SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_32psu_3_S3_L002_R1_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.6.4_dev Cutadapt version: 2.4 Python version: could not detect Number of cores used for trimming: 8 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Using Illumina adapter for trimming (count: 655761). Second best hit was smallRNA (count: 0) 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 All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /gscratch/scrubbed/strigg/analyses/20200427/TG_PE_FASTQS/FastQC --threads 28 Output file will be GZIP compressed This is cutadapt 2.4 with Python 3.7.6 Command line parameters: -j 8 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_32psu_3_S3_L002_R1_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 47.86 s (4 us/read; 17.14 M reads/minute). === Summary === Total reads processed: 13,670,957 Reads with adapters: 11,663,120 (85.3%) Reads written (passing filters): 13,670,957 (100.0%) Total basepairs processed: 2,050,643,550 bp Quality-trimmed: 4,231,959 bp (0.2%) Total written (filtered): 1,462,745,020 bp (71.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11663120 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.2% C: 13.5% G: 21.8% T: 35.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 1152864 3417739.2 0 1152864 2 186575 854434.8 0 186575 3 110892 213608.7 0 110892 4 68686 53402.2 0 68686 5 61523 13350.5 0 61523 6 61066 3337.6 0 61066 7 49563 834.4 0 49563 8 63725 208.6 0 63725 9 62710 52.2 0 61945 765 10 59136 13.0 1 55273 3863 11 67741 3.3 1 61750 5991 12 63923 0.8 1 59045 4878 13 66568 0.2 1 61427 5141 14 66808 0.2 1 61285 5523 15 71031 0.2 1 65247 5784 16 70289 0.2 1 63984 6305 17 86030 0.2 1 77755 8275 18 73739 0.2 1 68290 5449 19 63306 0.2 1 58569 4737 20 77355 0.2 1 71402 5953 21 85573 0.2 1 78654 6919 22 72710 0.2 1 67584 5126 23 86414 0.2 1 79515 6899 24 79027 0.2 1 71591 7436 25 86879 0.2 1 79866 7013 26 79473 0.2 1 73820 5653 27 90733 0.2 1 83035 7698 28 90102 0.2 1 83123 6979 29 92865 0.2 1 84237 8628 30 100457 0.2 1 93462 6995 31 79802 0.2 1 73917 5885 32 97719 0.2 1 90137 7582 33 93085 0.2 1 85177 7908 34 99262 0.2 1 90786 8476 35 104947 0.2 1 96795 8152 36 99380 0.2 1 91895 7485 37 106441 0.2 1 96879 9562 38 114379 0.2 1 105498 8881 39 96631 0.2 1 89100 7531 40 112490 0.2 1 103151 9339 41 123125 0.2 1 112471 10654 42 98677 0.2 1 90013 8664 43 172897 0.2 1 162100 10797 44 52704 0.2 1 47226 5478 45 117558 0.2 1 108914 8644 46 110418 0.2 1 102198 8220 47 119359 0.2 1 110565 8794 48 116841 0.2 1 108072 8769 49 129611 0.2 1 119238 10373 50 111895 0.2 1 104242 7653 51 123193 0.2 1 114083 9110 52 127566 0.2 1 117108 10458 53 137342 0.2 1 127459 9883 54 110167 0.2 1 102021 8146 55 130673 0.2 1 120967 9706 56 160643 0.2 1 149587 11056 57 104913 0.2 1 96311 8602 58 136727 0.2 1 128029 8698 59 118611 0.2 1 109706 8905 60 133859 0.2 1 123864 9995 61 131656 0.2 1 122381 9275 62 147218 0.2 1 137094 10124 63 117137 0.2 1 107812 9325 64 130610 0.2 1 121719 8891 65 145884 0.2 1 135248 10636 66 150729 0.2 1 139945 10784 67 163505 0.2 1 149584 13921 68 306709 0.2 1 289681 17028 69 62043 0.2 1 56562 5481 70 23965 0.2 1 19784 4181 71 84291 0.2 1 78568 5723 72 119692 0.2 1 111910 7782 73 127200 0.2 1 118724 8476 74 126943 0.2 1 118057 8886 75 127010 0.2 1 118252 8758 76 125373 0.2 1 116194 9179 77 125254 0.2 1 116388 8866 78 119533 0.2 1 110788 8745 79 118816 0.2 1 110233 8583 80 116241 0.2 1 107681 8560 81 114798 0.2 1 106595 8203 82 112468 0.2 1 104279 8189 83 109667 0.2 1 101888 7779 84 105890 0.2 1 98240 7650 85 103302 0.2 1 95804 7498 86 101064 0.2 1 93722 7342 87 97500 0.2 1 90687 6813 88 96898 0.2 1 89881 7017 89 91450 0.2 1 84968 6482 90 91495 0.2 1 84920 6575 91 86388 0.2 1 80232 6156 92 82291 0.2 1 76556 5735 93 78431 0.2 1 72788 5643 94 75874 0.2 1 70339 5535 95 70751 0.2 1 65675 5076 96 67352 0.2 1 62368 4984 97 63954 0.2 1 59443 4511 98 58850 0.2 1 54439 4411 99 58771 0.2 1 54248 4523 100 52467 0.2 1 48655 3812 101 49569 0.2 1 45811 3758 102 45464 0.2 1 42074 3390 103 41939 0.2 1 38904 3035 104 39055 0.2 1 36189 2866 105 34942 0.2 1 32296 2646 106 31969 0.2 1 29559 2410 107 29286 0.2 1 27065 2221 108 27282 0.2 1 25136 2146 109 24507 0.2 1 22544 1963 110 21811 0.2 1 20137 1674 111 19775 0.2 1 18232 1543 112 17157 0.2 1 15740 1417 113 14815 0.2 1 13543 1272 114 13327 0.2 1 12234 1093 115 11366 0.2 1 10408 958 116 9845 0.2 1 9004 841 117 8405 0.2 1 7663 742 118 7384 0.2 1 6703 681 119 6035 0.2 1 5477 558 120 4910 0.2 1 4438 472 121 4090 0.2 1 3702 388 122 3634 0.2 1 3283 351 123 3044 0.2 1 2741 303 124 2552 0.2 1 2281 271 125 2030 0.2 1 1827 203 126 1757 0.2 1 1559 198 127 1362 0.2 1 1204 158 128 1097 0.2 1 981 116 129 1002 0.2 1 874 128 130 785 0.2 1 685 100 131 638 0.2 1 562 76 132 540 0.2 1 480 60 133 462 0.2 1 415 47 134 556 0.2 1 494 62 135 352 0.2 1 314 38 136 204 0.2 1 176 28 137 149 0.2 1 133 16 138 114 0.2 1 99 15 139 71 0.2 1 62 9 140 64 0.2 1 52 12 141 32 0.2 1 25 7 142 45 0.2 1 42 3 143 51 0.2 1 43 8 144 31 0.2 1 25 6 145 45 0.2 1 31 14 146 90 0.2 1 77 13 147 226 0.2 1 201 25 148 203 0.2 1 185 18 149 84 0.2 1 77 7 150 819 0.2 1 651 168 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_32psu_3_S3_L002_R1_001.fastq.gz ============================================= 13670957 sequences processed in total