SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-167_S10_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 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-167_S10_L002_R1_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 474.76 s (19 us/read; 3.14 M reads/minute). === Summary === Total reads processed: 24,859,230 Reads with adapters: 13,309,382 (53.5%) Reads written (passing filters): 24,859,230 (100.0%) Total basepairs processed: 2,499,293,998 bp Total written (filtered): 2,298,095,482 bp (91.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 13309382 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 25.4% C: 9.4% G: 23.7% T: 41.2% none/other: 0.3% Overview of removed sequences length count expect max.err error counts 1 5079720 6214807.5 0 5079720 2 1201788 1553701.9 0 1201788 3 455870 388425.5 0 455870 4 314973 97106.4 0 314973 5 161437 24276.6 0 161437 6 154361 6069.1 0 154361 7 140803 1517.3 0 140803 8 147331 379.3 0 147331 9 155862 94.8 0 154346 1516 10 144320 23.7 1 138306 6014 11 151112 5.9 1 144135 6977 12 143788 1.5 1 137433 6355 13 137785 0.4 1 131615 6170 14 149147 0.4 1 141174 7973 15 139227 0.4 1 132332 6895 16 149312 0.4 1 141084 8228 17 143086 0.4 1 135505 7581 18 132310 0.4 1 126071 6239 19 143811 0.4 1 135287 8524 20 131290 0.4 1 124923 6367 21 145679 0.4 1 136781 8898 22 134890 0.4 1 128035 6855 23 126067 0.4 1 119640 6427 24 131665 0.4 1 124339 7326 25 122358 0.4 1 116289 6069 26 132225 0.4 1 124597 7628 27 119894 0.4 1 114131 5763 28 113340 0.4 1 107992 5348 29 123769 0.4 1 117559 6210 30 113297 0.4 1 108240 5057 31 120469 0.4 1 114168 6301 32 111183 0.4 1 106261 4922 33 114363 0.4 1 108986 5377 34 108844 0.4 1 103786 5058 35 104131 0.4 1 99505 4626 36 99526 0.4 1 95050 4476 37 106038 0.4 1 100981 5057 38 92323 0.4 1 88308 4015 39 93759 0.4 1 89399 4360 40 94519 0.4 1 89633 4886 41 129205 0.4 1 123873 5332 42 78110 0.4 1 74983 3127 43 35837 0.4 1 33746 2091 44 72367 0.4 1 69091 3276 45 67031 0.4 1 64106 2925 46 63610 0.4 1 60758 2852 47 65331 0.4 1 62355 2976 48 58472 0.4 1 55680 2792 49 59983 0.4 1 57145 2838 50 53971 0.4 1 51646 2325 51 50543 0.4 1 48295 2248 52 47005 0.4 1 44956 2049 53 43086 0.4 1 41326 1760 54 41670 0.4 1 39954 1716 55 40994 0.4 1 39370 1624 56 37127 0.4 1 35622 1505 57 34125 0.4 1 32652 1473 58 31505 0.4 1 30268 1237 59 30411 0.4 1 29237 1174 60 26925 0.4 1 25909 1016 61 26652 0.4 1 25578 1074 62 25545 0.4 1 24603 942 63 21912 0.4 1 21115 797 64 20166 0.4 1 19505 661 65 18118 0.4 1 17409 709 66 16596 0.4 1 15950 646 67 15516 0.4 1 14924 592 68 14125 0.4 1 13540 585 69 13654 0.4 1 13093 561 70 12496 0.4 1 12006 490 71 12383 0.4 1 11814 569 72 14176 0.4 1 13392 784 73 24770 0.4 1 22779 1991 74 80795 0.4 1 77743 3052 75 62980 0.4 1 60815 2165 76 34346 0.4 1 33049 1297 77 20015 0.4 1 19279 736 78 11561 0.4 1 11141 420 79 6228 0.4 1 5972 256 80 4035 0.4 1 3856 179 81 2455 0.4 1 2342 113 82 1682 0.4 1 1592 90 83 1305 0.4 1 1243 62 84 1169 0.4 1 1106 63 85 1034 0.4 1 975 59 86 988 0.4 1 940 48 87 884 0.4 1 824 60 88 755 0.4 1 703 52 89 848 0.4 1 797 51 90 941 0.4 1 890 51 91 1310 0.4 1 1224 86 92 2045 0.4 1 1916 129 93 4668 0.4 1 4448 220 94 13833 0.4 1 13196 637 95 24756 0.4 1 23645 1111 96 12039 0.4 1 11473 566 97 8920 0.4 1 8427 493 98 3872 0.4 1 3654 218 99 4141 0.4 1 3934 207 100 4419 0.4 1 4130 289 101 8269 0.4 1 7410 859 RUN STATISTICS FOR INPUT FILE: EPI-167_S10_L002_R1_001.fastq.gz ============================================= 24859230 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 2260450 (9.1%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 13070589 (52.6%) RRBS reads trimmed by 2 bp at the start when read started with CAA (225699) or CGA (129066) in total: 354765 (1.4%)