SUMMARISING RUN PARAMETERS ========================== Input filename: 2112_lane1_ATCACG.fastq.gz Trimming mode: single-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 before a sequence gets removed: 20 bp Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /home/sam/analyses/20180911_virginica_oil_trimgalore_01/20180911_virginica_oil_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 -q 20 -O 1 -a AGATCGGAAGAGC 2112_lane1_ATCACG.fastq.gz Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 749.44 s (22 us/read; 2.67 M reads/minute). === Summary === Total reads processed: 33,409,414 Reads with adapters: 17,611,436 (52.7%) Reads written (passing filters): 33,409,414 (100.0%) Total basepairs processed: 3,374,350,814 bp Quality-trimmed: 220,159,975 bp (6.5%) Total written (filtered): 2,847,951,372 bp (84.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 17611436 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 36.3% C: 16.1% G: 7.6% T: 18.9% none/other: 21.1% Overview of removed sequences length count expect max.err error counts 1 10442109 8352353.5 0 10442109 2 858531 2088088.4 0 858531 3 323059 522022.1 0 323059 4 208999 130505.5 0 208999 5 156468 32626.4 0 156468 6 150095 8156.6 0 150095 7 150683 2039.1 0 150683 8 112087 509.8 0 112087 9 121119 127.4 0 119789 1330 10 120185 31.9 1 118496 1689 11 82522 8.0 1 80895 1627 12 102396 2.0 1 100840 1556 13 83339 0.5 1 81773 1566 14 80199 0.5 1 78593 1606 15 80591 0.5 1 78931 1660 16 71183 0.5 1 69586 1597 17 78307 0.5 1 76360 1947 18 77111 0.5 1 75828 1283 19 37842 0.5 1 36894 948 20 53140 0.5 1 51938 1202 21 48734 0.5 1 47537 1197 22 51325 0.5 1 50222 1103 23 35379 0.5 1 34409 970 24 35467 0.5 1 34472 995 25 36003 0.5 1 34999 1004 26 29489 0.5 1 27823 1666 27 30967 0.5 1 28456 2511 28 35485 0.5 1 31877 3608 29 22082 0.5 1 19860 2222 30 27130 0.5 1 25572 1558 31 12798 0.5 1 11146 1652 32 21740 0.5 1 16029 5711 33 20199 0.5 1 13434 6765 34 19003 0.5 1 13472 5531 35 14389 0.5 1 11153 3236 36 11969 0.5 1 10095 1874 37 13574 0.5 1 8671 4903 38 13729 0.5 1 9035 4694 39 10171 0.5 1 6936 3235 40 11802 0.5 1 6610 5192 41 10036 0.5 1 4373 5663 42 10201 0.5 1 3897 6304 43 7546 0.5 1 3982 3564 44 7277 0.5 1 3278 3999 45 6507 0.5 1 3634 2873 46 5774 0.5 1 3093 2681 47 5356 0.5 1 1998 3358 48 4427 0.5 1 1669 2758 49 4043 0.5 1 1934 2109 50 5248 0.5 1 1453 3795 51 7087 0.5 1 1453 5634 52 6646 0.5 1 1797 4849 53 4822 0.5 1 1667 3155 54 5450 0.5 1 473 4977 55 5173 0.5 1 783 4390 56 6833 0.5 1 755 6078 57 10395 0.5 1 884 9511 58 11086 0.5 1 751 10335 59 7377 0.5 1 898 6479 60 12412 0.5 1 523 11889 61 16010 0.5 1 614 15396 62 40681 0.5 1 636 40045 63 71709 0.5 1 1313 70396 64 22353 0.5 1 1201 21152 65 27766 0.5 1 296 27470 66 60315 0.5 1 483 59832 67 205212 0.5 1 736 204476 68 445189 0.5 1 1601 443588 69 1354272 0.5 1 2421 1351851 70 645444 0.5 1 4623 640821 71 244073 0.5 1 1185 242888 72 91085 0.5 1 384 90701 73 26529 0.5 1 148 26381 74 13928 0.5 1 82 13846 75 8001 0.5 1 49 7952 76 6494 0.5 1 53 6441 77 8716 0.5 1 54 8662 78 8523 0.5 1 58 8465 79 8002 0.5 1 52 7950 80 6802 0.5 1 17 6785 81 6065 0.5 1 10 6055 82 5812 0.5 1 13 5799 83 5192 0.5 1 17 5175 84 4934 0.5 1 16 4918 85 4964 0.5 1 16 4948 86 5251 0.5 1 23 5228 87 5652 0.5 1 26 5626 88 5278 0.5 1 23 5255 89 5331 0.5 1 34 5297 90 5719 0.5 1 8 5711 91 6034 0.5 1 9 6025 92 6322 0.5 1 18 6304 93 6631 0.5 1 8 6623 94 7224 0.5 1 12 7212 95 7883 0.5 1 10 7873 96 9041 0.5 1 4 9037 97 9978 0.5 1 1 9977 98 11212 0.5 1 6 11206 99 12879 0.5 1 5 12874 100 25791 0.5 1 9 25782 101 108043 0.5 1 10 108033 RUN STATISTICS FOR INPUT FILE: 2112_lane1_ATCACG.fastq.gz ============================================= 33409414 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 3771783 (11.3%)