SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-220_S32_L004_R1_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-220_S32_L004_R1_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 334.14 s (19 us/read; 3.20 M reads/minute). === Summary === Total reads processed: 17,825,268 Reads with adapters: 11,471,469 (64.4%) Reads written (passing filters): 17,825,268 (100.0%) Total basepairs processed: 1,766,718,240 bp Total written (filtered): 1,406,582,519 bp (79.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11471469 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 21.6% C: 19.3% G: 23.6% T: 34.3% none/other: 1.1% Overview of removed sequences length count expect max.err error counts 1 2816787 4456317.0 0 2816787 2 665959 1114079.2 0 665959 3 271037 278519.8 0 271037 4 182007 69630.0 0 182007 5 103141 17407.5 0 103141 6 100596 4351.9 0 100596 7 93589 1088.0 0 93589 8 110206 272.0 0 110206 9 104696 68.0 0 103755 941 10 101241 17.0 1 97832 3409 11 97525 4.2 1 93793 3732 12 93057 1.1 1 89634 3423 13 94558 0.3 1 90815 3743 14 100444 0.3 1 96134 4310 15 100677 0.3 1 96567 4110 16 104281 0.3 1 99726 4555 17 101761 0.3 1 97344 4417 18 95997 0.3 1 92373 3624 19 101640 0.3 1 96901 4739 20 97475 0.3 1 93709 3766 21 105302 0.3 1 100434 4868 22 99864 0.3 1 95970 3894 23 95399 0.3 1 91404 3995 24 97593 0.3 1 93136 4457 25 95248 0.3 1 91345 3903 26 100412 0.3 1 95721 4691 27 95192 0.3 1 91157 4035 28 92989 0.3 1 89167 3822 29 100104 0.3 1 95688 4416 30 94291 0.3 1 90456 3835 31 97546 0.3 1 93132 4414 32 94908 0.3 1 90964 3944 33 98300 0.3 1 93984 4316 34 94803 0.3 1 90673 4130 35 90579 0.3 1 86751 3828 36 94010 0.3 1 89828 4182 37 95550 0.3 1 91689 3861 38 89786 0.3 1 85894 3892 39 89292 0.3 1 85486 3806 40 89965 0.3 1 85827 4138 41 124555 0.3 1 119414 5141 42 78287 0.3 1 75189 3098 43 55801 0.3 1 53363 2438 44 79191 0.3 1 75982 3209 45 79133 0.3 1 75822 3311 46 75215 0.3 1 72256 2959 47 78210 0.3 1 74798 3412 48 74470 0.3 1 71284 3186 49 76701 0.3 1 73405 3296 50 68671 0.3 1 66015 2656 51 68800 0.3 1 66039 2761 52 66645 0.3 1 63873 2772 53 62801 0.3 1 60483 2318 54 61376 0.3 1 58934 2442 55 64444 0.3 1 62039 2405 56 59266 0.3 1 57064 2202 57 54923 0.3 1 52854 2069 58 56982 0.3 1 54837 2145 59 52115 0.3 1 50168 1947 60 47297 0.3 1 45547 1750 61 49457 0.3 1 47631 1826 62 48315 0.3 1 46635 1680 63 44295 0.3 1 42747 1548 64 42067 0.3 1 40618 1449 65 39541 0.3 1 38241 1300 66 35984 0.3 1 34739 1245 67 34807 0.3 1 33560 1247 68 31532 0.3 1 30393 1139 69 33020 0.3 1 31755 1265 70 31981 0.3 1 30880 1101 71 32374 0.3 1 31101 1273 72 38341 0.3 1 36452 1889 73 67892 0.3 1 61702 6190 74 341575 0.3 1 329404 12171 75 398804 0.3 1 386831 11973 76 265894 0.3 1 257126 8768 77 185476 0.3 1 179528 5948 78 116424 0.3 1 112677 3747 79 64451 0.3 1 62327 2124 80 40238 0.3 1 38931 1307 81 22844 0.3 1 22076 768 82 14454 0.3 1 13892 562 83 10505 0.3 1 10072 433 84 8674 0.3 1 8309 365 85 7536 0.3 1 7201 335 86 6995 0.3 1 6710 285 87 6283 0.3 1 6033 250 88 5675 0.3 1 5430 245 89 5561 0.3 1 5320 241 90 7073 0.3 1 6775 298 91 9659 0.3 1 9242 417 92 15397 0.3 1 14771 626 93 37541 0.3 1 36017 1524 94 115148 0.3 1 110889 4259 95 197095 0.3 1 189902 7193 96 85515 0.3 1 82063 3452 97 52173 0.3 1 49912 2261 98 19660 0.3 1 18734 926 99 18939 0.3 1 18146 793 100 18180 0.3 1 17239 941 101 31404 0.3 1 29114 2290 RUN STATISTICS FOR INPUT FILE: EPI-220_S32_L004_R1_001.fastq.gz ============================================= 17825268 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 2772472 (15.6%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 11289404 (63.3%)