SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_26psu_4_S12_L001_R2_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: 414349). Second best hit was Nextera (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/8C_26psu_4_S12_L001_R2_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 53.00 s (4 us/read; 14.26 M reads/minute). === Summary === Total reads processed: 12,592,704 Reads with adapters: 8,852,263 (70.3%) Reads written (passing filters): 12,592,704 (100.0%) Total basepairs processed: 1,888,905,600 bp Quality-trimmed: 12,948,585 bp (0.7%) Total written (filtered): 1,572,160,709 bp (83.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 8852263 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.4% C: 12.6% G: 20.6% T: 36.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2390954 3148176.0 0 2390954 2 298677 787044.0 0 298677 3 170286 196761.0 0 170286 4 88634 49190.2 0 88634 5 67201 12297.6 0 67201 6 54871 3074.4 0 54871 7 42570 768.6 0 42570 8 63033 192.1 0 63033 9 50827 48.0 0 50608 219 10 54798 12.0 1 51719 3079 11 58410 3.0 1 54143 4267 12 59146 0.8 1 54631 4515 13 64024 0.2 1 59760 4264 14 60295 0.2 1 55485 4810 15 48131 0.2 1 44661 3470 16 72030 0.2 1 66991 5039 17 55432 0.2 1 51368 4064 18 54012 0.2 1 50286 3726 19 67964 0.2 1 63040 4924 20 63154 0.2 1 58908 4246 21 56080 0.2 1 52250 3830 22 62812 0.2 1 58598 4214 23 64652 0.2 1 60263 4389 24 64121 0.2 1 59590 4531 25 72378 0.2 1 67726 4652 26 60189 0.2 1 55991 4198 27 67272 0.2 1 62190 5082 28 62061 0.2 1 58469 3592 29 66706 0.2 1 62082 4624 30 64680 0.2 1 60760 3920 31 70875 0.2 1 66272 4603 32 63295 0.2 1 59659 3636 33 68948 0.2 1 64437 4511 34 89723 0.2 1 83808 5915 35 49481 0.2 1 46615 2866 36 69552 0.2 1 64903 4649 37 74271 0.2 1 69458 4813 38 69359 0.2 1 65691 3668 39 67616 0.2 1 63803 3813 40 75243 0.2 1 70372 4871 41 71025 0.2 1 67013 4012 42 73877 0.2 1 69581 4296 43 66995 0.2 1 63092 3903 44 76573 0.2 1 71945 4628 45 80934 0.2 1 76127 4807 46 59833 0.2 1 56439 3394 47 73828 0.2 1 69722 4106 48 73312 0.2 1 69349 3963 49 75078 0.2 1 70776 4302 50 70693 0.2 1 66714 3979 51 88709 0.2 1 83803 4906 52 62743 0.2 1 59451 3292 53 75598 0.2 1 71882 3716 54 57634 0.2 1 54617 3017 55 73802 0.2 1 70193 3609 56 76463 0.2 1 72320 4143 57 71883 0.2 1 68382 3501 58 68729 0.2 1 65597 3132 59 69792 0.2 1 66296 3496 60 72493 0.2 1 68898 3595 61 74181 0.2 1 70431 3750 62 80362 0.2 1 76257 4105 63 105716 0.2 1 100889 4827 64 86565 0.2 1 82909 3656 65 55528 0.2 1 52821 2707 66 61319 0.2 1 58488 2831 67 60096 0.2 1 57177 2919 68 60017 0.2 1 57079 2938 69 59676 0.2 1 56862 2814 70 62200 0.2 1 59177 3023 71 65595 0.2 1 62486 3109 72 62243 0.2 1 59355 2888 73 65321 0.2 1 62407 2914 74 60107 0.2 1 57408 2699 75 56927 0.2 1 54342 2585 76 56197 0.2 1 53642 2555 77 55543 0.2 1 53010 2533 78 53264 0.2 1 50829 2435 79 50917 0.2 1 48532 2385 80 50251 0.2 1 48020 2231 81 49279 0.2 1 47040 2239 82 47377 0.2 1 45259 2118 83 45689 0.2 1 43632 2057 84 44996 0.2 1 42952 2044 85 43197 0.2 1 41186 2011 86 43336 0.2 1 41365 1971 87 42821 0.2 1 40993 1828 88 42339 0.2 1 40455 1884 89 37924 0.2 1 36191 1733 90 36727 0.2 1 35019 1708 91 33632 0.2 1 32108 1524 92 32065 0.2 1 30559 1506 93 30818 0.2 1 29434 1384 94 30025 0.2 1 28706 1319 95 28433 0.2 1 27167 1266 96 27472 0.2 1 26315 1157 97 25080 0.2 1 23956 1124 98 23110 0.2 1 22057 1053 99 21635 0.2 1 20659 976 100 19482 0.2 1 18587 895 101 17939 0.2 1 17090 849 102 17260 0.2 1 16487 773 103 15967 0.2 1 15237 730 104 15618 0.2 1 14883 735 105 13954 0.2 1 13334 620 106 12766 0.2 1 12218 548 107 11338 0.2 1 10826 512 108 10218 0.2 1 9719 499 109 9371 0.2 1 8900 471 110 8643 0.2 1 8250 393 111 8343 0.2 1 7959 384 112 7194 0.2 1 6837 357 113 6183 0.2 1 5873 310 114 5369 0.2 1 5131 238 115 4668 0.2 1 4438 230 116 3833 0.2 1 3644 189 117 3219 0.2 1 3007 212 118 2818 0.2 1 2669 149 119 2453 0.2 1 2312 141 120 2060 0.2 1 1936 124 121 1912 0.2 1 1802 110 122 1619 0.2 1 1536 83 123 1396 0.2 1 1315 81 124 1132 0.2 1 1057 75 125 1047 0.2 1 976 71 126 972 0.2 1 915 57 127 819 0.2 1 758 61 128 624 0.2 1 581 43 129 486 0.2 1 450 36 130 458 0.2 1 430 28 131 510 0.2 1 482 28 132 584 0.2 1 562 22 133 1105 0.2 1 1055 50 134 2683 0.2 1 2615 68 135 802 0.2 1 778 24 136 171 0.2 1 159 12 137 100 0.2 1 93 7 138 80 0.2 1 73 7 139 45 0.2 1 40 5 140 54 0.2 1 48 6 141 22 0.2 1 17 5 142 19 0.2 1 18 1 143 19 0.2 1 16 3 144 60 0.2 1 57 3 145 202 0.2 1 195 7 146 219 0.2 1 210 9 147 1124 0.2 1 1091 33 148 721 0.2 1 692 29 149 428 0.2 1 410 18 150 2417 0.2 1 2310 107 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_26psu_4_S12_L001_R2_001.fastq.gz ============================================= 12592704 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 12592704 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 111446 (0.89%)