SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth18_R2_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 2.4 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 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/20200311/WGBS_MBD/FASTQC --threads 28 Output file will be GZIP compressed This is cutadapt 2.4 with Python 3.7.3 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth18_R2_001.fastq.gz WARNING: Option --format is deprecated and ignored because the input file format is always auto-detected Processing reads on 1 core in single-end mode ... Finished in 1945.42 s (31 us/read; 1.93 M reads/minute). === Summary === Total reads processed: 62,709,665 Reads with adapters: 38,470,962 (61.3%) Reads written (passing filters): 62,709,665 (100.0%) Total basepairs processed: 9,406,449,750 bp Quality-trimmed: 123,266,483 bp (1.3%) Total written (filtered): 8,293,089,887 bp (88.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 38470962 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 33.9% C: 15.7% G: 18.8% T: 31.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 13938102 15677416.2 0 13938102 2 1359085 3919354.1 0 1359085 3 655707 979838.5 0 655707 4 424350 244959.6 0 424350 5 319726 61239.9 0 319726 6 262112 15310.0 0 262112 7 271385 3827.5 0 271385 8 308619 956.9 0 308619 9 274806 239.2 0 270909 3897 10 289786 59.8 1 272669 17117 11 313346 15.0 1 288947 24399 12 342477 3.7 1 319651 22826 13 271931 0.9 1 249417 22514 14 304901 0.9 1 280810 24091 15 296605 0.9 1 274390 22215 16 317217 0.9 1 291435 25782 17 310223 0.9 1 287370 22853 18 285260 0.9 1 265121 20139 19 316262 0.9 1 293234 23028 20 313717 0.9 1 291447 22270 21 292460 0.9 1 269393 23067 22 306848 0.9 1 285978 20870 23 292904 0.9 1 272708 20196 24 305824 0.9 1 284026 21798 25 347412 0.9 1 324914 22498 26 260991 0.9 1 241945 19046 27 295345 0.9 1 274519 20826 28 289282 0.9 1 273557 15725 29 300009 0.9 1 282102 17907 30 291390 0.9 1 275828 15562 31 291938 0.9 1 275449 16489 32 285292 0.9 1 270572 14720 33 296526 0.9 1 280520 16006 34 290373 0.9 1 273385 16988 35 275373 0.9 1 261229 14144 36 309222 0.9 1 286985 22237 37 303293 0.9 1 287295 15998 38 263075 0.9 1 249446 13629 39 277927 0.9 1 261674 16253 40 281344 0.9 1 266350 14994 41 314164 0.9 1 285346 28818 42 859329 0.9 1 821915 37414 43 214873 0.9 1 177493 37380 44 2127916 0.9 1 2053251 74665 45 656389 0.9 1 629255 27134 46 95251 0.9 1 86718 8533 47 272611 0.9 1 261799 10812 48 64446 0.9 1 59424 5022 49 131431 0.9 1 124864 6567 50 74671 0.9 1 70255 4416 51 88881 0.9 1 83627 5254 52 108893 0.9 1 103315 5578 53 96814 0.9 1 90928 5886 54 181867 0.9 1 174468 7399 55 91933 0.9 1 85542 6391 56 202134 0.9 1 189063 13071 57 485918 0.9 1 467361 18557 58 222943 0.9 1 212802 10141 59 108710 0.9 1 98168 10542 60 533815 0.9 1 514315 19500 61 175316 0.9 1 168033 7283 62 110774 0.9 1 104147 6627 63 173022 0.9 1 162763 10259 64 302922 0.9 1 291617 11305 65 58519 0.9 1 54470 4049 66 76865 0.9 1 72536 4329 67 74982 0.9 1 70890 4092 68 67096 0.9 1 63594 3502 69 29767 0.9 1 27509 2258 70 42075 0.9 1 39471 2604 71 38108 0.9 1 35538 2570 72 45987 0.9 1 42773 3214 73 68951 0.9 1 64906 4045 74 80469 0.9 1 75872 4597 75 90238 0.9 1 84880 5358 76 95749 0.9 1 91000 4749 77 54195 0.9 1 51219 2976 78 32377 0.9 1 29925 2452 79 48931 0.9 1 45613 3318 80 77168 0.9 1 72494 4674 81 98659 0.9 1 93220 5439 82 110484 0.9 1 104341 6143 83 116379 0.9 1 110222 6157 84 113064 0.9 1 106708 6356 85 111232 0.9 1 105095 6137 86 100271 0.9 1 94615 5656 87 95678 0.9 1 90055 5623 88 92558 0.9 1 87256 5302 89 87143 0.9 1 82148 4995 90 83107 0.9 1 78387 4720 91 81141 0.9 1 76375 4766 92 75016 0.9 1 70683 4333 93 71384 0.9 1 67152 4232 94 68641 0.9 1 64479 4162 95 64919 0.9 1 60813 4106 96 61201 0.9 1 57219 3982 97 60034 0.9 1 55999 4035 98 55725 0.9 1 52200 3525 99 52598 0.9 1 49023 3575 100 50269 0.9 1 46953 3316 101 49968 0.9 1 46553 3415 102 43032 0.9 1 40044 2988 103 39766 0.9 1 36758 3008 104 42804 0.9 1 39652 3152 105 40656 0.9 1 37618 3038 106 42333 0.9 1 39247 3086 107 39304 0.9 1 36432 2872 108 33100 0.9 1 30480 2620 109 28032 0.9 1 25648 2384 110 25918 0.9 1 23678 2240 111 23406 0.9 1 21343 2063 112 22518 0.9 1 20530 1988 113 22972 0.9 1 20783 2189 114 22593 0.9 1 20364 2229 115 23108 0.9 1 21018 2090 116 25370 0.9 1 23152 2218 117 27684 0.9 1 25351 2333 118 21699 0.9 1 19859 1840 119 17433 0.9 1 15678 1755 120 16264 0.9 1 14745 1519 121 14027 0.9 1 12711 1316 122 14518 0.9 1 13046 1472 123 14995 0.9 1 13343 1652 124 12332 0.9 1 11021 1311 125 13155 0.9 1 11793 1362 126 21866 0.9 1 19754 2112 127 17451 0.9 1 15442 2009 128 11229 0.9 1 9967 1262 129 12020 0.9 1 10880 1140 130 29273 0.9 1 27237 2036 131 46913 0.9 1 44236 2677 132 45943 0.9 1 43119 2824 133 85100 0.9 1 80107 4993 134 80390 0.9 1 75630 4760 135 19109 0.9 1 17816 1293 136 5201 0.9 1 4669 532 137 3737 0.9 1 3340 397 138 2522 0.9 1 2120 402 139 1322 0.9 1 1011 311 140 1264 0.9 1 1049 215 141 542 0.9 1 422 120 142 433 0.9 1 261 172 143 414 0.9 1 288 126 144 602 0.9 1 523 79 145 2117 0.9 1 1982 135 146 1897 0.9 1 1712 185 147 11623 0.9 1 10545 1078 148 6005 0.9 1 5257 748 149 2018 0.9 1 1806 212 150 26536 0.9 1 25134 1402 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth18_R2_001.fastq.gz ============================================= 62709665 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 62709665 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1124265 (1.79%)