SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth1_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/Meth1_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 2350.59 s (31 us/read; 1.92 M reads/minute). === Summary === Total reads processed: 75,063,646 Reads with adapters: 48,328,955 (64.4%) Reads written (passing filters): 75,063,646 (100.0%) Total basepairs processed: 11,259,546,900 bp Quality-trimmed: 13,767,880 bp (0.1%) Total written (filtered): 10,038,125,535 bp (89.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 48328955 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 39.1% C: 16.0% G: 14.0% T: 30.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 18710709 18765911.5 0 18710709 2 1656344 4691477.9 0 1656344 3 816816 1172869.5 0 816816 4 516096 293217.4 0 516096 5 376016 73304.3 0 376016 6 315457 18326.1 0 315457 7 337109 4581.5 0 337109 8 369652 1145.4 0 369652 9 335509 286.3 0 327477 8032 10 357252 71.6 1 335442 21810 11 372080 17.9 1 345243 26837 12 376270 4.5 1 351799 24471 13 361054 1.1 1 335856 25198 14 375182 1.1 1 347566 27616 15 370274 1.1 1 344585 25689 16 378696 1.1 1 350698 27998 17 390340 1.1 1 361837 28503 18 369733 1.1 1 344851 24882 19 365329 1.1 1 340187 25142 20 372175 1.1 1 346848 25327 21 378433 1.1 1 351678 26755 22 371144 1.1 1 345973 25171 23 382287 1.1 1 355300 26987 24 374251 1.1 1 345132 29119 25 373180 1.1 1 347857 25323 26 369424 1.1 1 344363 25061 27 379615 1.1 1 354423 25192 28 369357 1.1 1 345908 23449 29 366320 1.1 1 342423 23897 30 366803 1.1 1 345225 21578 31 362760 1.1 1 340028 22732 32 400561 1.1 1 377808 22753 33 328870 1.1 1 307922 20948 34 370029 1.1 1 346926 23103 35 359381 1.1 1 337247 22134 36 366007 1.1 1 342210 23797 37 354073 1.1 1 333404 20669 38 359650 1.1 1 337399 22251 39 356932 1.1 1 335239 21693 40 358506 1.1 1 336483 22023 41 349540 1.1 1 327051 22489 42 381911 1.1 1 360544 21367 43 309857 1.1 1 287977 21880 44 342623 1.1 1 317606 25017 45 487516 1.1 1 466022 21494 46 182025 1.1 1 167416 14609 47 325619 1.1 1 306447 19172 48 330513 1.1 1 310694 19819 49 330610 1.1 1 311613 18997 50 313977 1.1 1 294522 19455 51 322321 1.1 1 301535 20786 52 317755 1.1 1 299076 18679 53 305793 1.1 1 287161 18632 54 308320 1.1 1 288750 19570 55 308849 1.1 1 290247 18602 56 296634 1.1 1 278525 18109 57 297862 1.1 1 279673 18189 58 311936 1.1 1 294182 17754 59 264874 1.1 1 248209 16665 60 281522 1.1 1 265089 16433 61 267748 1.1 1 251495 16253 62 273594 1.1 1 257005 16589 63 264311 1.1 1 248380 15931 64 271183 1.1 1 255859 15324 65 228552 1.1 1 214019 14533 66 252781 1.1 1 236108 16673 67 291928 1.1 1 273531 18397 68 298209 1.1 1 280575 17634 69 273052 1.1 1 248426 24626 70 535664 1.1 1 515290 20374 71 39169 1.1 1 36074 3095 72 29751 1.1 1 25209 4542 73 116623 1.1 1 107809 8814 74 174109 1.1 1 163139 10970 75 187073 1.1 1 175273 11800 76 183577 1.1 1 172180 11397 77 176884 1.1 1 165498 11386 78 170780 1.1 1 159859 10921 79 164622 1.1 1 154127 10495 80 159951 1.1 1 149653 10298 81 153932 1.1 1 143914 10018 82 147439 1.1 1 137900 9539 83 143214 1.1 1 134040 9174 84 137291 1.1 1 128259 9032 85 132225 1.1 1 123566 8659 86 125531 1.1 1 117378 8153 87 123532 1.1 1 115683 7849 88 107193 1.1 1 99639 7554 89 100482 1.1 1 93344 7138 90 98338 1.1 1 91292 7046 91 93064 1.1 1 86350 6714 92 89428 1.1 1 82811 6617 93 83308 1.1 1 77158 6150 94 79442 1.1 1 73600 5842 95 74504 1.1 1 68842 5662 96 69303 1.1 1 63977 5326 97 64086 1.1 1 58962 5124 98 59263 1.1 1 54478 4785 99 55431 1.1 1 50932 4499 100 51141 1.1 1 46801 4340 101 48209 1.1 1 44018 4191 102 43538 1.1 1 39871 3667 103 39805 1.1 1 36098 3707 104 38756 1.1 1 35097 3659 105 35421 1.1 1 31970 3451 106 33268 1.1 1 30122 3146 107 29612 1.1 1 26680 2932 108 26797 1.1 1 24049 2748 109 23707 1.1 1 21229 2478 110 21294 1.1 1 19095 2199 111 19347 1.1 1 16984 2363 112 16813 1.1 1 14814 1999 113 16091 1.1 1 14158 1933 114 13670 1.1 1 11893 1777 115 13296 1.1 1 11498 1798 116 11809 1.1 1 10128 1681 117 11544 1.1 1 10095 1449 118 9929 1.1 1 8552 1377 119 8573 1.1 1 7300 1273 120 7809 1.1 1 6511 1298 121 6728 1.1 1 5618 1110 122 7027 1.1 1 5901 1126 123 7546 1.1 1 6434 1112 124 6267 1.1 1 5356 911 125 7049 1.1 1 5992 1057 126 14598 1.1 1 12783 1815 127 13298 1.1 1 11606 1692 128 7112 1.1 1 6061 1051 129 6533 1.1 1 5591 942 130 10720 1.1 1 9489 1231 131 20639 1.1 1 19294 1345 132 24336 1.1 1 22602 1734 133 36762 1.1 1 34343 2419 134 35478 1.1 1 33207 2271 135 11882 1.1 1 10868 1014 136 3678 1.1 1 3202 476 137 2423 1.1 1 2056 367 138 2237 1.1 1 1784 453 139 911 1.1 1 660 251 140 744 1.1 1 534 210 141 277 1.1 1 188 89 142 192 1.1 1 107 85 143 207 1.1 1 148 59 144 361 1.1 1 291 70 145 1422 1.1 1 1247 175 146 1707 1.1 1 1433 274 147 10742 1.1 1 9315 1427 148 6295 1.1 1 5220 1075 149 2023 1.1 1 1738 285 150 23032 1.1 1 20646 2386 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth1_R1_001.fastq.gz ============================================= 75063646 sequences processed in total