SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-184_S18_L003_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-184_S18_L003_R1_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 394.01 s (19 us/read; 3.22 M reads/minute). === Summary === Total reads processed: 21,173,421 Reads with adapters: 12,717,638 (60.1%) Reads written (passing filters): 21,173,421 (100.0%) Total basepairs processed: 2,125,941,717 bp Total written (filtered): 1,847,026,952 bp (86.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 12717638 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 23.7% C: 11.3% G: 26.2% T: 38.4% none/other: 0.4% Overview of removed sequences length count expect max.err error counts 1 3638896 5293355.2 0 3638896 2 873706 1323338.8 0 873706 3 347067 330834.7 0 347067 4 245367 82708.7 0 245367 5 137692 20677.2 0 137692 6 135740 5169.3 0 135740 7 125886 1292.3 0 125886 8 135376 323.1 0 135376 9 136020 80.8 0 134882 1138 10 130093 20.2 1 124860 5233 11 133715 5.0 1 127805 5910 12 128505 1.3 1 122926 5579 13 126041 0.3 1 120383 5658 14 138675 0.3 1 129100 9575 15 131011 0.3 1 121708 9303 16 141676 0.3 1 131482 10194 17 138614 0.3 1 128469 10145 18 128181 0.3 1 119669 8512 19 139482 0.3 1 128114 11368 20 129953 0.3 1 120881 9072 21 145219 0.3 1 133803 11416 22 135841 0.3 1 126228 9613 23 130227 0.3 1 120727 9500 24 135870 0.3 1 125783 10087 25 127895 0.3 1 118621 9274 26 139656 0.3 1 128773 10883 27 132679 0.3 1 124985 7694 28 127791 0.3 1 121316 6475 29 137225 0.3 1 129834 7391 30 132565 0.3 1 126055 6510 31 137460 0.3 1 129663 7797 32 131453 0.3 1 124885 6568 33 141675 0.3 1 134279 7396 34 129247 0.3 1 122862 6385 35 127783 0.3 1 121156 6627 36 126687 0.3 1 120633 6054 37 134338 0.3 1 127788 6550 38 124681 0.3 1 118515 6166 39 125142 0.3 1 119430 5712 40 128701 0.3 1 122207 6494 41 184647 0.3 1 177291 7356 42 109541 0.3 1 105132 4409 43 49793 0.3 1 47072 2721 44 105120 0.3 1 100619 4501 45 101954 0.3 1 97679 4275 46 99033 0.3 1 94911 4122 47 103936 0.3 1 99234 4702 48 94066 0.3 1 89828 4238 49 98758 0.3 1 94243 4515 50 89947 0.3 1 86109 3838 51 87304 0.3 1 83661 3643 52 82421 0.3 1 78902 3519 53 78324 0.3 1 75252 3072 54 77712 0.3 1 74488 3224 55 77691 0.3 1 74622 3069 56 72474 0.3 1 69570 2904 57 66836 0.3 1 64162 2674 58 64961 0.3 1 62520 2441 59 62627 0.3 1 60303 2324 60 57474 0.3 1 55304 2170 61 57815 0.3 1 55564 2251 62 57438 0.3 1 55361 2077 63 50426 0.3 1 48587 1839 64 48374 0.3 1 46788 1586 65 44533 0.3 1 43049 1484 66 40613 0.3 1 39107 1506 67 39246 0.3 1 37817 1429 68 36242 0.3 1 34946 1296 69 36737 0.3 1 35522 1215 70 34357 0.3 1 33040 1317 71 35506 0.3 1 34109 1397 72 34813 0.3 1 33239 1574 73 50018 0.3 1 46836 3182 74 131890 0.3 1 127220 4670 75 106044 0.3 1 102569 3475 76 54686 0.3 1 52711 1975 77 31510 0.3 1 30361 1149 78 18928 0.3 1 18205 723 79 10874 0.3 1 10429 445 80 7355 0.3 1 7085 270 81 4733 0.3 1 4567 166 82 3262 0.3 1 3124 138 83 2635 0.3 1 2518 117 84 2135 0.3 1 2047 88 85 1743 0.3 1 1658 85 86 1461 0.3 1 1387 74 87 1240 0.3 1 1182 58 88 1022 0.3 1 978 44 89 933 0.3 1 887 46 90 1183 0.3 1 1120 63 91 1608 0.3 1 1538 70 92 2636 0.3 1 2493 143 93 6309 0.3 1 6028 281 94 19225 0.3 1 18474 751 95 32788 0.3 1 31456 1332 96 14467 0.3 1 13804 663 97 10014 0.3 1 9545 469 98 4186 0.3 1 3965 221 99 4250 0.3 1 4033 217 100 5203 0.3 1 4895 308 101 10750 0.3 1 9783 967 RUN STATISTICS FOR INPUT FILE: EPI-184_S18_L003_R1_001.fastq.gz ============================================= 21173421 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 2173165 (10.3%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 12657109 (59.8%)