SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-127_S33_L005_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 File was specified to be a non-directional MspI-digested RRBS sample. Sequences starting with either 'CAA' or 'CGA' will have the first 2 bp trimmed off to remove potential methylation-biased bases from the end-repair reaction Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /home/sam/data/geoduck_EPI/20180514_geoduck_trimgalore_rrbs/20180514_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/20180514_geoduck_trimgalore_rrbs/EPI-127_S33_L005_R1_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 428.55 s (19 us/read; 3.13 M reads/minute). === Summary === Total reads processed: 22,355,686 Reads with adapters: 11,417,507 (51.1%) Reads written (passing filters): 22,355,686 (100.0%) Total basepairs processed: 2,248,791,219 bp Total written (filtered): 2,093,991,891 bp (93.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11417507 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 27.0% C: 6.3% G: 23.3% T: 43.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 4882969 5588921.5 0 4882969 2 1116893 1397230.4 0 1116893 3 426930 349307.6 0 426930 4 276583 87326.9 0 276583 5 118160 21831.7 0 118160 6 121821 5457.9 0 121821 7 114560 1364.5 0 114560 8 149860 341.1 0 149860 9 114876 85.3 0 113781 1095 10 107364 21.3 1 102391 4973 11 108127 5.3 1 102176 5951 12 103053 1.3 1 97763 5290 13 96089 0.3 1 91121 4968 14 109531 0.3 1 102927 6604 15 102473 0.3 1 96856 5617 16 109111 0.3 1 102214 6897 17 101084 0.3 1 95374 5710 18 92253 0.3 1 87347 4906 19 100321 0.3 1 94053 6268 20 90871 0.3 1 86177 4694 21 102488 0.3 1 96176 6312 22 94446 0.3 1 89425 5021 23 88321 0.3 1 83308 5013 24 90456 0.3 1 84879 5577 25 82073 0.3 1 77613 4460 26 92242 0.3 1 86536 5706 27 81188 0.3 1 76859 4329 28 76347 0.3 1 72335 4012 29 83614 0.3 1 78848 4766 30 78095 0.3 1 74093 4002 31 82411 0.3 1 77389 5022 32 73913 0.3 1 70063 3850 33 78500 0.3 1 74044 4456 34 72121 0.3 1 68284 3837 35 67034 0.3 1 63480 3554 36 72399 0.3 1 68263 4136 37 72450 0.3 1 68647 3803 38 67294 0.3 1 63589 3705 39 66218 0.3 1 62461 3757 40 63261 0.3 1 59608 3653 41 95925 0.3 1 91533 4392 42 53069 0.3 1 50584 2485 43 32535 0.3 1 30532 2003 44 56150 0.3 1 53249 2901 45 53879 0.3 1 51207 2672 46 52991 0.3 1 50298 2693 47 56117 0.3 1 53036 3081 48 53298 0.3 1 50362 2936 49 52476 0.3 1 49494 2982 50 46861 0.3 1 44514 2347 51 44236 0.3 1 42074 2162 52 41665 0.3 1 39539 2126 53 41295 0.3 1 39349 1946 54 40768 0.3 1 38679 2089 55 42177 0.3 1 40291 1886 56 40266 0.3 1 38267 1999 57 39317 0.3 1 37475 1842 58 36448 0.3 1 34907 1541 59 35749 0.3 1 34183 1566 60 31938 0.3 1 30618 1320 61 32396 0.3 1 31041 1355 62 34700 0.3 1 33230 1470 63 34572 0.3 1 33159 1413 64 34911 0.3 1 33587 1324 65 32149 0.3 1 30758 1391 66 29926 0.3 1 28687 1239 67 26706 0.3 1 25582 1124 68 23018 0.3 1 22075 943 69 23700 0.3 1 22671 1029 70 22088 0.3 1 21142 946 71 20351 0.3 1 19515 836 72 20321 0.3 1 19467 854 73 21829 0.3 1 20603 1226 74 37648 0.3 1 36381 1267 75 17723 0.3 1 17017 706 76 8245 0.3 1 7914 331 77 4909 0.3 1 4683 226 78 3419 0.3 1 3270 149 79 2351 0.3 1 2250 101 80 1687 0.3 1 1599 88 81 1140 0.3 1 1102 38 82 773 0.3 1 743 30 83 547 0.3 1 521 26 84 389 0.3 1 367 22 85 220 0.3 1 200 20 86 147 0.3 1 135 12 87 117 0.3 1 109 8 88 78 0.3 1 68 10 89 67 0.3 1 60 7 90 102 0.3 1 94 8 91 127 0.3 1 118 9 92 232 0.3 1 212 20 93 409 0.3 1 376 33 94 1020 0.3 1 957 63 95 1596 0.3 1 1491 105 96 847 0.3 1 787 60 97 491 0.3 1 456 35 98 211 0.3 1 191 20 99 190 0.3 1 171 19 100 345 0.3 1 271 74 101 850 0.3 1 641 209 RUN STATISTICS FOR INPUT FILE: EPI-127_S33_L005_R1_001.fastq.gz ============================================= 22355686 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 2286517 (10.2%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 11274695 (50.4%) RRBS reads trimmed by 2 bp at the start when read started with CAA (143759) or CGA (138750) in total: 282509 (1.3%)