SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_26psu_2_S14_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/16C_26psu_2_S14_L002_R1_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 733.43 s (43 us/read; 1.40 M reads/minute). === Summary === Total reads processed: 17,174,050 Reads with adapters: 13,278,050 (77.3%) Reads written (passing filters): 17,174,050 (100.0%) Total basepairs processed: 2,576,107,500 bp Quality-trimmed: 5,444,792 bp (0.2%) Total written (filtered): 2,038,071,183 bp (79.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 13278050 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.9% C: 14.3% G: 20.5% T: 35.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2359801 4293512.5 0 2359801 2 349363 1073378.1 0 349363 3 195448 268344.5 0 195448 4 112766 67086.1 0 112766 5 92768 16771.5 0 92768 6 90305 4192.9 0 90305 7 71626 1048.2 0 71626 8 92261 262.1 0 92261 9 91976 65.5 0 90926 1050 10 85467 16.4 1 79925 5542 11 96691 4.1 1 88355 8336 12 91713 1.0 1 84839 6874 13 92754 0.3 1 85809 6945 14 95464 0.3 1 87621 7843 15 99277 0.3 1 91369 7908 16 97348 0.3 1 88681 8667 17 119420 0.3 1 108369 11051 18 98719 0.3 1 91552 7167 19 85310 0.3 1 78884 6426 20 103518 0.3 1 95770 7748 21 115588 0.3 1 106188 9400 22 95906 0.3 1 89272 6634 23 115386 0.3 1 106435 8951 24 102949 0.3 1 93582 9367 25 112836 0.3 1 104100 8736 26 100484 0.3 1 93502 6982 27 114811 0.3 1 105307 9504 28 113076 0.3 1 104189 8887 29 118710 0.3 1 108207 10503 30 126214 0.3 1 117742 8472 31 97121 0.3 1 89907 7214 32 120516 0.3 1 111427 9089 33 110848 0.3 1 101943 8905 34 122175 0.3 1 112281 9894 35 122064 0.3 1 111107 10957 36 119580 0.3 1 110830 8750 37 130636 0.3 1 120649 9987 38 115572 0.3 1 106536 9036 39 129905 0.3 1 119211 10694 40 124968 0.3 1 115039 9929 41 145398 0.3 1 132929 12469 42 108151 0.3 1 98831 9320 43 190551 0.3 1 178361 12190 44 58099 0.3 1 52480 5619 45 130794 0.3 1 121367 9427 46 121400 0.3 1 112370 9030 47 129048 0.3 1 119631 9417 48 126222 0.3 1 116730 9492 49 139750 0.3 1 128710 11040 50 117206 0.3 1 109130 8076 51 127012 0.3 1 117729 9283 52 132886 0.3 1 122231 10655 53 141918 0.3 1 132027 9891 54 110897 0.3 1 103000 7897 55 132094 0.3 1 122452 9642 56 162870 0.3 1 151676 11194 57 103170 0.3 1 94887 8283 58 132668 0.3 1 124347 8321 59 116116 0.3 1 107462 8654 60 129021 0.3 1 119747 9274 61 124026 0.3 1 115604 8422 62 137460 0.3 1 128199 9261 63 110698 0.3 1 102173 8525 64 120813 0.3 1 112906 7907 65 134938 0.3 1 125626 9312 66 138037 0.3 1 128352 9685 67 146504 0.3 1 134535 11969 68 277060 0.3 1 261442 15618 69 59870 0.3 1 54647 5223 70 22664 0.3 1 19044 3620 71 71972 0.3 1 67240 4732 72 103041 0.3 1 96552 6489 73 110046 0.3 1 102755 7291 74 107843 0.3 1 100538 7305 75 106162 0.3 1 98772 7390 76 105323 0.3 1 97926 7397 77 104408 0.3 1 97267 7141 78 97073 0.3 1 90169 6904 79 96839 0.3 1 89879 6960 80 93988 0.3 1 87339 6649 81 93546 0.3 1 86918 6628 82 90241 0.3 1 83957 6284 83 86944 0.3 1 80903 6041 84 83168 0.3 1 77255 5913 85 80437 0.3 1 74815 5622 86 77338 0.3 1 71860 5478 87 73439 0.3 1 68315 5124 88 73001 0.3 1 67818 5183 89 68544 0.3 1 63628 4916 90 68084 0.3 1 63234 4850 91 64534 0.3 1 60016 4518 92 61115 0.3 1 56823 4292 93 56566 0.3 1 52542 4024 94 55074 0.3 1 51146 3928 95 50909 0.3 1 47255 3654 96 48357 0.3 1 44862 3495 97 45610 0.3 1 42541 3069 98 41384 0.3 1 38355 3029 99 39655 0.3 1 36624 3031 100 36325 0.3 1 33739 2586 101 33659 0.3 1 31212 2447 102 31157 0.3 1 28883 2274 103 28746 0.3 1 26792 1954 104 26425 0.3 1 24518 1907 105 23705 0.3 1 22021 1684 106 21201 0.3 1 19619 1582 107 19613 0.3 1 18232 1381 108 17790 0.3 1 16434 1356 109 16006 0.3 1 14830 1176 110 14326 0.3 1 13263 1063 111 12771 0.3 1 11779 992 112 11222 0.3 1 10318 904 113 9534 0.3 1 8824 710 114 8358 0.3 1 7698 660 115 7285 0.3 1 6692 593 116 6411 0.3 1 5816 595 117 5570 0.3 1 5108 462 118 4832 0.3 1 4420 412 119 3906 0.3 1 3549 357 120 3397 0.3 1 3108 289 121 2929 0.3 1 2664 265 122 2444 0.3 1 2212 232 123 2198 0.3 1 1992 206 124 1767 0.3 1 1602 165 125 1386 0.3 1 1230 156 126 1228 0.3 1 1089 139 127 1105 0.3 1 989 116 128 786 0.3 1 705 81 129 664 0.3 1 591 73 130 581 0.3 1 508 73 131 479 0.3 1 435 44 132 414 0.3 1 361 53 133 450 0.3 1 408 42 134 646 0.3 1 602 44 135 289 0.3 1 262 27 136 173 0.3 1 154 19 137 125 0.3 1 108 17 138 98 0.3 1 88 10 139 90 0.3 1 77 13 140 54 0.3 1 46 8 141 52 0.3 1 45 7 142 38 0.3 1 35 3 143 50 0.3 1 43 7 144 42 0.3 1 37 5 145 46 0.3 1 45 1 146 125 0.3 1 116 9 147 651 0.3 1 623 28 148 442 0.3 1 421 21 149 216 0.3 1 204 12 150 2921 0.3 1 2713 208 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_26psu_2_S14_L002_R1_001.fastq.gz ============================================= 17174050 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 7457 (0.0%)