SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth16_R1_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/Meth16_R1_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 2293.21 s (31 us/read; 1.96 M reads/minute). === Summary === Total reads processed: 74,853,767 Reads with adapters: 48,037,292 (64.2%) Reads written (passing filters): 74,853,767 (100.0%) Total basepairs processed: 11,228,065,050 bp Quality-trimmed: 36,053,773 bp (0.3%) Total written (filtered): 9,837,986,914 bp (87.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 48037292 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 36.2% C: 18.3% G: 15.5% T: 30.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 17313868 18713441.8 0 17313868 2 1583328 4678360.4 0 1583328 3 734995 1169590.1 0 734995 4 484487 292397.5 0 484487 5 365747 73099.4 0 365747 6 306052 18274.8 0 306052 7 326825 4568.7 0 326825 8 355821 1142.2 0 355821 9 329077 285.5 0 318768 10309 10 350603 71.4 1 323517 27086 11 363844 17.8 1 332511 31333 12 370191 4.5 1 340171 30020 13 360136 1.1 1 329053 31083 14 364817 1.1 1 332231 32586 15 363063 1.1 1 331453 31610 16 367140 1.1 1 334097 33043 17 377091 1.1 1 343906 33185 18 369893 1.1 1 339507 30386 19 355969 1.1 1 326336 29633 20 368159 1.1 1 336773 31386 21 367387 1.1 1 336304 31083 22 368597 1.1 1 337612 30985 23 374460 1.1 1 342564 31896 24 360467 1.1 1 327479 32988 25 365354 1.1 1 334690 30664 26 358786 1.1 1 328491 30295 27 368523 1.1 1 338620 29903 28 354139 1.1 1 325824 28315 29 361461 1.1 1 333316 28145 30 357984 1.1 1 332552 25432 31 350548 1.1 1 325225 25323 32 352088 1.1 1 326296 25792 33 353494 1.1 1 326851 26643 34 357245 1.1 1 330047 27198 35 388681 1.1 1 361266 27415 36 323469 1.1 1 295859 27610 37 349230 1.1 1 323398 25832 38 356217 1.1 1 330275 25942 39 340660 1.1 1 314720 25940 40 344816 1.1 1 319567 25249 41 345993 1.1 1 317927 28066 42 432513 1.1 1 404984 27529 43 269958 1.1 1 241567 28391 44 341755 1.1 1 311467 30288 45 470912 1.1 1 442075 28837 46 207165 1.1 1 186995 20170 47 370164 1.1 1 317931 52233 48 1092468 1.1 1 1030000 62468 49 338111 1.1 1 314927 23184 50 250889 1.1 1 218205 32684 51 693389 1.1 1 655996 37393 52 216232 1.1 1 201252 14980 53 149513 1.1 1 127675 21838 54 515579 1.1 1 479477 36102 55 434588 1.1 1 409565 25023 56 195335 1.1 1 178481 16854 57 277121 1.1 1 261646 15475 58 150426 1.1 1 132871 17555 59 370147 1.1 1 351761 18386 60 96297 1.1 1 88498 7799 61 124619 1.1 1 110743 13876 62 295323 1.1 1 276486 18837 63 201374 1.1 1 190618 10756 64 97923 1.1 1 87928 9995 65 236194 1.1 1 218487 17707 66 263554 1.1 1 248715 14839 67 112345 1.1 1 101331 11014 68 218261 1.1 1 201501 16760 69 240572 1.1 1 213510 27062 70 463476 1.1 1 436848 26628 71 175158 1.1 1 165372 9786 72 66039 1.1 1 61303 4736 73 46538 1.1 1 40240 6298 74 127225 1.1 1 115404 11821 75 178458 1.1 1 163549 14909 76 195988 1.1 1 180316 15672 77 184658 1.1 1 169056 15602 78 182029 1.1 1 166775 15254 79 183405 1.1 1 168575 14830 80 172253 1.1 1 157933 14320 81 168491 1.1 1 154027 14464 82 172525 1.1 1 158471 14054 83 165173 1.1 1 151286 13887 84 155803 1.1 1 142247 13556 85 153354 1.1 1 139663 13691 86 147524 1.1 1 135117 12407 87 145467 1.1 1 133330 12137 88 130493 1.1 1 118765 11728 89 118194 1.1 1 106908 11286 90 113080 1.1 1 102483 10597 91 112244 1.1 1 101690 10554 92 109435 1.1 1 99380 10055 93 103795 1.1 1 94108 9687 94 102631 1.1 1 92932 9699 95 97961 1.1 1 88897 9064 96 91876 1.1 1 83190 8686 97 86589 1.1 1 78224 8365 98 80136 1.1 1 72237 7899 99 75024 1.1 1 67446 7578 100 71637 1.1 1 64122 7515 101 70871 1.1 1 63555 7316 102 64137 1.1 1 57054 7083 103 59036 1.1 1 52880 6156 104 62022 1.1 1 55212 6810 105 58151 1.1 1 51491 6660 106 58726 1.1 1 52266 6460 107 54282 1.1 1 47901 6381 108 46819 1.1 1 41236 5583 109 41970 1.1 1 36717 5253 110 39692 1.1 1 34953 4739 111 35311 1.1 1 30880 4431 112 33592 1.1 1 29203 4389 113 34643 1.1 1 30384 4259 114 32144 1.1 1 28069 4075 115 31532 1.1 1 27473 4059 116 33589 1.1 1 29399 4190 117 34762 1.1 1 30672 4090 118 29062 1.1 1 25800 3262 119 24079 1.1 1 21370 2709 120 22610 1.1 1 19799 2811 121 20137 1.1 1 17519 2618 122 21585 1.1 1 19057 2528 123 22643 1.1 1 19986 2657 124 18961 1.1 1 16765 2196 125 19089 1.1 1 16946 2143 126 36041 1.1 1 31917 4124 127 29177 1.1 1 25594 3583 128 16168 1.1 1 14106 2062 129 17006 1.1 1 15017 1989 130 38957 1.1 1 35348 3609 131 73329 1.1 1 69245 4084 132 72500 1.1 1 67887 4613 133 108649 1.1 1 101987 6662 134 103526 1.1 1 97141 6385 135 26937 1.1 1 24874 2063 136 7964 1.1 1 6962 1002 137 5443 1.1 1 4749 694 138 4256 1.1 1 3541 715 139 2400 1.1 1 1838 562 140 1986 1.1 1 1524 462 141 774 1.1 1 515 259 142 538 1.1 1 348 190 143 454 1.1 1 307 147 144 763 1.1 1 623 140 145 2455 1.1 1 2152 303 146 5761 1.1 1 5162 599 147 49520 1.1 1 44674 4846 148 26470 1.1 1 23282 3188 149 6519 1.1 1 5725 794 150 80163 1.1 1 74408 5755 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth16_R1_001.fastq.gz ============================================= 74853767 sequences processed in total