SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-119_S31_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-119_S31_L005_R1_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 555.88 s (19 us/read; 3.13 M reads/minute). === Summary === Total reads processed: 29,018,872 Reads with adapters: 14,945,774 (51.5%) Reads written (passing filters): 29,018,872 (100.0%) Total basepairs processed: 2,919,648,747 bp Total written (filtered): 2,701,752,596 bp (92.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14945774 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 26.6% C: 6.5% G: 23.9% T: 43.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 6190802 7254718.0 0 6190802 2 1416952 1813679.5 0 1416952 3 528181 453419.9 0 528181 4 341864 113355.0 0 341864 5 144965 28338.7 0 144965 6 152127 7084.7 0 152127 7 146993 1771.2 0 146993 8 170386 442.8 0 170386 9 152866 110.7 0 151486 1380 10 149965 27.7 1 143748 6217 11 142341 6.9 1 135647 6694 12 137753 1.7 1 131563 6190 13 128964 0.4 1 123370 5594 14 146517 0.4 1 138762 7755 15 134849 0.4 1 128728 6121 16 141865 0.4 1 134264 7601 17 132955 0.4 1 126797 6158 18 120614 0.4 1 115272 5342 19 132847 0.4 1 125556 7291 20 121479 0.4 1 116123 5356 21 137034 0.4 1 129542 7492 22 127895 0.4 1 122021 5874 23 114673 0.4 1 109056 5617 24 120904 0.4 1 114560 6344 25 109352 0.4 1 104420 4932 26 121103 0.4 1 114671 6432 27 109335 0.4 1 104391 4944 28 105003 0.4 1 100237 4766 29 112686 0.4 1 107259 5427 30 107490 0.4 1 102848 4642 31 110686 0.4 1 105216 5470 32 102107 0.4 1 97682 4425 33 108458 0.4 1 103361 5097 34 97708 0.4 1 93448 4260 35 97974 0.4 1 93317 4657 36 96228 0.4 1 91975 4253 37 102500 0.4 1 97670 4830 38 94200 0.4 1 89985 4215 39 92800 0.4 1 88304 4496 40 96886 0.4 1 92107 4779 41 141622 0.4 1 136489 5133 42 75579 0.4 1 72696 2883 43 35589 0.4 1 33546 2043 44 79104 0.4 1 75615 3489 45 73701 0.4 1 70467 3234 46 74415 0.4 1 71304 3111 47 81279 0.4 1 77578 3701 48 76890 0.4 1 73424 3466 49 76572 0.4 1 72916 3656 50 70076 0.4 1 67100 2976 51 66114 0.4 1 63314 2800 52 62234 0.4 1 59644 2590 53 62422 0.4 1 59971 2451 54 62231 0.4 1 59621 2610 55 63774 0.4 1 61322 2452 56 62691 0.4 1 60157 2534 57 60227 0.4 1 57872 2355 58 56514 0.4 1 54560 1954 59 55589 0.4 1 53567 2022 60 50300 0.4 1 48558 1742 61 50412 0.4 1 48691 1721 62 54716 0.4 1 52811 1905 63 54717 0.4 1 52767 1950 64 56115 0.4 1 54254 1861 65 50693 0.4 1 49025 1668 66 46957 0.4 1 45356 1601 67 40646 0.4 1 39235 1411 68 33548 0.4 1 32437 1111 69 34486 0.4 1 33331 1155 70 31256 0.4 1 30204 1052 71 30849 0.4 1 29811 1038 72 29471 0.4 1 28343 1128 73 32424 0.4 1 30970 1454 74 52965 0.4 1 51557 1408 75 22944 0.4 1 22288 656 76 10556 0.4 1 10180 376 77 6398 0.4 1 6165 233 78 4367 0.4 1 4215 152 79 2823 0.4 1 2736 87 80 2034 0.4 1 1954 80 81 1354 0.4 1 1292 62 82 986 0.4 1 945 41 83 706 0.4 1 682 24 84 448 0.4 1 420 28 85 272 0.4 1 257 15 86 168 0.4 1 154 14 87 141 0.4 1 125 16 88 108 0.4 1 100 8 89 109 0.4 1 98 11 90 116 0.4 1 106 10 91 190 0.4 1 175 15 92 268 0.4 1 250 18 93 432 0.4 1 401 31 94 901 0.4 1 857 44 95 1201 0.4 1 1138 63 96 1067 0.4 1 1011 56 97 562 0.4 1 519 43 98 169 0.4 1 151 18 99 105 0.4 1 85 20 100 213 0.4 1 163 50 101 651 0.4 1 465 186 RUN STATISTICS FOR INPUT FILE: EPI-119_S31_L005_R1_001.fastq.gz ============================================= 29018872 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 2899376 (10.0%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 14762462 (50.9%) RRBS reads trimmed by 2 bp at the start when read started with CAA (200033) or CGA (164596) in total: 364629 (1.3%)