SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth7_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/Meth7_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 2949.95 s (31 us/read; 1.96 M reads/minute). === Summary === Total reads processed: 96,207,245 Reads with adapters: 66,820,598 (69.5%) Reads written (passing filters): 96,207,245 (100.0%) Total basepairs processed: 14,431,086,750 bp Quality-trimmed: 19,271,839 bp (0.1%) Total written (filtered): 12,420,465,978 bp (86.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 66820598 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 36.6% C: 16.4% G: 16.1% T: 30.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 18893415 24051811.2 0 18893415 2 2075402 6012952.8 0 2075402 3 1074832 1503238.2 0 1074832 4 730565 375809.6 0 730565 5 580700 93952.4 0 580700 6 491843 23488.1 0 491843 7 522550 5872.0 0 522550 8 574535 1468.0 0 574535 9 523760 367.0 0 511010 12750 10 551855 91.8 1 517158 34697 11 582007 22.9 1 539163 42844 12 586589 5.7 1 548044 38545 13 567003 1.4 1 527337 39666 14 586004 1.4 1 542029 43975 15 586147 1.4 1 543616 42531 16 593848 1.4 1 549250 44598 17 620099 1.4 1 573194 46905 18 588658 1.4 1 548830 39828 19 579962 1.4 1 539737 40225 20 594745 1.4 1 553187 41558 21 607750 1.4 1 564289 43461 22 598226 1.4 1 557033 41193 23 635604 1.4 1 590527 45077 24 586555 1.4 1 539603 46952 25 605497 1.4 1 563591 41906 26 593682 1.4 1 552487 41195 27 612737 1.4 1 570472 42265 28 603319 1.4 1 562873 40446 29 601801 1.4 1 560787 41014 30 597397 1.4 1 560562 36835 31 589632 1.4 1 552154 37478 32 599864 1.4 1 562538 37326 33 600972 1.4 1 561842 39130 34 609415 1.4 1 570334 39081 35 596730 1.4 1 557997 38733 36 621741 1.4 1 581719 40022 37 598406 1.4 1 554479 43927 38 587255 1.4 1 552033 35222 39 606528 1.4 1 564104 42424 40 764827 1.4 1 726986 37841 41 404975 1.4 1 371970 33005 42 576453 1.4 1 541025 35428 43 612011 1.4 1 571195 40816 44 570091 1.4 1 527482 42609 45 797978 1.4 1 760167 37811 46 331195 1.4 1 305285 25910 47 554541 1.4 1 520335 34206 48 566789 1.4 1 531638 35151 49 558560 1.4 1 524333 34227 50 538884 1.4 1 503131 35753 51 560715 1.4 1 522963 37752 52 539256 1.4 1 506364 32892 53 524054 1.4 1 491032 33022 54 528681 1.4 1 494411 34270 55 534643 1.4 1 500987 33656 56 507072 1.4 1 475525 31547 57 515673 1.4 1 483351 32322 58 533527 1.4 1 501349 32178 59 459223 1.4 1 429002 30221 60 487148 1.4 1 457924 29224 61 460611 1.4 1 431426 29185 62 478646 1.4 1 448702 29944 63 469042 1.4 1 439966 29076 64 466395 1.4 1 438681 27714 65 397730 1.4 1 370996 26734 66 453532 1.4 1 423943 29589 67 508141 1.4 1 475422 32719 68 528689 1.4 1 495643 33046 69 491943 1.4 1 448180 43763 70 935459 1.4 1 897026 38433 71 66887 1.4 1 61349 5538 72 47925 1.4 1 40567 7358 73 198195 1.4 1 183494 14701 74 302845 1.4 1 283180 19665 75 326283 1.4 1 305671 20612 76 322166 1.4 1 301376 20790 77 312601 1.4 1 292445 20156 78 301088 1.4 1 281054 20034 79 294019 1.4 1 274810 19209 80 282610 1.4 1 263801 18809 81 270475 1.4 1 252551 17924 82 261004 1.4 1 243724 17280 83 251344 1.4 1 234576 16768 84 240432 1.4 1 224432 16000 85 232334 1.4 1 216933 15401 86 221499 1.4 1 206669 14830 87 215211 1.4 1 200849 14362 88 189862 1.4 1 176031 13831 89 178105 1.4 1 164999 13106 90 172068 1.4 1 159584 12484 91 166119 1.4 1 154162 11957 92 157287 1.4 1 146104 11183 93 146262 1.4 1 135496 10766 94 138741 1.4 1 128833 9908 95 129089 1.4 1 119561 9528 96 120481 1.4 1 111443 9038 97 110869 1.4 1 102513 8356 98 102578 1.4 1 94496 8082 99 94646 1.4 1 87244 7402 100 89245 1.4 1 82113 7132 101 81358 1.4 1 74573 6785 102 74918 1.4 1 68660 6258 103 68945 1.4 1 63064 5881 104 63207 1.4 1 57686 5521 105 57242 1.4 1 52246 4996 106 52314 1.4 1 47521 4793 107 47066 1.4 1 42551 4515 108 42246 1.4 1 38201 4045 109 38600 1.4 1 34623 3977 110 33927 1.4 1 30387 3540 111 30596 1.4 1 27273 3323 112 27117 1.4 1 24103 3014 113 24611 1.4 1 21688 2923 114 21494 1.4 1 18841 2653 115 19212 1.4 1 16899 2313 116 17131 1.4 1 14849 2282 117 15036 1.4 1 13033 2003 118 13359 1.4 1 11542 1817 119 11717 1.4 1 10030 1687 120 10232 1.4 1 8719 1513 121 9285 1.4 1 7764 1521 122 8582 1.4 1 7202 1380 123 7857 1.4 1 6556 1301 124 7039 1.4 1 5809 1230 125 6765 1.4 1 5698 1067 126 8112 1.4 1 6897 1215 127 7797 1.4 1 6701 1096 128 6069 1.4 1 5118 951 129 5321 1.4 1 4563 758 130 5103 1.4 1 4363 740 131 6000 1.4 1 5279 721 132 5773 1.4 1 5003 770 133 7617 1.4 1 6735 882 134 6688 1.4 1 5947 741 135 2292 1.4 1 1834 458 136 1048 1.4 1 766 282 137 826 1.4 1 531 295 138 753 1.4 1 528 225 139 505 1.4 1 270 235 140 421 1.4 1 268 153 141 292 1.4 1 159 133 142 235 1.4 1 136 99 143 174 1.4 1 110 64 144 168 1.4 1 104 64 145 287 1.4 1 221 66 146 324 1.4 1 266 58 147 2001 1.4 1 1767 234 148 1053 1.4 1 933 120 149 368 1.4 1 330 38 150 5131 1.4 1 4735 396 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth7_R1_001.fastq.gz ============================================= 96207245 sequences processed in total