SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth12_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/Meth12_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 3104.61 s (33 us/read; 1.84 M reads/minute). === Summary === Total reads processed: 95,078,293 Reads with adapters: 57,113,586 (60.1%) Reads written (passing filters): 95,078,293 (100.0%) Total basepairs processed: 14,261,743,950 bp Quality-trimmed: 92,575,641 bp (0.6%) Total written (filtered): 12,953,429,284 bp (90.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 57113586 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 37.6% C: 13.2% G: 17.1% T: 32.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 24193020 23769573.2 0 24193020 2 2321427 5942393.3 0 2321427 3 1112927 1485598.3 0 1112927 4 680627 371399.6 0 680627 5 483619 92849.9 0 483619 6 382658 23212.5 0 382658 7 400756 5803.1 0 400756 8 476670 1450.8 0 476670 9 382416 362.7 0 375652 6764 10 426382 90.7 1 397796 28586 11 452408 22.7 1 414474 37934 12 485108 5.7 1 449176 35932 13 411618 1.4 1 375474 36144 14 446720 1.4 1 409328 37392 15 434065 1.4 1 399571 34494 16 462921 1.4 1 423521 39400 17 453970 1.4 1 418071 35899 18 412189 1.4 1 381021 31168 19 465881 1.4 1 430523 35358 20 454382 1.4 1 420028 34354 21 417482 1.4 1 383546 33936 22 444470 1.4 1 412491 31979 23 425227 1.4 1 394687 30540 24 454574 1.4 1 419702 34872 25 515764 1.4 1 481969 33795 26 369041 1.4 1 340356 28685 27 406916 1.4 1 375617 31299 28 415828 1.4 1 392669 23159 29 425658 1.4 1 399987 25671 30 427967 1.4 1 404675 23292 31 404403 1.4 1 381603 22800 32 417365 1.4 1 394613 22752 33 421253 1.4 1 398025 23228 34 402594 1.4 1 378677 23917 35 411229 1.4 1 389344 21885 36 453720 1.4 1 428393 25327 37 426906 1.4 1 403017 23889 38 427072 1.4 1 401798 25274 39 370033 1.4 1 350285 19748 40 395729 1.4 1 373590 22139 41 354046 1.4 1 333306 20740 42 385438 1.4 1 367338 18100 43 351442 1.4 1 330773 20669 44 509041 1.4 1 483534 25507 45 594107 1.4 1 565356 28751 46 317778 1.4 1 296250 21528 47 639123 1.4 1 617320 21803 48 113143 1.4 1 103819 9324 49 276243 1.4 1 261915 14328 50 270853 1.4 1 258851 12002 51 213056 1.4 1 200612 12444 52 263221 1.4 1 249959 13262 53 314479 1.4 1 296892 17587 54 505518 1.4 1 486843 18675 55 130184 1.4 1 119778 10406 56 328479 1.4 1 302626 25853 57 1110749 1.4 1 1075017 35732 58 157937 1.4 1 147605 10332 59 133513 1.4 1 120361 13152 60 607224 1.4 1 584749 22475 61 162404 1.4 1 153913 8491 62 168482 1.4 1 150480 18002 63 783592 1.4 1 754929 28663 64 505892 1.4 1 487511 18381 65 72148 1.4 1 66779 5369 66 124265 1.4 1 115472 8793 67 232144 1.4 1 223086 9058 68 113041 1.4 1 106634 6407 69 114501 1.4 1 107433 7068 70 170025 1.4 1 162729 7296 71 82166 1.4 1 77671 4495 72 71726 1.4 1 67090 4636 73 96300 1.4 1 91117 5183 74 93733 1.4 1 89063 4670 75 78851 1.4 1 74152 4699 76 71610 1.4 1 67074 4536 77 100323 1.4 1 94686 5637 78 135245 1.4 1 128265 6980 79 146731 1.4 1 139375 7356 80 153260 1.4 1 145549 7711 81 140021 1.4 1 133104 6917 82 130993 1.4 1 124085 6908 83 128099 1.4 1 121346 6753 84 122775 1.4 1 116305 6470 85 115824 1.4 1 109797 6027 86 108084 1.4 1 102249 5835 87 101586 1.4 1 96167 5419 88 94186 1.4 1 88986 5200 89 89268 1.4 1 84454 4814 90 85446 1.4 1 80746 4700 91 79463 1.4 1 74923 4540 92 74553 1.4 1 70313 4240 93 69532 1.4 1 65452 4080 94 65867 1.4 1 61984 3883 95 62796 1.4 1 59022 3774 96 59091 1.4 1 55464 3627 97 54962 1.4 1 51600 3362 98 50891 1.4 1 47713 3178 99 47043 1.4 1 44089 2954 100 44441 1.4 1 41505 2936 101 40672 1.4 1 37829 2843 102 36611 1.4 1 34115 2496 103 33247 1.4 1 30785 2462 104 31409 1.4 1 29137 2272 105 29212 1.4 1 27062 2150 106 28217 1.4 1 26200 2017 107 25665 1.4 1 23681 1984 108 22174 1.4 1 20404 1770 109 20157 1.4 1 18482 1675 110 18992 1.4 1 17269 1723 111 17255 1.4 1 15590 1665 112 15341 1.4 1 13808 1533 113 15075 1.4 1 13656 1419 114 13564 1.4 1 12115 1449 115 13158 1.4 1 11734 1424 116 12995 1.4 1 11653 1342 117 12776 1.4 1 11406 1370 118 10678 1.4 1 9485 1193 119 9111 1.4 1 7944 1167 120 8420 1.4 1 7308 1112 121 7655 1.4 1 6652 1003 122 7350 1.4 1 6355 995 123 8082 1.4 1 7049 1033 124 6446 1.4 1 5619 827 125 6500 1.4 1 5610 890 126 10458 1.4 1 9294 1164 127 9129 1.4 1 8095 1034 128 6081 1.4 1 5290 791 129 5996 1.4 1 5228 768 130 8988 1.4 1 8142 846 131 12230 1.4 1 11354 876 132 10519 1.4 1 9681 838 133 16022 1.4 1 14912 1110 134 12285 1.4 1 11366 919 135 3865 1.4 1 3436 429 136 1669 1.4 1 1394 275 137 1290 1.4 1 1063 227 138 1185 1.4 1 977 208 139 704 1.4 1 527 177 140 741 1.4 1 575 166 141 476 1.4 1 343 133 142 294 1.4 1 213 81 143 286 1.4 1 174 112 144 224 1.4 1 171 53 145 534 1.4 1 487 47 146 450 1.4 1 389 61 147 2769 1.4 1 2540 229 148 1423 1.4 1 1291 132 149 450 1.4 1 429 21 150 4827 1.4 1 4616 211 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth12_R2_001.fastq.gz ============================================= 95078293 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 95078293 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 655588 (0.69%)