SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_26psu_3_S15_L001_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: 482987). 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_26psu_3_S15_L001_R1_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 54.90 s (4 us/read; 16.07 M reads/minute). === Summary === Total reads processed: 14,705,097 Reads with adapters: 11,084,660 (75.4%) Reads written (passing filters): 14,705,097 (100.0%) Total basepairs processed: 2,205,764,550 bp Quality-trimmed: 5,654,261 bp (0.3%) Total written (filtered): 1,768,343,252 bp (80.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11084660 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.1% C: 18.1% G: 19.4% T: 32.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2274798 3676274.2 0 2274798 2 348366 919068.6 0 348366 3 204139 229767.1 0 204139 4 102009 57441.8 0 102009 5 74565 14360.4 0 74565 6 72782 3590.1 0 72782 7 57000 897.5 0 57000 8 74016 224.4 0 74016 9 74077 56.1 0 73070 1007 10 67767 14.0 1 63550 4217 11 78426 3.5 1 71779 6647 12 73178 0.9 1 67904 5274 13 73121 0.2 1 67865 5256 14 76375 0.2 1 70227 6148 15 78023 0.2 1 72295 5728 16 76757 0.2 1 70359 6398 17 96301 0.2 1 87532 8769 18 78109 0.2 1 72884 5225 19 66841 0.2 1 61960 4881 20 81976 0.2 1 75979 5997 21 91230 0.2 1 84192 7038 22 74923 0.2 1 70026 4897 23 89318 0.2 1 82578 6740 24 80595 0.2 1 73239 7356 25 88530 0.2 1 81693 6837 26 80024 0.2 1 74706 5318 27 90563 0.2 1 83032 7531 28 88117 0.2 1 81366 6751 29 90600 0.2 1 82528 8072 30 100870 0.2 1 94452 6418 31 72291 0.2 1 67161 5130 32 93105 0.2 1 86376 6729 33 85828 0.2 1 79302 6526 34 93973 0.2 1 87113 6860 35 95201 0.2 1 86703 8498 36 98814 0.2 1 91143 7671 37 92594 0.2 1 86632 5962 38 92492 0.2 1 85700 6792 39 99594 0.2 1 92552 7042 40 99241 0.2 1 91728 7513 41 109705 0.2 1 100318 9387 42 91534 0.2 1 84273 7261 43 144391 0.2 1 135954 8437 44 48359 0.2 1 43755 4604 45 101091 0.2 1 93630 7461 46 97319 0.2 1 90173 7146 47 102355 0.2 1 95522 6833 48 95140 0.2 1 87635 7505 49 109171 0.2 1 100789 8382 50 88275 0.2 1 82648 5627 51 96905 0.2 1 90014 6891 52 106355 0.2 1 97463 8892 53 116272 0.2 1 109052 7220 54 82504 0.2 1 76626 5878 55 104155 0.2 1 97146 7009 56 117878 0.2 1 110588 7290 57 94064 0.2 1 87248 6816 58 98547 0.2 1 93098 5449 59 78147 0.2 1 72464 5683 60 103609 0.2 1 96779 6830 61 99715 0.2 1 93367 6348 62 96712 0.2 1 90590 6122 63 91683 0.2 1 85401 6282 64 88404 0.2 1 82993 5411 65 98564 0.2 1 92125 6439 66 106366 0.2 1 99301 7065 67 113416 0.2 1 104214 9202 68 212253 0.2 1 201102 11151 69 52200 0.2 1 48055 4145 70 18616 0.2 1 15750 2866 71 46522 0.2 1 43178 3344 72 78090 0.2 1 73258 4832 73 85268 0.2 1 79938 5330 74 84510 0.2 1 79145 5365 75 84172 0.2 1 78812 5360 76 82514 0.2 1 77266 5248 77 82709 0.2 1 77348 5361 78 77578 0.2 1 72635 4943 79 76394 0.2 1 71265 5129 80 74740 0.2 1 69853 4887 81 73428 0.2 1 68638 4790 82 72487 0.2 1 67836 4651 83 69366 0.2 1 64850 4516 84 68485 0.2 1 64014 4471 85 65855 0.2 1 61694 4161 86 63892 0.2 1 59720 4172 87 59968 0.2 1 56023 3945 88 59481 0.2 1 55667 3814 89 57389 0.2 1 53698 3691 90 56546 0.2 1 52783 3763 91 53907 0.2 1 50295 3612 92 51001 0.2 1 47631 3370 93 48245 0.2 1 45064 3181 94 47040 0.2 1 43981 3059 95 44130 0.2 1 41149 2981 96 41844 0.2 1 38970 2874 97 39077 0.2 1 36479 2598 98 36411 0.2 1 33904 2507 99 35258 0.2 1 32713 2545 100 32027 0.2 1 29780 2247 101 30331 0.2 1 28259 2072 102 28208 0.2 1 26138 2070 103 26173 0.2 1 24325 1848 104 24471 0.2 1 22816 1655 105 21780 0.2 1 20187 1593 106 20446 0.2 1 18956 1490 107 18149 0.2 1 16771 1378 108 17180 0.2 1 15945 1235 109 15082 0.2 1 13906 1176 110 14103 0.2 1 12998 1105 111 13190 0.2 1 12191 999 112 11450 0.2 1 10565 885 113 9717 0.2 1 8858 859 114 8899 0.2 1 8160 739 115 7941 0.2 1 7316 625 116 6735 0.2 1 6226 509 117 5866 0.2 1 5379 487 118 5055 0.2 1 4584 471 119 4372 0.2 1 3977 395 120 3711 0.2 1 3362 349 121 3540 0.2 1 3243 297 122 2903 0.2 1 2643 260 123 2410 0.2 1 2172 238 124 2227 0.2 1 2020 207 125 1832 0.2 1 1640 192 126 1658 0.2 1 1492 166 127 1471 0.2 1 1327 144 128 1080 0.2 1 953 127 129 958 0.2 1 848 110 130 709 0.2 1 628 81 131 795 0.2 1 718 77 132 862 0.2 1 774 88 133 1124 0.2 1 1033 91 134 1984 0.2 1 1883 101 135 812 0.2 1 780 32 136 310 0.2 1 269 41 137 196 0.2 1 180 16 138 185 0.2 1 168 17 139 138 0.2 1 131 7 140 94 0.2 1 84 10 141 74 0.2 1 68 6 142 62 0.2 1 50 12 143 92 0.2 1 84 8 144 74 0.2 1 67 7 145 205 0.2 1 196 9 146 780 0.2 1 755 25 147 4835 0.2 1 4652 183 148 3283 0.2 1 3150 133 149 1826 0.2 1 1757 69 150 16714 0.2 1 15810 904 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_26psu_3_S15_L001_R1_001.fastq.gz ============================================= 14705097 sequences processed in total