SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-152_S3_L002_R2_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.9.1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected) 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 File was specified to be an MspI-digested RRBS sample. Read 1 sequences with adapter contamination will be trimmed a further 2 bp from their 3' end, and Read 2 sequences will be trimmed by 2 bp from their 5' end to remove potential methylation-biased bases from the end-repair reaction All Read 2 sequences will be trimmed by 2 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /home/sam/data/geoduck_EPI/20180516_geoduck_trimgalore_rrbs/20180516_geoduck_trimmed_fastqc --threads 16 Output file will be GZIP compressed This is cutadapt 1.9.1 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -O 1 -a AGATCGGAAGAGC /home/sam/data/geoduck_EPI/20180516_geoduck_trimgalore_rrbs/EPI-152_S3_L002_R2_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 583.85 s (19 us/read; 3.12 M reads/minute). === Summary === Total reads processed: 30,318,886 Reads with adapters: 19,145,564 (63.1%) Reads written (passing filters): 30,318,886 (100.0%) Total basepairs processed: 3,034,698,503 bp Total written (filtered): 2,759,491,028 bp (90.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 19145564 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 38.2% C: 23.6% G: 8.1% T: 29.8% none/other: 0.3% Overview of removed sequences length count expect max.err error counts 1 9990747 7579721.5 0 9990747 2 288732 1894930.4 0 288732 3 257148 473732.6 0 257148 4 205744 118433.1 0 205744 5 206057 29608.3 0 206057 6 206130 7402.1 0 206130 7 196063 1850.5 0 196063 8 218017 462.6 0 218017 9 195335 115.7 0 194517 818 10 196212 28.9 1 190862 5350 11 184814 7.2 1 177952 6862 12 187199 1.8 1 180653 6546 13 178629 0.5 1 172160 6469 14 192604 0.5 1 185615 6989 15 182210 0.5 1 175580 6630 16 180401 0.5 1 174167 6234 17 184940 0.5 1 178583 6357 18 165907 0.5 1 160048 5859 19 173764 0.5 1 167684 6080 20 172432 0.5 1 166012 6420 21 173719 0.5 1 166798 6921 22 176536 0.5 1 169855 6681 23 165340 0.5 1 159298 6042 24 171350 0.5 1 164926 6424 25 155463 0.5 1 149626 5837 26 156769 0.5 1 150216 6553 27 159452 0.5 1 151946 7506 28 158987 0.5 1 153050 5937 29 153139 0.5 1 146505 6634 30 161380 0.5 1 155721 5659 31 141278 0.5 1 135645 5633 32 140777 0.5 1 136013 4764 33 148289 0.5 1 142455 5834 34 151530 0.5 1 145311 6219 35 136233 0.5 1 131949 4284 36 134315 0.5 1 129180 5135 37 131144 0.5 1 126416 4728 38 116231 0.5 1 112046 4185 39 120477 0.5 1 116115 4362 40 116677 0.5 1 112473 4204 41 114771 0.5 1 111067 3704 42 111951 0.5 1 108674 3277 43 98589 0.5 1 95094 3495 44 99616 0.5 1 96379 3237 45 121738 0.5 1 118344 3394 46 95474 0.5 1 92448 3026 47 68969 0.5 1 66535 2434 48 93963 0.5 1 91301 2662 49 66969 0.5 1 64774 2195 50 69076 0.5 1 66716 2360 51 92170 0.5 1 89792 2378 52 58388 0.5 1 56450 1938 53 59663 0.5 1 57733 1930 54 51748 0.5 1 49962 1786 55 61616 0.5 1 59715 1901 56 58278 0.5 1 56319 1959 57 53490 0.5 1 51720 1770 58 51518 0.5 1 49790 1728 59 48327 0.5 1 46668 1659 60 45570 0.5 1 43949 1621 61 45000 0.5 1 43441 1559 62 45077 0.5 1 43410 1667 63 45597 0.5 1 43821 1776 64 44777 0.5 1 43034 1743 65 45428 0.5 1 43673 1755 66 49394 0.5 1 47327 2067 67 67707 0.5 1 62852 4855 68 218564 0.5 1 213221 5343 69 80301 0.5 1 77677 2624 70 39409 0.5 1 37907 1502 71 21155 0.5 1 20253 902 72 15454 0.5 1 14669 785 73 11661 0.5 1 11022 639 74 9418 0.5 1 8874 544 75 7969 0.5 1 7521 448 76 6933 0.5 1 6544 389 77 6155 0.5 1 5771 384 78 5494 0.5 1 5167 327 79 4722 0.5 1 4439 283 80 3972 0.5 1 3734 238 81 3330 0.5 1 3101 229 82 2692 0.5 1 2527 165 83 2243 0.5 1 2083 160 84 1669 0.5 1 1558 111 85 1350 0.5 1 1258 92 86 1152 0.5 1 1055 97 87 1044 0.5 1 946 98 88 1008 0.5 1 909 99 89 1043 0.5 1 943 100 90 1238 0.5 1 1112 126 91 1692 0.5 1 1534 158 92 2496 0.5 1 2251 245 93 5194 0.5 1 4779 415 94 14811 0.5 1 13702 1109 95 26195 0.5 1 24309 1886 96 12307 0.5 1 11405 902 97 9881 0.5 1 9136 745 98 4126 0.5 1 3800 326 99 4315 0.5 1 3956 359 100 5774 0.5 1 5341 433 101 13762 0.5 1 12363 1399 RUN STATISTICS FOR INPUT FILE: EPI-152_S3_L002_R2_001.fastq.gz ============================================= 30318886 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 3132019 (10.3%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 0 (0.0%) Total number of sequences analysed for the sequence pair length validation: 30318886 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 463868 (1.53%)