SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-43_S40_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-43_S40_L005_R1_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 542.40 s (18 us/read; 3.25 M reads/minute). === Summary === Total reads processed: 29,360,787 Reads with adapters: 20,620,662 (70.2%) Reads written (passing filters): 29,360,787 (100.0%) Total basepairs processed: 2,857,460,638 bp Total written (filtered): 1,998,784,073 bp (69.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 20620662 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 20.0% C: 26.5% G: 21.6% T: 30.4% none/other: 1.5% Overview of removed sequences length count expect max.err error counts 1 3895309 7340196.8 0 3895309 2 911786 1835049.2 0 911786 3 364394 458762.3 0 364394 4 245445 114690.6 0 245445 5 137427 28672.6 0 137427 6 130590 7168.2 0 130590 7 118550 1792.0 0 118550 8 128937 448.0 0 128937 9 134687 112.0 0 133531 1156 10 128672 28.0 1 122607 6065 11 133534 7.0 1 126414 7120 12 124322 1.8 1 118184 6138 13 126893 0.4 1 120474 6419 14 137165 0.4 1 128979 8186 15 134894 0.4 1 127260 7634 16 141806 0.4 1 133073 8733 17 143893 0.4 1 135223 8670 18 126217 0.4 1 119575 6642 19 140931 0.4 1 131535 9396 20 132861 0.4 1 125609 7252 21 150744 0.4 1 140261 10483 22 138844 0.4 1 130921 7923 23 132812 0.4 1 125079 7733 24 140093 0.4 1 130865 9228 25 136841 0.4 1 128749 8092 26 145127 0.4 1 135527 9600 27 140613 0.4 1 132746 7867 28 135087 0.4 1 127863 7224 29 147522 0.4 1 138906 8616 30 137145 0.4 1 130148 6997 31 149534 0.4 1 140339 9195 32 140476 0.4 1 133050 7426 33 143670 0.4 1 135704 7966 34 141834 0.4 1 134174 7660 35 150971 0.4 1 142012 8959 36 139448 0.4 1 132506 6942 37 147735 0.4 1 139832 7903 38 144478 0.4 1 136801 7677 39 139182 0.4 1 132134 7048 40 159075 0.4 1 149579 9496 41 211374 0.4 1 200982 10392 42 124477 0.4 1 118619 5858 43 69394 0.4 1 65348 4046 44 126800 0.4 1 120451 6349 45 129981 0.4 1 122803 7178 46 124010 0.4 1 117422 6588 47 137187 0.4 1 129398 7789 48 126428 0.4 1 119319 7109 49 136024 0.4 1 127949 8075 50 117632 0.4 1 111322 6310 51 123096 0.4 1 116072 7024 52 122457 0.4 1 115148 7309 53 112318 0.4 1 106214 6104 54 109531 0.4 1 103176 6355 55 122692 0.4 1 115625 7067 56 111022 0.4 1 104673 6349 57 99646 0.4 1 93864 5782 58 109067 0.4 1 103391 5676 59 103507 0.4 1 98170 5337 60 90490 0.4 1 85927 4563 61 103419 0.4 1 98033 5386 62 104191 0.4 1 98953 5238 63 89905 0.4 1 85415 4490 64 87225 0.4 1 83121 4104 65 80646 0.4 1 76974 3672 66 77685 0.4 1 74120 3565 67 79888 0.4 1 76267 3621 68 80567 0.4 1 76905 3662 69 91569 0.4 1 87446 4123 70 94166 0.4 1 89765 4401 71 113625 0.4 1 108163 5462 72 160639 0.4 1 150732 9907 73 445515 0.4 1 410099 35416 74 1830536 0.4 1 1771323 59213 75 1038058 0.4 1 999743 38315 76 575820 0.4 1 553705 22115 77 318777 0.4 1 306268 12509 78 184889 0.4 1 177546 7343 79 100125 0.4 1 95908 4217 80 66140 0.4 1 63314 2826 81 41376 0.4 1 39548 1828 82 28595 0.4 1 27253 1342 83 22547 0.4 1 21372 1175 84 19040 0.4 1 18051 989 85 17791 0.4 1 16841 950 86 17093 0.4 1 16158 935 87 15693 0.4 1 14835 858 88 14265 0.4 1 13497 768 89 15479 0.4 1 14615 864 90 20502 0.4 1 19472 1030 91 31226 0.4 1 29708 1518 92 52453 0.4 1 49824 2629 93 134451 0.4 1 128032 6419 94 399545 0.4 1 382017 17528 95 644966 0.4 1 616839 28127 96 263844 0.4 1 251156 12688 97 137147 0.4 1 129773 7374 98 50714 0.4 1 47862 2852 99 47408 0.4 1 44737 2671 100 44576 0.4 1 41826 2750 101 71889 0.4 1 66438 5451 RUN STATISTICS FOR INPUT FILE: EPI-43_S40_L005_R1_001.fastq.gz ============================================= 29360787 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 7933123 (27.0%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 19823584 (67.5%) RRBS reads trimmed by 2 bp at the start when read started with CAA (278001) or CGA (204642) in total: 482643 (1.6%)