SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth11_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/Meth11_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 1776.03 s (31 us/read; 1.93 M reads/minute). === Summary === Total reads processed: 57,269,773 Reads with adapters: 36,706,809 (64.1%) Reads written (passing filters): 57,269,773 (100.0%) Total basepairs processed: 8,590,465,950 bp Quality-trimmed: 10,574,753 bp (0.1%) Total written (filtered): 7,658,565,162 bp (89.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 36706809 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 38.8% C: 16.9% G: 13.9% T: 30.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 13982278 14317443.2 0 13982278 2 1272605 3579360.8 0 1272605 3 616626 894840.2 0 616626 4 399599 223710.1 0 399599 5 297560 55927.5 0 297560 6 250136 13981.9 0 250136 7 266111 3495.5 0 266111 8 288918 873.9 0 288918 9 271113 218.5 0 265390 5723 10 279544 54.6 1 264129 15415 11 294465 13.7 1 274988 19477 12 298990 3.4 1 281558 17432 13 283809 0.9 1 266082 17727 14 291926 0.9 1 272443 19483 15 289444 0.9 1 270991 18453 16 291726 0.9 1 271848 19878 17 301649 0.9 1 281196 20453 18 287390 0.9 1 270155 17235 19 282484 0.9 1 265004 17480 20 288996 0.9 1 271191 17805 21 293094 0.9 1 274500 18594 22 289715 0.9 1 272137 17578 23 294469 0.9 1 275458 19011 24 291501 0.9 1 270616 20885 25 286994 0.9 1 268986 18008 26 286191 0.9 1 268476 17715 27 293187 0.9 1 275154 18033 28 280749 0.9 1 264395 16354 29 285836 0.9 1 268364 17472 30 282183 0.9 1 267200 14983 31 276439 0.9 1 261052 15387 32 278845 0.9 1 263555 15290 33 278270 0.9 1 261863 16407 34 280484 0.9 1 264520 15964 35 270772 0.9 1 256556 14216 36 273552 0.9 1 258558 14994 37 270503 0.9 1 256113 14390 38 269801 0.9 1 254354 15447 39 307927 0.9 1 292977 14950 40 228292 0.9 1 213693 14599 41 262916 0.9 1 247928 14988 42 310441 0.9 1 295775 14666 43 214783 0.9 1 200500 14283 44 261094 0.9 1 244473 16621 45 348358 0.9 1 333791 14567 46 155990 0.9 1 145446 10544 47 246315 0.9 1 233080 13235 48 253542 0.9 1 239845 13697 49 242860 0.9 1 229843 13017 50 236542 0.9 1 222793 13749 51 256172 0.9 1 241268 14904 52 230905 0.9 1 218690 12215 53 225380 0.9 1 213051 12329 54 232326 0.9 1 219163 13163 55 232548 0.9 1 220387 12161 56 218193 0.9 1 206384 11809 57 223916 0.9 1 211977 11939 58 230390 0.9 1 218148 12242 59 207275 0.9 1 195384 11891 60 206194 0.9 1 195797 10397 61 195645 0.9 1 185124 10521 62 208679 0.9 1 197641 11038 63 208281 0.9 1 197739 10542 64 194879 0.9 1 184959 9920 65 174970 0.9 1 164625 10345 66 200053 0.9 1 189080 10973 67 204501 0.9 1 193222 11279 68 217395 0.9 1 205150 12245 69 211131 0.9 1 194236 16895 70 433015 0.9 1 417582 15433 71 38685 0.9 1 36188 2497 72 21854 0.9 1 19319 2535 73 72469 0.9 1 67203 5266 74 127570 0.9 1 120370 7200 75 140965 0.9 1 133156 7809 76 141040 0.9 1 133125 7915 77 136732 0.9 1 129051 7681 78 133000 0.9 1 125447 7553 79 130736 0.9 1 123441 7295 80 123899 0.9 1 116847 7052 81 120530 0.9 1 113828 6702 82 116290 0.9 1 109538 6752 83 113154 0.9 1 106811 6343 84 108150 0.9 1 101817 6333 85 104580 0.9 1 98445 6135 86 100366 0.9 1 94548 5818 87 98603 0.9 1 93171 5432 88 86456 0.9 1 81142 5314 89 82757 0.9 1 77660 5097 90 79793 0.9 1 74838 4955 91 77171 0.9 1 72293 4878 92 72816 0.9 1 68413 4403 93 69895 0.9 1 65420 4475 94 65365 0.9 1 61111 4254 95 61385 0.9 1 57350 4035 96 57430 0.9 1 53681 3749 97 54052 0.9 1 50321 3731 98 50877 0.9 1 47462 3415 99 47187 0.9 1 43985 3202 100 43700 0.9 1 40634 3066 101 40961 0.9 1 37957 3004 102 37929 0.9 1 35132 2797 103 35167 0.9 1 32514 2653 104 32627 0.9 1 30181 2446 105 29931 0.9 1 27484 2447 106 28066 0.9 1 25789 2277 107 25817 0.9 1 23703 2114 108 22839 0.9 1 20877 1962 109 19830 0.9 1 18204 1626 110 17973 0.9 1 16390 1583 111 16561 0.9 1 14903 1658 112 14658 0.9 1 13236 1422 113 13084 0.9 1 11717 1367 114 11483 0.9 1 10188 1295 115 10860 0.9 1 9574 1286 116 9285 0.9 1 8192 1093 117 8359 0.9 1 7430 929 118 7648 0.9 1 6652 996 119 6490 0.9 1 5641 849 120 5765 0.9 1 4943 822 121 5033 0.9 1 4278 755 122 4865 0.9 1 4139 726 123 4372 0.9 1 3730 642 124 3987 0.9 1 3368 619 125 4223 0.9 1 3593 630 126 7107 0.9 1 6256 851 127 6334 0.9 1 5554 780 128 3487 0.9 1 2933 554 129 3044 0.9 1 2511 533 130 4342 0.9 1 3706 636 131 8508 0.9 1 7754 754 132 11085 0.9 1 10293 792 133 17731 0.9 1 16507 1224 134 18066 0.9 1 16825 1241 135 5794 0.9 1 5274 520 136 1625 0.9 1 1370 255 137 938 0.9 1 721 217 138 798 0.9 1 569 229 139 380 0.9 1 255 125 140 308 0.9 1 208 100 141 151 0.9 1 74 77 142 113 0.9 1 55 58 143 76 0.9 1 46 30 144 164 0.9 1 131 33 145 570 0.9 1 476 94 146 636 0.9 1 513 123 147 3935 0.9 1 3353 582 148 2549 0.9 1 2094 455 149 1118 0.9 1 939 179 150 13768 0.9 1 12403 1365 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth11_R1_001.fastq.gz ============================================= 57269773 sequences processed in total