SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-169_S12_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-169_S12_L002_R1_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 412.67 s (19 us/read; 3.18 M reads/minute). === Summary === Total reads processed: 21,849,611 Reads with adapters: 13,767,429 (63.0%) Reads written (passing filters): 21,849,611 (100.0%) Total basepairs processed: 2,194,351,039 bp Total written (filtered): 1,859,208,225 bp (84.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 13767429 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 22.7% C: 10.7% G: 27.8% T: 38.2% none/other: 0.6% Overview of removed sequences length count expect max.err error counts 1 3452710 5462402.8 0 3452710 2 883846 1365600.7 0 883846 3 346804 341400.2 0 346804 4 247235 85350.0 0 247235 5 138986 21337.5 0 138986 6 137165 5334.4 0 137165 7 128137 1333.6 0 128137 8 140982 333.4 0 140982 9 144748 83.3 0 143298 1450 10 138479 20.8 1 132681 5798 11 141188 5.2 1 134441 6747 12 137071 1.3 1 130933 6138 13 131819 0.3 1 126000 5819 14 147936 0.3 1 139931 8005 15 140154 0.3 1 133297 6857 16 154056 0.3 1 145311 8745 17 145212 0.3 1 137452 7760 18 140661 0.3 1 133678 6983 19 148281 0.3 1 139722 8559 20 140923 0.3 1 133926 6997 21 153636 0.3 1 144809 8827 22 145797 0.3 1 138448 7349 23 144859 0.3 1 137260 7599 24 148762 0.3 1 140420 8342 25 141603 0.3 1 134305 7298 26 157228 0.3 1 147717 9511 27 143846 0.3 1 136786 7060 28 138636 0.3 1 132130 6506 29 154789 0.3 1 146905 7884 30 144150 0.3 1 137787 6363 31 160953 0.3 1 152288 8665 32 145594 0.3 1 139051 6543 33 154229 0.3 1 146602 7627 34 154085 0.3 1 146676 7409 35 145885 0.3 1 139179 6706 36 139625 0.3 1 133499 6126 37 152260 0.3 1 145690 6570 38 145892 0.3 1 139147 6745 39 144154 0.3 1 137244 6910 40 148119 0.3 1 140526 7593 41 210181 0.3 1 200934 9247 42 123384 0.3 1 117945 5439 43 83249 0.3 1 78945 4304 44 126656 0.3 1 120748 5908 45 125464 0.3 1 119926 5538 46 121102 0.3 1 115617 5485 47 129265 0.3 1 123109 6156 48 118980 0.3 1 113284 5696 49 127065 0.3 1 120826 6239 50 115322 0.3 1 110286 5036 51 113215 0.3 1 108221 4994 52 108080 0.3 1 103320 4760 53 102607 0.3 1 98567 4040 54 101008 0.3 1 96718 4290 55 103431 0.3 1 99263 4168 56 97158 0.3 1 93237 3921 57 90769 0.3 1 86976 3793 58 89671 0.3 1 86147 3524 59 86481 0.3 1 83057 3424 60 79333 0.3 1 76277 3056 61 81826 0.3 1 78682 3144 62 81355 0.3 1 78352 3003 63 73528 0.3 1 70700 2828 64 70977 0.3 1 68584 2393 65 65070 0.3 1 62747 2323 66 60937 0.3 1 58592 2345 67 59537 0.3 1 57286 2251 68 56160 0.3 1 53935 2225 69 57563 0.3 1 55377 2186 70 54060 0.3 1 51936 2124 71 54890 0.3 1 52671 2219 72 59911 0.3 1 57276 2635 73 74957 0.3 1 69857 5100 74 165354 0.3 1 159292 6062 75 115811 0.3 1 112025 3786 76 51661 0.3 1 49786 1875 77 29388 0.3 1 28252 1136 78 18224 0.3 1 17555 669 79 10971 0.3 1 10496 475 80 8075 0.3 1 7777 298 81 5690 0.3 1 5494 196 82 4117 0.3 1 3965 152 83 3604 0.3 1 3432 172 84 2835 0.3 1 2693 142 85 2176 0.3 1 2074 102 86 1540 0.3 1 1465 75 87 1279 0.3 1 1214 65 88 953 0.3 1 907 46 89 831 0.3 1 778 53 90 998 0.3 1 950 48 91 1307 0.3 1 1238 69 92 1924 0.3 1 1823 101 93 4060 0.3 1 3854 206 94 11206 0.3 1 10722 484 95 20380 0.3 1 19483 897 96 11252 0.3 1 10721 531 97 8949 0.3 1 8470 479 98 3622 0.3 1 3378 244 99 3805 0.3 1 3564 241 100 6092 0.3 1 5640 452 101 17638 0.3 1 15830 1808 RUN STATISTICS FOR INPUT FILE: EPI-169_S12_L002_R1_001.fastq.gz ============================================= 21849611 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 2295840 (10.5%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 13675084 (62.6%)