136886 0.2 1 127696 9190 86 134793 0.2 1 125685 9108 87 130207 0.2 1 121771 8436 88 129730 0.2 1 121003 8727 89 125338 0.2 1 117059 8279 90 125920 0.2 1 117611 8309 91 120727 0.2 1 112765 7962 92 116230 0.2 1 108426 7804 93 110261 0.2 1 102836 7425 94 107731 0.2 1 100461 7270 95 101765 0.2 1 94845 6920 96 97730 0.2 1 91189 6541 97 92862 0.2 1 86658 6204 98 87553 0.2 1 81547 6006 99 87158 0.2 1 80825 6333 100 78638 0.2 1 73170 5468 101 74653 0.2 1 69508 5145 102 70275 0.2 1 65468 4807 103 65373 0.2 1 60911 4462 104 61766 0.2 1 57502 4264 105 55492 0.2 1 51811 3681 106 51179 0.2 1 47624 3555 107 46618 0.2 1 43293 3325 108 44553 0.2 1 41440 3113 109 39712 0.2 1 36840 2872 110 36630 0.2 1 33977 2653 111 32740 0.2 1 30268 2472 112 29144 0.2 1 26890 2254 113 25615 0.2 1 23550 2065 114 22855 0.2 1 21063 1792 115 19838 0.2 1 18299 1539 116 17636 0.2 1 16221 1415 117 14547 0.2 1 13334 1213 118 13235 0.2 1 12137 1098 119 10988 0.2 1 10016 972 120 9462 0.2 1 8648 814 121 7752 0.2 1 7051 701 122 6591 0.2 1 5988 603 123 5413 0.2 1 4917 496 124 4773 0.2 1 4290 483 125 3899 0.2 1 3520 379 126 3211 0.2 1 2920 291 127 2698 0.2 1 2418 280 128 2171 0.2 1 1932 239 129 1648 0.2 1 1461 187 130 1400 0.2 1 1257 143 131 1218 0.2 1 1094 124 132 1037 0.2 1 929 108 133 1169 0.2 1 1044 125 134 1204 0.2 1 1109 95 135 602 0.2 1 535 67 136 395 0.2 1 343 52 137 232 0.2 1 196 36 138 155 0.2 1 142 13 139 118 0.2 1 95 23 140 87 0.2 1 71 16 141 57 0.2 1 45 12 142 68 0.2 1 58 10 143 37 0.2 1 32 5 144 24 0.2 1 22 2 145 36 0.2 1 30 6 146 26 0.2 1 23 3 147 105 0.2 1 86 19 148 85 0.2 1 66 19 149 76 0.2 1 64 12 150 640 0.2 1 546 94 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_32psu_1_S5_L002_R1_001.fastq.gz ============================================= 13980098 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 7427 (0.1%)