SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_32psu_3_S7_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: 631984). Second best hit was smallRNA (count: 1) 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_32psu_3_S7_L001_R2_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 52.01 s (4 us/read; 16.34 M reads/minute). === Summary === Total reads processed: 14,166,205 Reads with adapters: 11,771,953 (83.1%) Reads written (passing filters): 14,166,205 (100.0%) Total basepairs processed: 2,124,930,750 bp Quality-trimmed: 10,797,724 bp (0.5%) Total written (filtered): 1,563,454,753 bp (73.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11771953 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 27.6% C: 13.3% G: 24.5% T: 34.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 1427757 3541551.2 0 1427757 2 222493 885387.8 0 222493 3 133332 221347.0 0 133332 4 79137 55336.7 0 79137 5 75786 13834.2 0 75786 6 65915 3458.5 0 65915 7 53576 864.6 0 53576 8 76744 216.2 0 76744 9 61976 54.0 0 61779 197 10 67080 13.5 1 64106 2974 11 71681 3.4 1 67501 4180 12 72222 0.8 1 68053 4169 13 80561 0.2 1 76346 4215 14 76520 0.2 1 71606 4914 15 62607 0.2 1 59130 3477 16 91383 0.2 1 86350 5033 17 72745 0.2 1 68212 4533 18 70883 0.2 1 67020 3863 19 89801 0.2 1 84529 5272 20 83841 0.2 1 79367 4474 21 75027 0.2 1 70918 4109 22 84425 0.2 1 79923 4502 23 88024 0.2 1 83097 4927 24 88855 0.2 1 83891 4964 25 101226 0.2 1 95974 5252 26 83308 0.2 1 78591 4717 27 92909 0.2 1 87066 5843 28 87156 0.2 1 83145 4011 29 93947 0.2 1 88848 5099 30 93821 0.2 1 89436 4385 31 101908 0.2 1 96520 5388 32 92154 0.2 1 87903 4251 33 101850 0.2 1 96541 5309 34 132968 0.2 1 125972 6996 35 75102 0.2 1 71554 3548 36 106526 0.2 1 100872 5654 37 112114 0.2 1 106255 5859 38 106187 0.2 1 101516 4671 39 103250 0.2 1 98795 4455 40 116350 0.2 1 110242 6108 41 111543 0.2 1 106565 4978 42 115913 0.2 1 110317 5596 43 105510 0.2 1 100613 4897 44 121504 0.2 1 115737 5767 45 131840 0.2 1 125697 6143 46 94875 0.2 1 90604 4271 47 121018 0.2 1 115877 5141 48 118842 0.2 1 113797 5045 49 124446 0.2 1 118832 5614 50 118268 0.2 1 112777 5491 51 147285 0.2 1 140570 6715 52 109448 0.2 1 105060 4388 53 130385 0.2 1 125319 5066 54 99487 0.2 1 95470 4017 55 129239 0.2 1 124277 4962 56 133599 0.2 1 127967 5632 57 126390 0.2 1 121587 4803 58 121811 0.2 1 117475 4336 59 124529 0.2 1 119540 4989 60 130401 0.2 1 125258 5143 61 134015 0.2 1 128535 5480 62 145629 0.2 1 139763 5866 63 197423 0.2 1 190204 7219 64 168240 0.2 1 162928 5312 65 106543 0.2 1 102625 3918 66 114942 0.2 1 110706 4236 67 114164 0.2 1 109736 4428 68 116350 0.2 1 112096 4254 69 114565 0.2 1 110115 4450 70 124406 0.2 1 119762 4644 71 128031 0.2 1 123514 4517 72 120687 0.2 1 116066 4621 73 126907 0.2 1 122307 4600 74 117912 0.2 1 113666 4246 75 113448 0.2 1 109343 4105 76 111278 0.2 1 107269 4009 77 112780 0.2 1 108679 4101 78 106864 0.2 1 102856 4008 79 103353 0.2 1 99664 3689 80 103266 0.2 1 99595 3671 81 101983 0.2 1 98265 3718 82 97716 0.2 1 94285 3431 83 95425 0.2 1 92073 3352 84 92931 0.2 1 89513 3418 85 92256 0.2 1 88832 3424 86 91168 0.2 1 87863 3305 87 91423 0.2 1 88169 3254 88 89550 0.2 1 86420 3130 89 80366 0.2 1 77566 2800 90 77351 0.2 1 74500 2851 91 72940 0.2 1 70306 2634 92 68488 0.2 1 66133 2355 93 65935 0.2 1 63542 2393 94 63561 0.2 1 61328 2233 95 59923 0.2 1 57811 2112 96 58074 0.2 1 56092 1982 97 54057 0.2 1 52194 1863 98 50980 0.2 1 49204 1776 99 50084 0.2 1 48441 1643 100 43642 0.2 1 42153 1489 101 40618 0.2 1 39288 1330 102 38299 0.2 1 37001 1298 103 34998 0.2 1 33809 1189 104 34454 0.2 1 33375 1079 105 29814 0.2 1 28817 997 106 27473 0.2 1 26595 878 107 24384 0.2 1 23578 806 108 22338 0.2 1 21561 777 109 19549 0.2 1 18854 695 110 18085 0.2 1 17505 580 111 16893 0.2 1 16326 567 112 14541 0.2 1 14060 481 113 12649 0.2 1 12207 442 114 11108 0.2 1 10661 447 115 9325 0.2 1 9006 319 116 7950 0.2 1 7620 330 117 6499 0.2 1 6272 227 118 5695 0.2 1 5463 232 119 4844 0.2 1 4637 207 120 4029 0.2 1 3868 161 121 3484 0.2 1 3355 129 122 2831 0.2 1 2700 131 123 2522 0.2 1 2436 86 124 2113 0.2 1 2005 108 125 1739 0.2 1 1651 88 126 1465 0.2 1 1407 58 127 1198 0.2 1 1145 53 128 931 0.2 1 888 43 129 754 0.2 1 713 41 130 539 0.2 1 514 25 131 443 0.2 1 421 22 132 375 0.2 1 351 24 133 401 0.2 1 386 15 134 477 0.2 1 456 21 135 242 0.2 1 234 8 136 136 0.2 1 132 4 137 103 0.2 1 99 4 138 81 0.2 1 73 8 139 54 0.2 1 51 3 140 37 0.2 1 32 5 141 20 0.2 1 19 1 142 21 0.2 1 20 1 143 18 0.2 1 16 2 144 17 0.2 1 16 1 145 18 0.2 1 16 2 146 15 0.2 1 14 1 147 32 0.2 1 29 3 148 19 0.2 1 17 2 149 11 0.2 1 10 1 150 176 0.2 1 165 11 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_32psu_3_S7_L001_R2_001.fastq.gz ============================================= 14166205 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 14166205 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 151334 (1.07%)