SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth18_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/Meth18_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 1915.67 s (31 us/read; 1.96 M reads/minute). === Summary === Total reads processed: 62,709,665 Reads with adapters: 40,276,846 (64.2%) Reads written (passing filters): 62,709,665 (100.0%) Total basepairs processed: 9,406,449,750 bp Quality-trimmed: 13,181,420 bp (0.1%) Total written (filtered): 8,278,807,374 bp (88.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 40276846 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 36.4% C: 19.3% G: 14.9% T: 29.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 14603394 15677416.2 0 14603394 2 1307142 3919354.1 0 1307142 3 620947 979838.5 0 620947 4 414208 244959.6 0 414208 5 316368 61239.9 0 316368 6 270939 15310.0 0 270939 7 287587 3827.5 0 287587 8 307571 956.9 0 307571 9 291943 239.2 0 282290 9653 10 307212 59.8 1 282437 24775 11 324430 15.0 1 295685 28745 12 324931 3.7 1 297576 27355 13 310057 0.9 1 281854 28203 14 319835 0.9 1 290105 29730 15 316897 0.9 1 288199 28698 16 320152 0.9 1 289773 30379 17 331126 0.9 1 300877 30249 18 316149 0.9 1 288328 27821 19 309858 0.9 1 281474 28384 20 317463 0.9 1 289824 27639 21 322446 0.9 1 292983 29463 22 315246 0.9 1 287741 27505 23 318776 0.9 1 290279 28497 24 317130 0.9 1 287444 29686 25 316748 0.9 1 288506 28242 26 312623 0.9 1 284985 27638 27 315963 0.9 1 289143 26820 28 308124 0.9 1 282067 26057 29 313104 0.9 1 286542 26562 30 305952 0.9 1 281690 24262 31 304134 0.9 1 279368 24766 32 303558 0.9 1 279370 24188 33 303893 0.9 1 278900 24993 34 309218 0.9 1 284210 25008 35 297568 0.9 1 272333 25235 36 298995 0.9 1 275445 23550 37 294671 0.9 1 271449 23222 38 297407 0.9 1 272901 24506 39 293165 0.9 1 269627 23538 40 289296 0.9 1 265392 23904 41 291360 0.9 1 265470 25890 42 355817 0.9 1 330018 25799 43 228920 0.9 1 205404 23516 44 283541 0.9 1 256980 26561 45 382574 0.9 1 357752 24822 46 170015 0.9 1 153114 16901 47 274307 0.9 1 251167 23140 48 288981 0.9 1 266366 22615 49 267341 0.9 1 246164 21177 50 262545 0.9 1 238827 23718 51 309854 0.9 1 285611 24243 52 234312 0.9 1 214802 19510 53 239120 0.9 1 218787 20333 54 265265 0.9 1 242029 23236 55 267428 0.9 1 245787 21641 56 237662 0.9 1 217530 20132 57 261343 0.9 1 239988 21355 58 250492 0.9 1 229315 21177 59 255887 0.9 1 235257 20630 60 216508 0.9 1 199315 17193 61 201088 0.9 1 182910 18178 62 241115 0.9 1 220874 20241 63 251346 0.9 1 232213 19133 64 197045 0.9 1 180407 16638 65 201530 0.9 1 182837 18693 66 237722 0.9 1 218444 19278 67 209414 0.9 1 190744 18670 68 230710 0.9 1 210503 20207 69 240393 0.9 1 211428 28965 70 474752 0.9 1 447253 27499 71 70131 0.9 1 64871 5260 72 34318 0.9 1 30099 4219 73 73975 0.9 1 65127 8848 74 141387 0.9 1 128289 13098 75 159757 0.9 1 145916 13841 76 161791 0.9 1 147865 13926 77 155984 0.9 1 142301 13683 78 151988 0.9 1 137458 14530 79 148788 0.9 1 135487 13301 80 143094 0.9 1 129829 13265 81 138762 0.9 1 125718 13044 82 139690 0.9 1 126839 12851 83 134840 0.9 1 122736 12104 84 130580 0.9 1 118601 11979 85 123383 0.9 1 111910 11473 86 117432 0.9 1 106943 10489 87 116497 0.9 1 105948 10549 88 102840 0.9 1 93024 9816 89 96936 0.9 1 87251 9685 90 92329 0.9 1 82936 9393 91 92315 0.9 1 82931 9384 92 85579 0.9 1 77148 8431 93 81824 0.9 1 73594 8230 94 80538 0.9 1 72344 8194 95 76259 0.9 1 68343 7916 96 71614 0.9 1 63843 7771 97 68904 0.9 1 61350 7554 98 62679 0.9 1 55862 6817 99 58401 0.9 1 51652 6749 100 56028 0.9 1 49611 6417 101 55872 0.9 1 49522 6350 102 49325 0.9 1 43305 6020 103 46128 0.9 1 40440 5688 104 49109 0.9 1 43181 5928 105 45999 0.9 1 40385 5614 106 47857 0.9 1 41726 6131 107 43913 0.9 1 38515 5398 108 37490 0.9 1 32533 4957 109 31238 0.9 1 27191 4047 110 29474 0.9 1 25395 4079 111 26769 0.9 1 22915 3854 112 25120 0.9 1 21522 3598 113 25299 0.9 1 21691 3608 114 24400 0.9 1 21060 3340 115 23839 0.9 1 20669 3170 116 23656 0.9 1 20243 3413 117 24613 0.9 1 21161 3452 118 20639 0.9 1 17969 2670 119 17306 0.9 1 14902 2404 120 16945 0.9 1 14510 2435 121 14466 0.9 1 12437 2029 122 15550 0.9 1 13404 2146 123 16818 0.9 1 14662 2156 124 13836 0.9 1 11819 2017 125 13708 0.9 1 11782 1926 126 23751 0.9 1 20650 3101 127 19283 0.9 1 16602 2681 128 11956 0.9 1 10235 1721 129 12417 0.9 1 10865 1552 130 24411 0.9 1 21918 2493 131 44236 0.9 1 41265 2971 132 46490 0.9 1 43176 3314 133 74517 0.9 1 69869 4648 134 82144 0.9 1 76941 5203 135 20244 0.9 1 18592 1652 136 5533 0.9 1 4741 792 137 3702 0.9 1 3172 530 138 3027 0.9 1 2388 639 139 1479 0.9 1 1075 404 140 1311 0.9 1 959 352 141 530 0.9 1 342 188 142 344 0.9 1 214 130 143 337 0.9 1 246 91 144 611 0.9 1 484 127 145 2283 0.9 1 2061 222 146 3252 0.9 1 2855 397 147 25656 0.9 1 22355 3301 148 13908 0.9 1 11832 2076 149 4146 0.9 1 3549 597 150 58653 0.9 1 53591 5062 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth18_R1_001.fastq.gz ============================================= 62709665 sequences processed in total