SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth14_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; 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 File was specified to be an MspI-digested RRBS sample. Read 1 sequences with adapter contamination will be trimmed a further 2 bp from their 3' end, and Read 2 sequences will be trimmed by 2 bp from their 5' end to remove potential methylation-biased bases from the end-repair reaction File was specified to be a non-directional MspI-digested RRBS sample. Sequences starting with either 'CAA' or 'CGA' will have the first 2 bp trimmed off to remove potential methylation-biased bases from the end-repair reaction Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /gscratch/scrubbed/strigg/analyses/20200311/RRBS/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 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/strigg/analyses/20200311/RRBS/Meth14_R1_001.fastq.gz_qual_trimmed.fastq 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 1651.33 s (24 us/read; 2.52 M reads/minute). === Summary === Total reads processed: 69,473,196 Reads with adapters: 55,400,990 (79.7%) Reads written (passing filters): 69,473,196 (100.0%) Total basepairs processed: 10,409,777,720 bp Total written (filtered): 7,291,489,780 bp (70.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 55400990 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 40.9% C: 2.5% G: 51.1% T: 5.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 8782866 17368299.0 0 8782866 2 857608 4342074.8 0 857608 3 658045 1085518.7 0 658045 4 300067 271379.7 0 300067 5 207375 67844.9 0 207375 6 181801 16961.2 0 181801 7 219369 4240.3 0 219369 8 219799 1060.1 0 219799 9 205689 265.0 0 202777 2912 10 246677 66.3 1 226049 20628 11 418235 16.6 1 378095 40140 12 254220 4.1 1 229651 24569 13 229447 1.0 1 205325 24122 14 231819 1.0 1 206513 25306 15 197934 1.0 1 176411 21523 16 207582 1.0 1 184590 22992 17 239494 1.0 1 213264 26230 18 227732 1.0 1 204314 23418 19 240456 1.0 1 215059 25397 20 243286 1.0 1 218005 25281 21 270542 1.0 1 241962 28580 22 261114 1.0 1 233681 27433 23 324289 1.0 1 290172 34117 24 304424 1.0 1 270683 33741 25 268262 1.0 1 239785 28477 26 230253 1.0 1 205804 24449 27 266605 1.0 1 238152 28453 28 422673 1.0 1 378173 44500 29 273666 1.0 1 242704 30962 30 258507 1.0 1 230975 27532 31 260642 1.0 1 232758 27884 32 282796 1.0 1 252895 29901 33 251359 1.0 1 223613 27746 34 270491 1.0 1 241227 29264 35 261946 1.0 1 233346 28600 36 264319 1.0 1 234923 29396 37 363860 1.0 1 324492 39368 38 330615 1.0 1 294792 35823 39 317729 1.0 1 281947 35782 40 443709 1.0 1 396553 47156 41 439031 1.0 1 392495 46536 42 293226 1.0 1 261246 31980 43 349316 1.0 1 310324 38992 44 278944 1.0 1 247166 31778 45 430265 1.0 1 386344 43921 46 209795 1.0 1 186554 23241 47 270492 1.0 1 241475 29017 48 338914 1.0 1 301468 37446 49 608396 1.0 1 543874 64522 50 345036 1.0 1 305958 39078 51 393371 1.0 1 346977 46394 52 434189 1.0 1 387030 47159 53 375166 1.0 1 333040 42126 54 677937 1.0 1 602728 75209 55 438277 1.0 1 389961 48316 56 336391 1.0 1 299219 37172 57 381521 1.0 1 338996 42525 58 578958 1.0 1 514594 64364 59 348832 1.0 1 309050 39782 60 690597 1.0 1 616628 73969 61 378363 1.0 1 335286 43077 62 371312 1.0 1 328574 42738 63 325780 1.0 1 288761 37019 64 360043 1.0 1 320109 39934 65 299565 1.0 1 265521 34044 66 351273 1.0 1 310428 40845 67 446381 1.0 1 393754 52627 68 581169 1.0 1 513322 67847 69 555370 1.0 1 477063 78307 70 1821958 1.0 1 1645415 176543 71 159722 1.0 1 141530 18192 72 66696 1.0 1 57291 9405 73 388987 1.0 1 339110 49877 74 1374358 1.0 1 1216794 157564 75 332841 1.0 1 292206 40635 76 416417 1.0 1 367866 48551 77 460145 1.0 1 406050 54095 78 331342 1.0 1 291983 39359 79 366128 1.0 1 323010 43118 80 382456 1.0 1 336936 45520 81 326902 1.0 1 287716 39186 82 348100 1.0 1 306813 41287 83 332056 1.0 1 292244 39812 84 475457 1.0 1 419007 56450 85 420225 1.0 1 369669 50556 86 345642 1.0 1 303706 41936 87 426380 1.0 1 375165 51215 88 363082 1.0 1 318909 44173 89 441663 1.0 1 388095 53568 90 420556 1.0 1 368610 51946 91 461064 1.0 1 404128 56936 92 336462 1.0 1 294241 42221 93 393138 1.0 1 344342 48796 94 443807 1.0 1 388607 55200 95 316764 1.0 1 276823 39941 96 338920 1.0 1 295107 43813 97 449770 1.0 1 391931 57839 98 424585 1.0 1 369668 54917 99 375734 1.0 1 327187 48547 100 399744 1.0 1 347485 52259 101 306235 1.0 1 266586 39649 102 303444 1.0 1 263487 39957 103 381845 1.0 1 331309 50536 104 325653 1.0 1 282316 43337 105 312837 1.0 1 271156 41681 106 518166 1.0 1 449072 69094 107 394290 1.0 1 340403 53887 108 400937 1.0 1 346365 54572 109 457671 1.0 1 394132 63539 110 296032 1.0 1 255379 40653 111 290983 1.0 1 250446 40537 112 324856 1.0 1 279357 45499 113 280038 1.0 1 240483 39555 114 482507 1.0 1 414788 67719 115 943892 1.0 1 812500 131392 116 271430 1.0 1 232083 39347 117 382741 1.0 1 327790 54951 118 350788 1.0 1 300238 50550 119 368835 1.0 1 315411 53424 120 207719 1.0 1 177597 30122 121 211750 1.0 1 180751 30999 122 191203 1.0 1 162999 28204 123 206942 1.0 1 176595 30347 124 200886 1.0 1 171101 29785 125 263147 1.0 1 224479 38668 126 157461 1.0 1 133795 23666 127 132546 1.0 1 112871 19675 128 82021 1.0 1 69657 12364 129 66010 1.0 1 56158 9852 130 47701 1.0 1 40590 7111 131 65077 1.0 1 55570 9507 132 29191 1.0 1 24701 4490 133 10959 1.0 1 9307 1652 134 6055 1.0 1 5140 915 135 1656 1.0 1 1395 261 136 705 1.0 1 608 97 137 41 1.0 1 32 9 138 10 1.0 1 10 139 6 1.0 1 6 140 9 1.0 1 9 141 6 1.0 1 4 2 142 2 1.0 1 2 144 1 1.0 1 0 1 145 2 1.0 1 1 1 148 59 1.0 1 52 7 149 26 1.0 1 17 9 150 306 1.0 1 266 40 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth14_R1_001.fastq.gz ============================================= 69473196 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 3888847 (5.6%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 30667943 (44.1%) RRBS reads trimmed by 2 bp at the start when read started with CAA (641373) or CGA (30028291) in total: 30669664 (44.1%)