SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth11_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/Meth11_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 1845.06 s (32 us/read; 1.86 M reads/minute). === Summary === Total reads processed: 57,269,773 Reads with adapters: 35,875,658 (62.6%) Reads written (passing filters): 57,269,773 (100.0%) Total basepairs processed: 8,590,465,950 bp Quality-trimmed: 49,403,829 bp (0.6%) Total written (filtered): 7,661,639,634 bp (89.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 35875658 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 36.6% C: 13.2% G: 17.9% T: 32.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 13652070 14317443.2 0 13652070 2 1371554 3579360.8 0 1371554 3 670390 894840.2 0 670390 4 417479 223710.1 0 417479 5 303084 55927.5 0 303084 6 241419 13981.9 0 241419 7 247953 3495.5 0 247953 8 300759 873.9 0 300759 9 244986 218.5 0 241363 3623 10 267107 54.6 1 251813 15294 11 288379 13.7 1 266578 21801 12 308750 3.4 1 288531 20219 13 263280 0.9 1 242595 20685 14 283158 0.9 1 261771 21387 15 273211 0.9 1 254413 18798 16 295565 0.9 1 272704 22861 17 291590 0.9 1 270953 20637 18 257791 0.9 1 240881 16910 19 298939 0.9 1 278827 20112 20 294388 0.9 1 275007 19381 21 259793 0.9 1 240679 19114 22 288102 0.9 1 269983 18119 23 272758 0.9 1 255357 17401 24 302255 0.9 1 282101 20154 25 346143 0.9 1 327110 19033 26 221906 0.9 1 206394 15512 27 257508 0.9 1 239993 17515 28 266794 0.9 1 253852 12942 29 278302 0.9 1 262931 15371 30 273410 0.9 1 259852 13558 31 269441 0.9 1 255190 14251 32 265656 0.9 1 252921 12735 33 274926 0.9 1 259601 15325 34 266938 0.9 1 254391 12547 35 325149 0.9 1 310396 14753 36 211849 0.9 1 198782 13067 37 275447 0.9 1 260850 14597 38 262895 0.9 1 248000 14895 39 250310 0.9 1 239428 10882 40 261993 0.9 1 247371 14622 41 267420 0.9 1 254707 12713 42 268773 0.9 1 255253 13520 43 234071 0.9 1 222435 11636 44 301151 0.9 1 286586 14565 45 280759 0.9 1 265724 15035 46 299635 0.9 1 284753 14882 47 312695 0.9 1 301613 11082 48 157512 0.9 1 149001 8511 49 213512 0.9 1 203376 10136 50 235473 0.9 1 226110 9363 51 178012 0.9 1 169464 8548 52 234813 0.9 1 224858 9955 53 209236 0.9 1 199293 9943 54 316092 0.9 1 305412 10680 55 112244 0.9 1 105473 6771 56 220830 0.9 1 208113 12717 57 508437 0.9 1 492031 16406 58 107616 0.9 1 101036 6580 59 141028 0.9 1 132803 8225 60 328748 0.9 1 317231 11517 61 170989 0.9 1 163213 7776 62 190271 0.9 1 176527 13744 63 598469 0.9 1 582057 16412 64 196175 0.9 1 189111 7064 65 75303 0.9 1 71391 3912 66 93127 0.9 1 86983 6144 67 252236 0.9 1 243838 8398 68 139122 0.9 1 133347 5775 69 101848 0.9 1 96919 4929 70 148277 0.9 1 142823 5454 71 96395 0.9 1 92108 4287 72 94572 0.9 1 89902 4670 73 122596 0.9 1 117135 5461 74 117845 0.9 1 112409 5436 75 114732 0.9 1 109854 4878 76 85369 0.9 1 81892 3477 77 49961 0.9 1 47013 2948 78 91492 0.9 1 87404 4088 79 112415 0.9 1 107577 4838 80 115758 0.9 1 110808 4950 81 110029 0.9 1 105236 4793 82 106598 0.9 1 101879 4719 83 107411 0.9 1 102853 4558 84 102221 0.9 1 97792 4429 85 99548 0.9 1 95304 4244 86 91834 0.9 1 88022 3812 87 87435 0.9 1 83652 3783 88 82206 0.9 1 78618 3588 89 78920 0.9 1 75577 3343 90 75420 0.9 1 72180 3240 91 71229 0.9 1 68159 3070 92 66879 0.9 1 63939 2940 93 63376 0.9 1 60471 2905 94 58378 0.9 1 55732 2646 95 55848 0.9 1 53239 2609 96 52506 0.9 1 49995 2511 97 49733 0.9 1 47319 2414 98 47175 0.9 1 44951 2224 99 44576 0.9 1 42258 2318 100 41299 0.9 1 39149 2150 101 37729 0.9 1 35880 1849 102 34327 0.9 1 32542 1785 103 31505 0.9 1 29933 1572 104 29038 0.9 1 27496 1542 105 27014 0.9 1 25593 1421 106 25246 0.9 1 23877 1369 107 23541 0.9 1 22243 1298 108 20574 0.9 1 19364 1210 109 18140 0.9 1 17020 1120 110 16344 0.9 1 15303 1041 111 14718 0.9 1 13778 940 112 13229 0.9 1 12375 854 113 11880 0.9 1 10969 911 114 10325 0.9 1 9514 811 115 9876 0.9 1 9056 820 116 8659 0.9 1 7917 742 117 7984 0.9 1 7254 730 118 7051 0.9 1 6346 705 119 6120 0.9 1 5502 618 120 5404 0.9 1 4811 593 121 4475 0.9 1 3981 494 122 4366 0.9 1 3809 557 123 4026 0.9 1 3465 561 124 3652 0.9 1 3170 482 125 3933 0.9 1 3413 520 126 6525 0.9 1 5801 724 127 5731 0.9 1 5038 693 128 3229 0.9 1 2781 448 129 2875 0.9 1 2498 377 130 4906 0.9 1 4365 541 131 9003 0.9 1 8372 631 132 11425 0.9 1 10654 771 133 20494 0.9 1 19096 1398 134 19061 0.9 1 17759 1302 135 5795 0.9 1 5297 498 136 1682 0.9 1 1494 188 137 1060 0.9 1 890 170 138 733 0.9 1 578 155 139 345 0.9 1 259 86 140 325 0.9 1 255 70 141 178 0.9 1 98 80 142 100 0.9 1 57 43 143 102 0.9 1 66 36 144 193 0.9 1 140 53 145 617 0.9 1 561 56 146 465 0.9 1 385 80 147 2118 0.9 1 1805 313 148 1327 0.9 1 1096 231 149 604 0.9 1 524 80 150 6552 0.9 1 6036 516 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth11_R2_001.fastq.gz ============================================= 57269773 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 57269773 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 424184 (0.74%)