SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth2_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/Meth2_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 2693.95 s (31 us/read; 1.91 M reads/minute). === Summary === Total reads processed: 85,631,206 Reads with adapters: 56,009,490 (65.4%) Reads written (passing filters): 85,631,206 (100.0%) Total basepairs processed: 12,844,680,900 bp Quality-trimmed: 167,513,930 bp (1.3%) Total written (filtered): 11,245,362,120 bp (87.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 56009490 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 36.9% C: 12.3% G: 18.3% T: 32.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 19526925 21407801.5 0 19526925 2 1919744 5351950.4 0 1919744 3 1000302 1337987.6 0 1000302 4 624387 334496.9 0 624387 5 454674 83624.2 0 454674 6 362196 20906.1 0 362196 7 377034 5226.5 0 377034 8 444785 1306.6 0 444785 9 388832 326.7 0 383436 5396 10 407705 81.7 1 386713 20992 11 436143 20.4 1 405334 30809 12 474952 5.1 1 446573 28379 13 399014 1.3 1 369972 29042 14 433402 1.3 1 402382 31020 15 423608 1.3 1 394967 28641 16 458900 1.3 1 424925 33975 17 450236 1.3 1 420648 29588 18 404648 1.3 1 378999 25649 19 457394 1.3 1 428403 28991 20 455617 1.3 1 427230 28387 21 416268 1.3 1 386706 29562 22 445263 1.3 1 419296 25967 23 427498 1.3 1 401454 26044 24 468136 1.3 1 438862 29274 25 539381 1.3 1 510526 28855 26 359179 1.3 1 334286 24893 27 414622 1.3 1 386523 28099 28 424441 1.3 1 404630 19811 29 439823 1.3 1 415917 23906 30 438325 1.3 1 418035 20290 31 426447 1.3 1 405301 21146 32 426641 1.3 1 407330 19311 33 437578 1.3 1 415263 22315 34 450100 1.3 1 422845 27255 35 458814 1.3 1 435678 23136 36 416993 1.3 1 398079 18914 37 480885 1.3 1 458188 22697 38 411691 1.3 1 391665 20026 39 416205 1.3 1 393247 22958 40 435739 1.3 1 408154 27585 41 457623 1.3 1 433245 24378 42 434135 1.3 1 413545 20590 43 572046 1.3 1 486118 85928 44 4439629 1.3 1 4327289 112340 45 943878 1.3 1 911234 32644 46 128272 1.3 1 113627 14645 47 649748 1.3 1 632500 17248 48 112027 1.3 1 103900 8127 49 226791 1.3 1 217697 9094 50 87315 1.3 1 81645 5670 51 160416 1.3 1 152783 7633 52 131115 1.3 1 124683 6432 53 165120 1.3 1 156944 8176 54 288967 1.3 1 279986 8981 55 127760 1.3 1 119298 8462 56 303442 1.3 1 286641 16801 57 668371 1.3 1 649676 18695 58 276318 1.3 1 265945 10373 59 152522 1.3 1 138015 14507 60 753840 1.3 1 734648 19192 61 274683 1.3 1 266406 8277 62 121713 1.3 1 112855 8858 63 377150 1.3 1 360264 16886 64 665350 1.3 1 649400 15950 65 104039 1.3 1 97711 6328 66 185040 1.3 1 178240 6800 67 116812 1.3 1 112189 4623 68 75589 1.3 1 72032 3557 69 48396 1.3 1 45577 2819 70 67820 1.3 1 64844 2976 71 48667 1.3 1 45837 2830 72 50159 1.3 1 46982 3177 73 70809 1.3 1 67074 3735 74 79735 1.3 1 75654 4081 75 87261 1.3 1 82766 4495 76 99775 1.3 1 95872 3903 77 59243 1.3 1 56439 2804 78 41631 1.3 1 39083 2548 79 62831 1.3 1 59486 3345 80 105952 1.3 1 101110 4842 81 143806 1.3 1 137879 5927 82 165444 1.3 1 158559 6885 83 182667 1.3 1 175483 7184 84 179947 1.3 1 172375 7572 85 183023 1.3 1 175727 7296 86 170339 1.3 1 163207 7132 87 160845 1.3 1 154267 6578 88 154171 1.3 1 147653 6518 89 147406 1.3 1 141317 6089 90 140259 1.3 1 134485 5774 91 132661 1.3 1 127057 5604 92 126408 1.3 1 121113 5295 93 120125 1.3 1 114920 5205 94 113174 1.3 1 108198 4976 95 105900 1.3 1 101224 4676 96 100579 1.3 1 96075 4504 97 95543 1.3 1 91403 4140 98 89238 1.3 1 85105 4133 99 84749 1.3 1 80958 3791 100 80264 1.3 1 76639 3625 101 71563 1.3 1 68287 3276 102 65843 1.3 1 62764 3079 103 59920 1.3 1 56915 3005 104 55387 1.3 1 52561 2826 105 51457 1.3 1 48888 2569 106 47709 1.3 1 45121 2588 107 43372 1.3 1 41022 2350 108 38957 1.3 1 36799 2158 109 34416 1.3 1 32322 2094 110 31685 1.3 1 29917 1768 111 28010 1.3 1 26357 1653 112 25151 1.3 1 23577 1574 113 21258 1.3 1 19851 1407 114 19115 1.3 1 17637 1478 115 17407 1.3 1 16078 1329 116 15372 1.3 1 14247 1125 117 14590 1.3 1 13440 1150 118 12148 1.3 1 11131 1017 119 10485 1.3 1 9606 879 120 8898 1.3 1 8119 779 121 7605 1.3 1 6869 736 122 7263 1.3 1 6440 823 123 6993 1.3 1 6244 749 124 5779 1.3 1 5103 676 125 6277 1.3 1 5595 682 126 11920 1.3 1 10762 1158 127 11003 1.3 1 9795 1208 128 5654 1.3 1 4913 741 129 4491 1.3 1 3966 525 130 8303 1.3 1 7551 752 131 14370 1.3 1 13513 857 132 17188 1.3 1 16250 938 133 30441 1.3 1 28534 1907 134 29014 1.3 1 27337 1677 135 8819 1.3 1 8235 584 136 2701 1.3 1 2413 288 137 1834 1.3 1 1630 204 138 1309 1.3 1 1091 218 139 635 1.3 1 515 120 140 514 1.3 1 400 114 141 238 1.3 1 153 85 142 181 1.3 1 106 75 143 179 1.3 1 128 51 144 334 1.3 1 282 52 145 1211 1.3 1 1101 110 146 966 1.3 1 827 139 147 4175 1.3 1 3631 544 148 2504 1.3 1 2101 403 149 1025 1.3 1 894 131 150 10756 1.3 1 9962 794 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth2_R2_001.fastq.gz ============================================= 85631206 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 85631206 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 671988 (0.78%)