SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-214_S30_L004_R2_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-214_S30_L004_R2_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 573.48 s (19 us/read; 3.21 M reads/minute). === Summary === Total reads processed: 30,640,077 Reads with adapters: 20,717,151 (67.6%) Reads written (passing filters): 30,640,077 (100.0%) Total basepairs processed: 3,038,979,722 bp Total written (filtered): 2,584,239,826 bp (85.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 20717151 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 35.3% C: 23.2% G: 11.0% T: 30.0% none/other: 0.5% Overview of removed sequences length count expect max.err error counts 1 8977279 7660019.2 0 8977279 2 260046 1915004.8 0 260046 3 216509 478751.2 0 216509 4 185940 119687.8 0 185940 5 184627 29922.0 0 184627 6 190328 7480.5 0 190328 7 184050 1870.1 0 184050 8 198228 467.5 0 198228 9 181718 116.9 0 180957 761 10 183550 29.2 1 179143 4407 11 171939 7.3 1 166976 4963 12 178044 1.8 1 172611 5433 13 172116 0.5 1 167220 4896 14 184202 0.5 1 178596 5606 15 175262 0.5 1 170155 5107 16 176487 0.5 1 171552 4935 17 184297 0.5 1 178860 5437 18 165624 0.5 1 160977 4647 19 172800 0.5 1 167698 5102 20 171600 0.5 1 166534 5066 21 173258 0.5 1 168026 5232 22 176511 0.5 1 171044 5467 23 173750 0.5 1 168514 5236 24 178484 0.5 1 172939 5545 25 163728 0.5 1 158781 4947 26 163032 0.5 1 157360 5672 27 163473 0.5 1 157157 6316 28 169998 0.5 1 164647 5351 29 164208 0.5 1 158621 5587 30 178365 0.5 1 173025 5340 31 155241 0.5 1 150235 5006 32 165394 0.5 1 160587 4807 33 170030 0.5 1 164542 5488 34 166761 0.5 1 160883 5878 35 160354 0.5 1 155865 4489 36 155891 0.5 1 150877 5014 37 153886 0.5 1 149021 4865 38 141812 0.5 1 137328 4484 39 142562 0.5 1 137875 4687 40 142048 0.5 1 137214 4834 41 144893 0.5 1 140165 4728 42 141160 0.5 1 136956 4204 43 128161 0.5 1 123996 4165 44 130969 0.5 1 126576 4393 45 154564 0.5 1 150009 4555 46 125551 0.5 1 121742 3809 47 98577 0.5 1 95287 3290 48 129428 0.5 1 125610 3818 49 99737 0.5 1 96794 2943 50 101669 0.5 1 98465 3204 51 136348 0.5 1 132701 3647 52 92110 0.5 1 89351 2759 53 93650 0.5 1 90943 2707 54 82745 0.5 1 80220 2525 55 99347 0.5 1 96700 2647 56 93862 0.5 1 91171 2691 57 88010 0.5 1 85408 2602 58 85201 0.5 1 82519 2682 59 82063 0.5 1 79521 2542 60 79335 0.5 1 76927 2408 61 79626 0.5 1 77109 2517 62 80039 0.5 1 77423 2616 63 79084 0.5 1 76402 2682 64 77639 0.5 1 74986 2653 65 82342 0.5 1 79266 3076 66 89153 0.5 1 85314 3839 67 139943 0.5 1 127986 11957 68 760396 0.5 1 740236 20160 69 343613 0.5 1 332336 11277 70 182596 0.5 1 176225 6371 71 91223 0.5 1 87469 3754 72 56545 0.5 1 54137 2408 73 36446 0.5 1 34641 1805 74 26608 0.5 1 25249 1359 75 20521 0.5 1 19367 1154 76 16962 0.5 1 15979 983 77 14403 0.5 1 13553 850 78 12746 0.5 1 11938 808 79 10867 0.5 1 10142 725 80 9324 0.5 1 8715 609 81 7907 0.5 1 7360 547 82 6774 0.5 1 6286 488 83 5711 0.5 1 5296 415 84 5249 0.5 1 4825 424 85 4540 0.5 1 4139 401 86 4155 0.5 1 3774 381 87 4500 0.5 1 4068 432 88 4664 0.5 1 4204 460 89 5480 0.5 1 4903 577 90 6949 0.5 1 6256 693 91 10283 0.5 1 9328 955 92 15523 0.5 1 14097 1426 93 33943 0.5 1 31062 2881 94 103132 0.5 1 95458 7674 95 164213 0.5 1 152860 11353 96 65731 0.5 1 61264 4467 97 36448 0.5 1 33863 2585 98 13936 0.5 1 12951 985 99 12821 0.5 1 11866 955 100 12329 0.5 1 11445 884 101 21975 0.5 1 20214 1761 RUN STATISTICS FOR INPUT FILE: EPI-214_S30_L004_R2_001.fastq.gz ============================================= 30640077 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 3851793 (12.6%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 0 (0.0%) Total number of sequences analysed for the sequence pair length validation: 30640077 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1980034 (6.46%)