SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_26psu_2_S14_L001_R1_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.6.4_dev Cutadapt version: 2.4 Python version: could not detect Number of cores used for trimming: 8 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Using Illumina adapter for trimming (count: 522594). Second best hit was smallRNA (count: 1) Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /gscratch/scrubbed/strigg/analyses/20200427/TG_PE_FASTQS/FastQC --threads 28 Output file will be GZIP compressed This is cutadapt 2.4 with Python 3.7.6 Command line parameters: -j 8 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_26psu_2_S14_L001_R1_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 62.70 s (4 us/read; 16.50 M reads/minute). === Summary === Total reads processed: 17,243,447 Reads with adapters: 13,329,210 (77.3%) Reads written (passing filters): 17,243,447 (100.0%) Total basepairs processed: 2,586,517,050 bp Quality-trimmed: 5,286,503 bp (0.2%) Total written (filtered): 2,048,045,774 bp (79.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 13329210 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.9% C: 14.2% G: 20.5% T: 35.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2371278 4310861.8 0 2371278 2 355428 1077715.4 0 355428 3 196735 269428.9 0 196735 4 114807 67357.2 0 114807 5 92976 16839.3 0 92976 6 90363 4209.8 0 90363 7 74432 1052.5 0 74432 8 93807 263.1 0 93807 9 93533 65.8 0 92435 1098 10 87230 16.4 1 82587 4643 11 96624 4.1 1 89271 7353 12 92957 1.0 1 86987 5970 13 93747 0.3 1 87764 5983 14 96011 0.3 1 89197 6814 15 98978 0.3 1 92592 6386 16 98159 0.3 1 90785 7374 17 119944 0.3 1 110196 9748 18 100650 0.3 1 94699 5951 19 86734 0.3 1 81180 5554 20 104244 0.3 1 97548 6696 21 115327 0.3 1 107159 8168 22 97273 0.3 1 91575 5698 23 115900 0.3 1 108235 7665 24 104136 0.3 1 95675 8461 25 112997 0.3 1 105393 7604 26 102184 0.3 1 96084 6100 27 114471 0.3 1 106298 8173 28 113184 0.3 1 105296 7888 29 118291 0.3 1 108737 9554 30 125680 0.3 1 118630 7050 31 99517 0.3 1 93132 6385 32 120246 0.3 1 112659 7587 33 112299 0.3 1 104687 7612 34 122051 0.3 1 114065 7986 35 122132 0.3 1 112527 9605 36 121056 0.3 1 113558 7498 37 131245 0.3 1 122809 8436 38 117529 0.3 1 109870 7659 39 130463 0.3 1 121802 8661 40 125603 0.3 1 117585 8018 41 145134 0.3 1 134544 10590 42 108964 0.3 1 101116 7848 43 193675 0.3 1 183736 9939 44 56524 0.3 1 51515 5009 45 130295 0.3 1 122170 8125 46 121941 0.3 1 114229 7712 47 128745 0.3 1 120966 7779 48 126992 0.3 1 118817 8175 49 138745 0.3 1 128994 9751 50 118346 0.3 1 111437 6909 51 127998 0.3 1 119617 8381 52 132118 0.3 1 122819 9299 53 142995 0.3 1 134373 8622 54 111526 0.3 1 104331 7195 55 132598 0.3 1 124212 8386 56 162335 0.3 1 152964 9371 57 103809 0.3 1 96508 7301 58 132526 0.3 1 125372 7154 59 115914 0.3 1 108457 7457 60 128350 0.3 1 120205 8145 61 126189 0.3 1 118700 7489 62 137584 0.3 1 129699 7885 63 110035 0.3 1 102791 7244 64 120964 0.3 1 114082 6882 65 135744 0.3 1 127467 8277 66 140396 0.3 1 131867 8529 67 145532 0.3 1 134835 10697 68 287021 0.3 1 273202 13819 69 48096 0.3 1 43999 4097 70 18303 0.3 1 15162 3141 71 72881 0.3 1 68623 4258 72 103446 0.3 1 97521 5925 73 109833 0.3 1 103450 6383 74 107925 0.3 1 101499 6426 75 106292 0.3 1 100152 6140 76 104330 0.3 1 98203 6127 77 104241 0.3 1 98017 6224 78 98088 0.3 1 92293 5795 79 96948 0.3 1 91096 5852 80 94252 0.3 1 88790 5462 81 93362 0.3 1 87783 5579 82 90202 0.3 1 84811 5391 83 87147 0.3 1 81902 5245 84 83793 0.3 1 78976 4817 85 80030 0.3 1 75251 4779 86 77694 0.3 1 73076 4618 87 74005 0.3 1 69629 4376 88 72748 0.3 1 68492 4256 89 68708 0.3 1 64648 4060 90 68047 0.3 1 63799 4248 91 64435 0.3 1 60450 3985 92 60503 0.3 1 56736 3767 93 56921 0.3 1 53460 3461 94 55199 0.3 1 51895 3304 95 50827 0.3 1 47651 3176 96 48189 0.3 1 45189 3000 97 45155 0.3 1 42374 2781 98 41036 0.3 1 38566 2470 99 40350 0.3 1 37693 2657 100 35870 0.3 1 33662 2208 101 33328 0.3 1 31103 2225 102 30823 0.3 1 28817 2006 103 28586 0.3 1 26749 1837 104 26108 0.3 1 24403 1705 105 23329 0.3 1 21857 1472 106 21254 0.3 1 19878 1376 107 19359 0.3 1 18082 1277 108 18005 0.3 1 16770 1235 109 16024 0.3 1 14870 1154 110 14310 0.3 1 13331 979 111 12919 0.3 1 11980 939 112 11039 0.3 1 10251 788 113 9662 0.3 1 8961 701 114 8278 0.3 1 7631 647 115 7400 0.3 1 6862 538 116 6380 0.3 1 5871 509 117 5590 0.3 1 5116 474 118 4883 0.3 1 4498 385 119 3958 0.3 1 3624 334 120 3465 0.3 1 3177 288 121 3026 0.3 1 2769 257 122 2531 0.3 1 2300 231 123 2116 0.3 1 1896 220 124 1699 0.3 1 1542 157 125 1434 0.3 1 1302 132 126 1188 0.3 1 1073 115 127 1126 0.3 1 995 131 128 869 0.3 1 759 110 129 701 0.3 1 622 79 130 549 0.3 1 500 49 131 448 0.3 1 398 50 132 432 0.3 1 385 47 133 454 0.3 1 410 44 134 600 0.3 1 564 36 135 275 0.3 1 252 23 136 173 0.3 1 157 16 137 109 0.3 1 101 8 138 92 0.3 1 82 10 139 63 0.3 1 54 9 140 64 0.3 1 52 12 141 59 0.3 1 51 8 142 40 0.3 1 37 3 143 53 0.3 1 48 5 144 32 0.3 1 31 1 145 53 0.3 1 50 3 146 166 0.3 1 154 12 147 548 0.3 1 525 23 148 402 0.3 1 390 12 149 263 0.3 1 250 13 150 2873 0.3 1 2693 180 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_26psu_2_S14_L001_R1_001.fastq.gz ============================================= 17243447 sequences processed in total