SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-41_S38_L005_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-41_S38_L005_R2_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 489.64 s (19 us/read; 3.16 M reads/minute). === Summary === Total reads processed: 25,784,248 Reads with adapters: 17,635,068 (68.4%) Reads written (passing filters): 25,784,248 (100.0%) Total basepairs processed: 2,562,234,225 bp Total written (filtered): 2,163,399,405 bp (84.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 17635068 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 34.7% C: 22.8% G: 10.7% T: 31.1% none/other: 0.7% Overview of removed sequences length count expect max.err error counts 1 6957145 6446062.0 0 6957145 2 248720 1611515.5 0 248720 3 177146 402878.9 0 177146 4 147721 100719.7 0 147721 5 146383 25179.9 0 146383 6 147588 6295.0 0 147588 7 143620 1573.7 0 143620 8 145419 393.4 0 145419 9 141858 98.4 0 141272 586 10 149959 24.6 1 143538 6421 11 140286 6.1 1 132752 7534 12 148660 1.5 1 141080 7580 13 139864 0.4 1 132960 6904 14 160334 0.4 1 152041 8293 15 144459 0.4 1 137324 7135 16 148496 0.4 1 141560 6936 17 162802 0.4 1 154906 7896 18 137481 0.4 1 130751 6730 19 153879 0.4 1 146538 7341 20 149179 0.4 1 141558 7621 21 151701 0.4 1 143629 8072 22 159907 0.4 1 151511 8396 23 154426 0.4 1 146841 7585 24 178770 0.4 1 169739 9031 25 143506 0.4 1 136287 7219 26 149615 0.4 1 141325 8290 27 155343 0.4 1 145723 9620 28 172140 0.4 1 163604 8536 29 156523 0.4 1 147083 9440 30 185894 0.4 1 177226 8668 31 150699 0.4 1 142404 8295 32 171077 0.4 1 163743 7334 33 178894 0.4 1 169644 9250 34 178132 0.4 1 168112 10020 35 184751 0.4 1 177685 7066 36 161903 0.4 1 153644 8259 37 163689 0.4 1 155607 8082 38 149582 0.4 1 142404 7178 39 161959 0.4 1 153762 8197 40 158742 0.4 1 150981 7761 41 163485 0.4 1 156739 6746 42 166614 0.4 1 160560 6054 43 139347 0.4 1 132745 6602 44 151828 0.4 1 145128 6700 45 217396 0.4 1 210163 7233 46 141747 0.4 1 135687 6060 47 95032 0.4 1 90229 4803 48 155242 0.4 1 149534 5708 49 101736 0.4 1 97225 4511 50 111533 0.4 1 106532 5001 51 174495 0.4 1 168770 5725 52 96871 0.4 1 92497 4374 53 99529 0.4 1 94809 4720 54 90510 0.4 1 86254 4256 55 115293 0.4 1 110603 4690 56 111307 0.4 1 106246 5061 57 104012 0.4 1 99736 4276 58 103731 0.4 1 99505 4226 59 99979 0.4 1 95616 4363 60 99179 0.4 1 94781 4398 61 102532 0.4 1 97938 4594 62 107723 0.4 1 102747 4976 63 110480 0.4 1 105467 5013 64 110148 0.4 1 104800 5348 65 117677 0.4 1 112276 5401 66 128289 0.4 1 122114 6175 67 170411 0.4 1 159239 11172 68 446369 0.4 1 432858 13511 69 156375 0.4 1 149378 6997 70 77641 0.4 1 73323 4318 71 47002 0.4 1 43677 3325 72 36015 0.4 1 33402 2613 73 29924 0.4 1 27658 2266 74 24372 0.4 1 22530 1842 75 21368 0.4 1 19692 1676 76 18615 0.4 1 17137 1478 77 16874 0.4 1 15521 1353 78 14849 0.4 1 13623 1226 79 12362 0.4 1 11274 1088 80 10110 0.4 1 9245 865 81 8355 0.4 1 7660 695 82 6782 0.4 1 6191 591 83 5173 0.4 1 4682 491 84 4062 0.4 1 3646 416 85 3043 0.4 1 2737 306 86 2320 0.4 1 2068 252 87 1958 0.4 1 1700 258 88 1487 0.4 1 1281 206 89 1551 0.4 1 1293 258 90 1883 0.4 1 1623 260 91 2632 0.4 1 2233 399 92 3854 0.4 1 3297 557 93 7594 0.4 1 6518 1076 94 20459 0.4 1 17981 2478 95 33935 0.4 1 30160 3775 96 17519 0.4 1 15550 1969 97 12444 0.4 1 10959 1485 98 4894 0.4 1 4309 585 99 4685 0.4 1 4123 562 100 7746 0.4 1 6706 1040 101 26438 0.4 1 22711 3727 RUN STATISTICS FOR INPUT FILE: EPI-41_S38_L005_R2_001.fastq.gz ============================================= 25784248 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 4536015 (17.6%) 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: 25784248 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 728931 (2.83%)