SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth1_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/Meth1_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 2419.51 s (32 us/read; 1.86 M reads/minute). === Summary === Total reads processed: 75,063,646 Reads with adapters: 47,220,569 (62.9%) Reads written (passing filters): 75,063,646 (100.0%) Total basepairs processed: 11,259,546,900 bp Quality-trimmed: 59,942,666 bp (0.5%) Total written (filtered): 10,051,947,808 bp (89.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 47220569 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 37.3% C: 12.8% G: 17.4% T: 32.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 18441421 18765911.5 0 18441421 2 1750991 4691477.9 0 1750991 3 877760 1172869.5 0 877760 4 542351 293217.4 0 542351 5 379149 73304.3 0 379149 6 303548 18326.1 0 303548 7 312527 4581.5 0 312527 8 362510 1145.4 0 362510 9 328504 286.3 0 323925 4579 10 338715 71.6 1 321858 16857 11 365879 17.9 1 339451 26428 12 397669 4.5 1 374189 23480 13 325125 1.1 1 301399 23726 14 360991 1.1 1 335177 25814 15 349921 1.1 1 325228 24693 16 382894 1.1 1 354217 28677 17 367351 1.1 1 342834 24517 18 338458 1.1 1 316318 22140 19 376286 1.1 1 352494 23792 20 379077 1.1 1 354928 24149 21 343774 1.1 1 318864 24910 22 366212 1.1 1 344159 22053 23 350055 1.1 1 328241 21814 24 376199 1.1 1 352432 23767 25 423461 1.1 1 399691 23770 26 307403 1.1 1 285842 21561 27 359312 1.1 1 334581 24731 28 345619 1.1 1 329168 16451 29 359270 1.1 1 339106 20164 30 354441 1.1 1 337793 16648 31 355057 1.1 1 336449 18608 32 350452 1.1 1 334307 16145 33 352943 1.1 1 335135 17808 34 358015 1.1 1 338908 19107 35 464708 1.1 1 445740 18968 36 273302 1.1 1 255292 18010 37 325079 1.1 1 311126 13953 38 335525 1.1 1 318863 16662 39 337577 1.1 1 322860 14717 40 367020 1.1 1 349128 17892 41 319224 1.1 1 304174 15050 42 332649 1.1 1 318337 14312 43 323823 1.1 1 308429 15394 44 334118 1.1 1 319822 14296 45 343494 1.1 1 326408 17086 46 358115 1.1 1 338836 19279 47 402427 1.1 1 387903 14524 48 283932 1.1 1 271129 12803 49 274857 1.1 1 261030 13827 50 315849 1.1 1 303139 12710 51 266831 1.1 1 254373 12458 52 311199 1.1 1 297931 13268 53 287934 1.1 1 274634 13300 54 385122 1.1 1 371431 13691 55 190442 1.1 1 179926 10516 56 295821 1.1 1 280546 15275 57 513539 1.1 1 495845 17694 58 168861 1.1 1 159586 9275 59 223841 1.1 1 212609 11232 60 384551 1.1 1 370691 13860 61 242884 1.1 1 232450 10434 62 233434 1.1 1 216179 17255 63 771347 1.1 1 750613 20734 64 193966 1.1 1 186184 7782 65 119008 1.1 1 112900 6108 66 137693 1.1 1 128970 8723 67 347444 1.1 1 336043 11401 68 204788 1.1 1 196327 8461 69 171955 1.1 1 164002 7953 70 219714 1.1 1 211438 8276 71 159973 1.1 1 153139 6834 72 143819 1.1 1 136598 7221 73 175548 1.1 1 167699 7849 74 158126 1.1 1 150516 7610 75 153760 1.1 1 147027 6733 76 103682 1.1 1 99086 4596 77 77177 1.1 1 72994 4183 78 125043 1.1 1 119651 5392 79 142945 1.1 1 136911 6034 80 147419 1.1 1 141242 6177 81 137880 1.1 1 131886 5994 82 133886 1.1 1 128062 5824 83 133032 1.1 1 127354 5678 84 127298 1.1 1 121870 5428 85 123895 1.1 1 118634 5261 86 113116 1.1 1 108201 4915 87 108156 1.1 1 103506 4650 88 101256 1.1 1 96922 4334 89 94739 1.1 1 90468 4271 90 91660 1.1 1 87538 4122 91 85089 1.1 1 81271 3818 92 80648 1.1 1 76884 3764 93 74350 1.1 1 70748 3602 94 70493 1.1 1 67010 3483 95 66098 1.1 1 62873 3225 96 62060 1.1 1 58962 3098 97 57590 1.1 1 54784 2806 98 54344 1.1 1 51575 2769 99 51367 1.1 1 48831 2536 100 47029 1.1 1 44560 2469 101 43951 1.1 1 41556 2395 102 38875 1.1 1 36878 1997 103 35306 1.1 1 33351 1955 104 34244 1.1 1 32195 2049 105 31669 1.1 1 29822 1847 106 29834 1.1 1 28041 1793 107 26571 1.1 1 24760 1811 108 23726 1.1 1 22206 1520 109 21391 1.1 1 19943 1448 110 19404 1.1 1 18072 1332 111 17107 1.1 1 15751 1356 112 14754 1.1 1 13496 1258 113 14189 1.1 1 13010 1179 114 12289 1.1 1 11217 1072 115 12191 1.1 1 11066 1125 116 11581 1.1 1 10479 1102 117 11369 1.1 1 10357 1012 118 9875 1.1 1 8914 961 119 7988 1.1 1 7169 819 120 7173 1.1 1 6327 846 121 6417 1.1 1 5647 770 122 6411 1.1 1 5646 765 123 6823 1.1 1 5985 838 124 6037 1.1 1 5272 765 125 6389 1.1 1 5701 688 126 13004 1.1 1 11810 1194 127 11807 1.1 1 10602 1205 128 6653 1.1 1 5821 832 129 6063 1.1 1 5404 659 130 12206 1.1 1 11167 1039 131 21489 1.1 1 20251 1238 132 23857 1.1 1 22552 1305 133 40790 1.1 1 38491 2299 134 36238 1.1 1 34039 2199 135 11536 1.1 1 10764 772 136 3632 1.1 1 3307 325 137 2534 1.1 1 2245 289 138 1913 1.1 1 1618 295 139 782 1.1 1 648 134 140 600 1.1 1 481 119 141 277 1.1 1 192 85 142 223 1.1 1 147 76 143 239 1.1 1 171 68 144 420 1.1 1 341 79 145 1534 1.1 1 1415 119 146 1169 1.1 1 1053 116 147 5852 1.1 1 5228 624 148 3276 1.1 1 2839 437 149 1056 1.1 1 928 128 150 10964 1.1 1 10259 705 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth1_R2_001.fastq.gz ============================================= 75063646 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 75063646 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 638951 (0.85%)