SUMMARISING RUN PARAMETERS ========================== Input filename: 2112_lane1_CAGATC.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_CAGATC.fastq.gz Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 908.94 s (23 us/read; 2.63 M reads/minute). === Summary === Total reads processed: 39,780,221 Reads with adapters: 23,668,832 (59.5%) Reads written (passing filters): 39,780,221 (100.0%) Total basepairs processed: 4,017,802,321 bp Quality-trimmed: 316,184,920 bp (7.9%) Total written (filtered): 3,168,106,786 bp (78.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 23668832 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 33.0% C: 15.7% G: 6.0% T: 18.1% none/other: 27.2% Overview of removed sequences length count expect max.err error counts 1 11462116 9945055.2 0 11462116 2 913629 2486263.8 0 913629 3 452027 621566.0 0 452027 4 350618 155391.5 0 350618 5 306933 38847.9 0 306933 6 287673 9712.0 0 287673 7 281622 2428.0 0 281622 8 223594 607.0 0 223594 9 240116 151.7 0 238205 1911 10 227281 37.9 1 224750 2531 11 163868 9.5 1 161288 2580 12 192839 2.4 1 190444 2395 13 162948 0.6 1 160373 2575 14 155026 0.6 1 152612 2414 15 156135 0.6 1 153474 2661 16 136091 0.6 1 133382 2709 17 150211 0.6 1 146876 3335 18 140793 0.6 1 138808 1985 19 77443 0.6 1 75897 1546 20 101254 0.6 1 99368 1886 21 93085 0.6 1 91238 1847 22 92927 0.6 1 91104 1823 23 72275 0.6 1 70493 1782 24 72096 0.6 1 70374 1722 25 70407 0.6 1 68697 1710 26 59212 0.6 1 56603 2609 27 60402 0.6 1 56761 3641 28 69540 0.6 1 64651 4889 29 44622 0.6 1 41133 3489 30 56254 0.6 1 53841 2413 31 26735 0.6 1 24281 2454 32 44698 0.6 1 38863 5835 33 37973 0.6 1 24758 13215 34 33790 0.6 1 29226 4564 35 32081 0.6 1 27180 4901 36 29448 0.6 1 22077 7371 37 24821 0.6 1 20313 4508 38 22225 0.6 1 17979 4246 39 18973 0.6 1 16137 2836 40 18644 0.6 1 12986 5658 41 17506 0.6 1 12014 5492 42 18109 0.6 1 11098 7011 43 14861 0.6 1 10066 4795 44 15499 0.6 1 8463 7036 45 14330 0.6 1 9724 4606 46 11858 0.6 1 7524 4334 47 10333 0.6 1 4854 5479 48 9714 0.6 1 3768 5946 49 9608 0.6 1 4719 4889 50 9483 0.6 1 3478 6005 51 14031 0.6 1 3385 10646 52 13293 0.6 1 4130 9163 53 8936 0.6 1 3526 5410 54 9880 0.6 1 942 8938 55 9118 0.6 1 1651 7467 56 13037 0.6 1 1504 11533 57 18891 0.6 1 1702 17189 58 20513 0.6 1 1377 19136 59 11927 0.6 1 1601 10326 60 19127 0.6 1 774 18353 61 23847 0.6 1 954 22893 62 75729 0.6 1 1023 74706 63 106543 0.6 1 2066 104477 64 28953 0.6 1 1537 27416 65 37265 0.6 1 412 36853 66 83783 0.6 1 586 83197 67 294910 0.6 1 1013 293897 68 680760 0.6 1 2305 678455 69 2319080 0.6 1 3770 2315310 70 1329812 0.6 1 8452 1321360 71 474084 0.6 1 2222 471862 72 166586 0.6 1 691 165895 73 46783 0.6 1 227 46556 74 24031 0.6 1 123 23908 75 13845 0.6 1 81 13764 76 11129 0.6 1 88 11041 77 15028 0.6 1 90 14938 78 14602 0.6 1 103 14499 79 13582 0.6 1 91 13491 80 11830 0.6 1 47 11783 81 10270 0.6 1 32 10238 82 9814 0.6 1 16 9798 83 9005 0.6 1 15 8990 84 8662 0.6 1 18 8644 85 8888 0.6 1 26 8862 86 9233 0.6 1 24 9209 87 9845 0.6 1 42 9803 88 9350 0.6 1 37 9313 89 9508 0.6 1 55 9453 90 10077 0.6 1 20 10057 91 10706 0.6 1 17 10689 92 11285 0.6 1 25 11260 93 11770 0.6 1 9 11761 94 12970 0.6 1 17 12953 95 13873 0.6 1 6 13867 96 16173 0.6 1 6 16167 97 17692 0.6 1 7 17685 98 19791 0.6 1 6 19785 99 22589 0.6 1 7 22582 100 45074 0.6 1 7 45067 101 187596 0.6 1 13 187583 RUN STATISTICS FOR INPUT FILE: 2112_lane1_CAGATC.fastq.gz ============================================= 39780221 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 6470690 (16.3%)