SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-154_S5_L002_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-154_S5_L002_R1_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 484.33 s (19 us/read; 3.15 M reads/minute). === Summary === Total reads processed: 25,441,933 Reads with adapters: 14,159,132 (55.7%) Reads written (passing filters): 25,441,933 (100.0%) Total basepairs processed: 2,559,902,726 bp Total written (filtered): 2,322,233,124 bp (90.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14159132 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 24.2% C: 8.5% G: 27.3% T: 39.8% none/other: 0.2% Overview of removed sequences length count expect max.err error counts 1 4758910 6360483.2 0 4758910 2 1182718 1590120.8 0 1182718 3 465026 397530.2 0 465026 4 323948 99382.6 0 323948 5 176498 24845.6 0 176498 6 174421 6211.4 0 174421 7 162919 1552.9 0 162919 8 173295 388.2 0 173295 9 171648 97.1 0 170121 1527 10 166755 24.3 1 160174 6581 11 167389 6.1 1 159845 7544 12 161202 1.5 1 154370 6832 13 155055 0.4 1 148382 6673 14 170743 0.4 1 161936 8807 15 159522 0.4 1 152107 7415 16 168621 0.4 1 159784 8837 17 162480 0.4 1 154109 8371 18 150706 0.4 1 143737 6969 19 165938 0.4 1 156352 9586 20 150811 0.4 1 143729 7082 21 166692 0.4 1 156931 9761 22 154673 0.4 1 147026 7647 23 145687 0.4 1 138377 7310 24 154467 0.4 1 146227 8240 25 144058 0.4 1 137099 6959 26 153835 0.4 1 145288 8547 27 143130 0.4 1 136426 6704 28 134100 0.4 1 127948 6152 29 145821 0.4 1 138517 7304 30 135915 0.4 1 130165 5750 31 143656 0.4 1 136355 7301 32 130968 0.4 1 125307 5661 33 135057 0.4 1 129013 6044 34 128038 0.4 1 122283 5755 35 131746 0.4 1 125391 6355 36 121513 0.4 1 116245 5268 37 129951 0.4 1 124043 5908 38 118793 0.4 1 113629 5164 39 110155 0.4 1 105590 4565 40 121421 0.4 1 115278 6143 41 158528 0.4 1 151754 6774 42 100839 0.4 1 96875 3964 43 47675 0.4 1 45082 2593 44 93325 0.4 1 89387 3938 45 87939 0.4 1 83992 3947 46 84309 0.4 1 80676 3633 47 87970 0.4 1 83989 3981 48 78885 0.4 1 75290 3595 49 82591 0.4 1 78718 3873 50 72665 0.4 1 69627 3038 51 70307 0.4 1 67324 2983 52 65488 0.4 1 62614 2874 53 61130 0.4 1 58839 2291 54 59022 0.4 1 56613 2409 55 59448 0.4 1 57170 2278 56 54510 0.4 1 52354 2156 57 49603 0.4 1 47627 1976 58 47918 0.4 1 46109 1809 59 46530 0.4 1 44825 1705 60 41065 0.4 1 39467 1598 61 41346 0.4 1 39833 1513 62 40509 0.4 1 38998 1511 63 35478 0.4 1 34197 1281 64 33128 0.4 1 31995 1133 65 30070 0.4 1 28986 1084 66 27659 0.4 1 26642 1017 67 27224 0.4 1 26257 967 68 24740 0.4 1 23790 950 69 25094 0.4 1 24224 870 70 22646 0.4 1 21825 821 71 21959 0.4 1 21115 844 72 22360 0.4 1 21299 1061 73 31617 0.4 1 29623 1994 74 72964 0.4 1 70602 2362 75 38484 0.4 1 37051 1433 76 19874 0.4 1 19117 757 77 11502 0.4 1 11039 463 78 7477 0.4 1 7172 305 79 4421 0.4 1 4238 183 80 3225 0.4 1 3100 125 81 2161 0.4 1 2066 95 82 1622 0.4 1 1543 79 83 1314 0.4 1 1256 58 84 1133 0.4 1 1079 54 85 855 0.4 1 809 46 86 639 0.4 1 600 39 87 561 0.4 1 515 46 88 416 0.4 1 380 36 89 426 0.4 1 395 31 90 509 0.4 1 471 38 91 628 0.4 1 589 39 92 988 0.4 1 923 65 93 2001 0.4 1 1858 143 94 5574 0.4 1 5284 290 95 9561 0.4 1 9093 468 96 4891 0.4 1 4617 274 97 3696 0.4 1 3471 225 98 1500 0.4 1 1395 105 99 1548 0.4 1 1439 109 100 2417 0.4 1 2191 226 101 6887 0.4 1 6051 836 RUN STATISTICS FOR INPUT FILE: EPI-154_S5_L002_R1_001.fastq.gz ============================================= 25441933 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 2357140 (9.3%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 14123870 (55.5%)