SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-152_S3_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-152_S3_L002_R1_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 582.47 s (19 us/read; 3.12 M reads/minute). === Summary === Total reads processed: 30,318,886 Reads with adapters: 16,719,337 (55.1%) Reads written (passing filters): 30,318,886 (100.0%) Total basepairs processed: 3,048,694,114 bp Total written (filtered): 2,765,158,127 bp (90.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 16719337 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 24.3% C: 8.6% G: 26.3% T: 40.5% none/other: 0.4% Overview of removed sequences length count expect max.err error counts 1 5845533 7579721.5 0 5845533 2 1453641 1894930.4 0 1453641 3 576011 473732.6 0 576011 4 389315 118433.1 0 389315 5 204393 29608.3 0 204393 6 201330 7402.1 0 201330 7 187781 1850.5 0 187781 8 211436 462.6 0 211436 9 196485 115.7 0 194823 1662 10 189452 28.9 1 182041 7411 11 189613 7.2 1 181409 8204 12 182027 1.8 1 174561 7466 13 173790 0.5 1 166523 7267 14 189147 0.5 1 179568 9579 15 181024 0.5 1 172787 8237 16 190563 0.5 1 181005 9558 17 178571 0.5 1 169952 8619 18 166254 0.5 1 158714 7540 19 181742 0.5 1 171663 10079 20 167919 0.5 1 160255 7664 21 185146 0.5 1 174903 10243 22 172236 0.5 1 164117 8119 23 158172 0.5 1 150540 7632 24 166286 0.5 1 157552 8734 25 154128 0.5 1 146945 7183 26 168632 0.5 1 159565 9067 27 153171 0.5 1 146199 6972 28 144472 0.5 1 138128 6344 29 155889 0.5 1 148392 7497 30 141485 0.5 1 135614 5871 31 150439 0.5 1 143174 7265 32 137205 0.5 1 131524 5681 33 148481 0.5 1 141304 7177 34 137527 0.5 1 131342 6185 35 127833 0.5 1 122022 5811 36 132526 0.5 1 126855 5671 37 129827 0.5 1 124349 5478 38 120186 0.5 1 115060 5126 39 115780 0.5 1 111040 4740 40 123296 0.5 1 117048 6248 41 162465 0.5 1 155705 6760 42 97769 0.5 1 93593 4176 43 68007 0.5 1 64797 3210 44 98963 0.5 1 94600 4363 45 95660 0.5 1 91467 4193 46 91542 0.5 1 87556 3986 47 94301 0.5 1 89894 4407 48 87105 0.5 1 83268 3837 49 88899 0.5 1 84783 4116 50 79496 0.5 1 75953 3543 51 76087 0.5 1 72903 3184 52 72047 0.5 1 69060 2987 53 68090 0.5 1 65495 2595 54 66340 0.5 1 63729 2611 55 67201 0.5 1 64575 2626 56 62170 0.5 1 59786 2384 57 58768 0.5 1 56434 2334 58 56355 0.5 1 54383 1972 59 53788 0.5 1 51807 1981 60 48103 0.5 1 46303 1800 61 47999 0.5 1 46278 1721 62 47483 0.5 1 45834 1649 63 44107 0.5 1 42520 1587 64 42462 0.5 1 41135 1327 65 38173 0.5 1 36835 1338 66 35958 0.5 1 34667 1291 67 34155 0.5 1 32897 1258 68 31494 0.5 1 30341 1153 69 32962 0.5 1 31765 1197 70 31170 0.5 1 29990 1180 71 29901 0.5 1 28762 1139 72 31753 0.5 1 30244 1509 73 45471 0.5 1 42188 3283 74 127773 0.5 1 123392 4381 75 86283 0.5 1 83423 2860 76 48960 0.5 1 47069 1891 77 29952 0.5 1 28788 1164 78 18384 0.5 1 17707 677 79 10711 0.5 1 10260 451 80 7048 0.5 1 6781 267 81 4594 0.5 1 4384 210 82 3225 0.5 1 3079 146 83 2620 0.5 1 2508 112 84 2170 0.5 1 2072 98 85 1776 0.5 1 1683 93 86 1443 0.5 1 1380 63 87 1243 0.5 1 1185 58 88 1014 0.5 1 941 73 89 996 0.5 1 926 70 90 1191 0.5 1 1114 77 91 1626 0.5 1 1537 89 92 2310 0.5 1 2200 110 93 5191 0.5 1 4942 249 94 15403 0.5 1 14748 655 95 27425 0.5 1 26318 1107 96 13045 0.5 1 12423 622 97 10089 0.5 1 9586 503 98 4489 0.5 1 4218 271 99 4757 0.5 1 4483 274 100 6376 0.5 1 5997 379 101 14255 0.5 1 12804 1451 RUN STATISTICS FOR INPUT FILE: EPI-152_S3_L002_R1_001.fastq.gz ============================================= 30318886 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 2694171 (8.9%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 16641638 (54.9%)