SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-206_S27_L004_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-206_S27_L004_R2_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 654.27 s (18 us/read; 3.37 M reads/minute). === Summary === Total reads processed: 36,712,077 Reads with adapters: 30,322,462 (82.6%) Reads written (passing filters): 36,712,077 (100.0%) Total basepairs processed: 3,384,922,184 bp Total written (filtered): 1,864,918,199 bp (55.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 30322462 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 23.7% C: 17.6% G: 25.9% T: 30.9% none/other: 2.0% Overview of removed sequences length count expect max.err error counts 1 5622341 9178019.2 0 5622341 2 190369 2294504.8 0 190369 3 150690 573626.2 0 150690 4 125873 143406.6 0 125873 5 123489 35851.6 0 123489 6 125773 8962.9 0 125773 7 126157 2240.7 0 126157 8 133915 560.2 0 133915 9 128158 140.0 0 127569 589 10 132863 35.0 1 128916 3947 11 121949 8.8 1 117724 4225 12 128132 2.2 1 123614 4518 13 124301 0.5 1 120318 3983 14 136486 0.5 1 131739 4747 15 129839 0.5 1 125669 4170 16 131812 0.5 1 127710 4102 17 136414 0.5 1 131790 4624 18 123385 0.5 1 119457 3928 19 130565 0.5 1 126142 4423 20 132794 0.5 1 128367 4427 21 134290 0.5 1 129611 4679 22 139484 0.5 1 134426 5058 23 133722 0.5 1 129042 4680 24 140305 0.5 1 134792 5513 25 129333 0.5 1 124859 4474 26 131594 0.5 1 126262 5332 27 134581 0.5 1 128440 6141 28 140321 0.5 1 135143 5178 29 137785 0.5 1 132238 5547 30 151515 0.5 1 146205 5310 31 134322 0.5 1 129182 5140 32 142872 0.5 1 137849 5023 33 151382 0.5 1 145131 6251 34 151066 0.5 1 144465 6601 35 146602 0.5 1 141537 5065 36 144136 0.5 1 138544 5592 37 144004 0.5 1 138564 5440 38 134186 0.5 1 129146 5040 39 138978 0.5 1 133309 5669 40 138499 0.5 1 133043 5456 41 144209 0.5 1 138946 5263 42 144984 0.5 1 139894 5090 43 127622 0.5 1 122754 4868 44 137213 0.5 1 131857 5356 45 185227 0.5 1 178452 6775 46 137845 0.5 1 132770 5075 47 108610 0.5 1 104485 4125 48 152067 0.5 1 146718 5349 49 115441 0.5 1 111552 3889 50 117413 0.5 1 113089 4324 51 171377 0.5 1 166347 5030 52 113394 0.5 1 109530 3864 53 115666 0.5 1 111939 3727 54 103141 0.5 1 99793 3348 55 127932 0.5 1 123954 3978 56 125112 0.5 1 120947 4165 57 119922 0.5 1 115798 4124 58 119783 0.5 1 115678 4105 59 117233 0.5 1 113089 4144 60 116238 0.5 1 112175 4063 61 121429 0.5 1 116919 4510 62 130711 0.5 1 125554 5157 63 140255 0.5 1 134198 6057 64 155643 0.5 1 148295 7348 65 187952 0.5 1 178456 9496 66 263322 0.5 1 247913 15409 67 640107 0.5 1 563705 76402 68 4965984 0.5 1 4826306 139678 69 2368827 0.5 1 2287436 81391 70 1321641 0.5 1 1274606 47035 71 640187 0.5 1 614021 26166 72 374506 0.5 1 358174 16332 73 220700 0.5 1 209758 10942 74 154443 0.5 1 146187 8256 75 115470 0.5 1 108703 6767 76 93584 0.5 1 87818 5766 77 80555 0.5 1 75430 5125 78 70562 0.5 1 65919 4643 79 62444 0.5 1 58139 4305 80 56824 0.5 1 52810 4014 81 50394 0.5 1 46686 3708 82 45432 0.5 1 41937 3495 83 41786 0.5 1 38378 3408 84 38983 0.5 1 35686 3297 85 36714 0.5 1 33423 3291 86 35521 0.5 1 32253 3268 87 36696 0.5 1 33261 3435 88 39983 0.5 1 36192 3791 89 46623 0.5 1 42249 4374 90 60528 0.5 1 55047 5481 91 89469 0.5 1 81391 8078 92 136733 0.5 1 124878 11855 93 302377 0.5 1 277839 24538 94 906082 0.5 1 841594 64488 95 1470100 0.5 1 1372383 97717 96 582477 0.5 1 543730 38747 97 286056 0.5 1 266739 19317 98 101563 0.5 1 94970 6593 99 83732 0.5 1 77951 5781 100 75131 0.5 1 70053 5078 101 136225 0.5 1 125789 10436 RUN STATISTICS FOR INPUT FILE: EPI-206_S27_L004_R2_001.fastq.gz ============================================= 36712077 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 14447723 (39.4%) 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: 36712077 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 15781059 (42.99%)