SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-127_S33_L005_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 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_R2_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 436.88 s (20 us/read; 3.07 M reads/minute). === Summary === Total reads processed: 22,355,686 Reads with adapters: 13,351,729 (59.7%) Reads written (passing filters): 22,355,686 (100.0%) Total basepairs processed: 2,240,582,928 bp Total written (filtered): 2,091,363,431 bp (93.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 13351729 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 39.8% C: 24.8% G: 6.7% T: 28.7% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 8212965 5588921.5 0 8212965 2 170746 1397230.4 0 170746 3 160618 349307.6 0 160618 4 122619 87326.9 0 122619 5 121424 21831.7 0 121424 6 124969 5457.9 0 124969 7 119036 1364.5 0 119036 8 157552 341.1 0 157552 9 112936 85.3 0 112499 437 10 112494 21.3 1 108309 4185 11 105698 5.3 1 100319 5379 12 105599 1.3 1 100697 4902 13 100727 0.3 1 95797 4930 14 113161 0.3 1 107739 5422 15 102104 0.3 1 97140 4964 16 102127 0.3 1 97177 4950 17 108571 0.3 1 103463 5108 18 89996 0.3 1 85728 4268 19 96273 0.3 1 91885 4388 20 92999 0.3 1 88394 4605 21 97808 0.3 1 92524 5284 22 99430 0.3 1 94318 5112 23 91359 0.3 1 86920 4439 24 97126 0.3 1 92467 4659 25 81277 0.3 1 77125 4152 26 86033 0.3 1 81253 4780 27 88562 0.3 1 82976 5586 28 89581 0.3 1 85314 4267 29 85610 0.3 1 80417 5193 30 94968 0.3 1 90831 4137 31 75926 0.3 1 71785 4141 32 80401 0.3 1 77047 3354 33 82795 0.3 1 78464 4331 34 85330 0.3 1 80534 4796 35 79259 0.3 1 76176 3083 36 72385 0.3 1 68604 3781 37 68993 0.3 1 65562 3431 38 63070 0.3 1 59853 3217 39 63892 0.3 1 60516 3376 40 64897 0.3 1 61535 3362 41 62791 0.3 1 60014 2777 42 66872 0.3 1 64374 2498 43 51627 0.3 1 48924 2703 44 58050 0.3 1 55314 2736 45 87377 0.3 1 84553 2824 46 50126 0.3 1 47826 2300 47 32995 0.3 1 31065 1930 48 57165 0.3 1 55118 2047 49 31760 0.3 1 30265 1495 50 36087 0.3 1 34185 1902 51 57437 0.3 1 55568 1869 52 27589 0.3 1 26176 1413 53 30956 0.3 1 29335 1621 54 26764 0.3 1 25407 1357 55 36220 0.3 1 34555 1665 56 35043 0.3 1 33311 1732 57 31459 0.3 1 30053 1406 58 30543 0.3 1 29236 1307 59 29066 0.3 1 27645 1421 60 29050 0.3 1 27574 1476 61 29559 0.3 1 28123 1436 62 32135 0.3 1 30502 1633 63 34722 0.3 1 33029 1693 64 35048 0.3 1 33390 1658 65 35913 0.3 1 34269 1644 66 36376 0.3 1 34668 1708 67 39603 0.3 1 37516 2087 68 76873 0.3 1 74822 2051 69 23807 0.3 1 22745 1062 70 11759 0.3 1 11091 668 71 7475 0.3 1 6934 541 72 6057 0.3 1 5614 443 73 5032 0.3 1 4625 407 74 4319 0.3 1 3978 341 75 3576 0.3 1 3320 256 76 3169 0.3 1 2904 265 77 2644 0.3 1 2434 210 78 2225 0.3 1 2064 161 79 1728 0.3 1 1623 105 80 1288 0.3 1 1187 101 81 947 0.3 1 870 77 82 696 0.3 1 631 65 83 477 0.3 1 442 35 84 300 0.3 1 274 26 85 161 0.3 1 141 20 86 101 0.3 1 92 9 87 93 0.3 1 85 8 88 49 0.3 1 46 3 89 67 0.3 1 58 9 90 81 0.3 1 75 6 91 114 0.3 1 103 11 92 178 0.3 1 156 22 93 354 0.3 1 310 44 94 857 0.3 1 768 89 95 1307 0.3 1 1166 141 96 705 0.3 1 639 66 97 427 0.3 1 381 46 98 155 0.3 1 141 14 99 145 0.3 1 135 10 100 243 0.3 1 219 24 101 671 0.3 1 577 94 RUN STATISTICS FOR INPUT FILE: EPI-127_S33_L005_R2_001.fastq.gz ============================================= 22355686 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 2519166 (11.3%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 0 (0.0%) RRBS reads trimmed by 2 bp at the start when read started with CAA (726743) or CGA (217864) in total: 944607 (4.2%) Total number of sequences analysed for the sequence pair length validation: 22355686 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 92528 (0.41%)