SUMMARISING RUN PARAMETERS ========================== Input filename: Geoduck-NMP-gDNA-5to7kb-6_S23_L006_R2_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 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 Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/20180328_fastqc_trimmed_hiseq_geoduck --threads 28 Output file will be GZIP compressed This is cutadapt 1.16 with Python 2.7.14 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC Geoduck-NMP-gDNA-5to7kb-6_S23_L006_R2_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 9759.48 s (29 us/read; 2.07 M reads/minute). === Summary === Total reads processed: 337,457,885 Reads with adapters: 75,968,497 (22.5%) Reads written (passing filters): 337,457,885 (100.0%) Total basepairs processed: 37,962,561,744 bp Quality-trimmed: 3,715,982,260 bp (9.8%) Total written (filtered): 33,913,014,949 bp (89.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 75968497 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.2% C: 25.2% G: 14.2% T: 28.9% none/other: 1.5% Overview of removed sequences length count expect max.err error counts 1 53251749 84364471.2 0 53251749 2 14161587 21091117.8 0 14161587 3 3179820 5272779.5 0 3179820 4 1308712 1318194.9 0 1308712 5 276711 329548.7 0 276711 6 47612 82387.2 0 47612 7 50159 20596.8 0 50159 8 31236 5149.2 0 31236 9 7152 1287.3 0 4833 2319 10 29137 321.8 1 14994 14143 11 9597 80.5 1 3893 5704 12 20461 20.1 1 12760 7701 13 12152 5.0 1 6201 5951 14 48001 5.0 1 33146 14855 15 14011 5.0 1 9416 4595 16 10339 5.0 1 5973 4366 17 30716 5.0 1 21418 9298 18 5537 5.0 1 3060 2477 19 26499 5.0 1 19207 7292 20 21365 5.0 1 15652 5713 21 2611 5.0 1 1064 1547 22 4464 5.0 1 2049 2415 23 20803 5.0 1 13909 6894 24 52787 5.0 1 37075 15712 25 20236 5.0 1 14323 5913 26 28710 5.0 1 22712 5998 27 3016 5.0 1 1487 1529 28 21615 5.0 1 15433 6182 29 3924 5.0 1 2008 1916 30 23411 5.0 1 16521 6890 31 5858 5.0 1 3606 2252 32 29414 5.0 1 21792 7622 33 54062 5.0 1 44170 9892 34 3908 5.0 1 2000 1908 35 10710 5.0 1 5873 4837 36 10168 5.0 1 6091 4077 37 27495 5.0 1 21809 5686 38 11004 5.0 1 6714 4290 39 15794 5.0 1 12033 3761 40 6979 5.0 1 4028 2951 41 25050 5.0 1 18098 6952 42 43309 5.0 1 32363 10946 43 7876 5.0 1 5266 2610 44 26271 5.0 1 19250 7021 45 42065 5.0 1 31775 10290 46 19945 5.0 1 15226 4719 47 7061 5.0 1 4422 2639 48 48106 5.0 1 36674 11432 49 27182 5.0 1 20418 6764 50 14509 5.0 1 9484 5025 51 89691 5.0 1 68589 21102 52 19465 5.0 1 13784 5681 53 13751 5.0 1 9746 4005 54 20076 5.0 1 16168 3908 55 30874 5.0 1 23545 7329 56 15533 5.0 1 11006 4527 57 25782 5.0 1 20205 5577 58 35697 5.0 1 29237 6460 59 22596 5.0 1 17784 4812 60 22217 5.0 1 17697 4520 61 22491 5.0 1 18065 4426 62 24733 5.0 1 19684 5049 63 30241 5.0 1 24303 5938 64 33275 5.0 1 26611 6664 65 36902 5.0 1 29376 7526 66 43287 5.0 1 32157 11130 67 331963 5.0 1 47956 284007 68 745425 5.0 1 476908 268517 69 398389 5.0 1 307966 90423 70 153354 5.0 1 85773 67581 71 85512 5.0 1 57848 27664 72 37770 5.0 1 23517 14253 73 24470 5.0 1 15464 9006 74 16010 5.0 1 9974 6036 75 14434 5.0 1 8652 5782 76 12957 5.0 1 8042 4915 77 11765 5.0 1 7049 4716 78 11632 5.0 1 6945 4687 79 11427 5.0 1 6937 4490 80 11082 5.0 1 6653 4429 81 11034 5.0 1 6729 4305 82 10713 5.0 1 6557 4156 83 10088 5.0 1 6223 3865 84 9550 5.0 1 5904 3646 85 9398 5.0 1 5814 3584 86 9162 5.0 1 5702 3460 87 8671 5.0 1 5258 3413 88 9147 5.0 1 5508 3639 89 8911 5.0 1 5425 3486 90 9110 5.0 1 5487 3623 91 9038 5.0 1 5551 3487 92 8167 5.0 1 4909 3258 93 7995 5.0 1 4873 3122 94 7900 5.0 1 4988 2912 95 7276 5.0 1 4334 2942 96 7328 5.0 1 4499 2829 97 7443 5.0 1 4702 2741 98 6685 5.0 1 4128 2557 99 6935 5.0 1 4292 2643 100 7462 5.0 1 4767 2695 101 7130 5.0 1 4606 2524 102 7202 5.0 1 4595 2607 103 7260 5.0 1 4724 2536 104 7176 5.0 1 4687 2489 105 6893 5.0 1 4602 2291 106 6915 5.0 1 4662 2253 107 6727 5.0 1 4610 2117 108 6563 5.0 1 4522 2041 109 6441 5.0 1 4481 1960 110 6217 5.0 1 4378 1839 111 6006 5.0 1 4113 1893 112 5795 5.0 1 4022 1773 113 5504 5.0 1 3787 1717 114 5530 5.0 1 3745 1785 115 5024 5.0 1 3416 1608 116 5078 5.0 1 3466 1612 117 4816 5.0 1 3328 1488 118 4569 5.0 1 3148 1421 119 4359 5.0 1 2991 1368 120 4355 5.0 1 2988 1367 121 4076 5.0 1 2852 1224 122 3904 5.0 1 2713 1191 123 3548 5.0 1 2496 1052 124 3595 5.0 1 2559 1036 125 3438 5.0 1 2400 1038 126 3352 5.0 1 2401 951 127 3064 5.0 1 2244 820 128 3581 5.0 1 2749 832 129 2520 5.0 1 1830 690 130 2482 5.0 1 1841 641 131 1918 5.0 1 1383 535 132 1859 5.0 1 1380 479 133 1573 5.0 1 1122 451 134 1618 5.0 1 1188 430 135 1448 5.0 1 1071 377 136 1463 5.0 1 1031 432 137 1287 5.0 1 919 368 138 1164 5.0 1 805 359 139 1100 5.0 1 733 367 140 1100 5.0 1 661 439 141 1026 5.0 1 585 441 142 1029 5.0 1 544 485 143 979 5.0 1 498 481 144 1017 5.0 1 502 515 145 1081 5.0 1 416 665 146 1227 5.0 1 426 801 147 1605 5.0 1 509 1096 148 5468 5.0 1 1477 3991 149 15278 5.0 1 4203 11075 150 68349 5.0 1 18398 49951 151 18078 5.0 1 4811 13267 RUN STATISTICS FOR INPUT FILE: Geoduck-NMP-gDNA-5to7kb-6_S23_L006_R2_001.fastq.gz ============================================= 337457885 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 337457885 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 99581376 (29.51%)