SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_26psu_4_S16_L002_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: 551300). 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/16C_26psu_4_S16_L002_R2_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 67.98 s (4 us/read; 15.19 M reads/minute). === Summary === Total reads processed: 17,208,353 Reads with adapters: 13,587,185 (79.0%) Reads written (passing filters): 17,208,353 (100.0%) Total basepairs processed: 2,581,252,950 bp Quality-trimmed: 13,418,385 bp (0.5%) Total written (filtered): 1,981,075,586 bp (76.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 13587185 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 27.8% C: 13.6% G: 24.4% T: 34.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2180320 4302088.2 0 2180320 2 324825 1075522.1 0 324825 3 196027 268880.5 0 196027 4 105938 67220.1 0 105938 5 93022 16805.0 0 93022 6 82169 4201.3 0 82169 7 65208 1050.3 0 65208 8 94076 262.6 0 94076 9 75651 65.6 0 75373 278 10 79743 16.4 1 74241 5502 11 88328 4.1 1 81010 7318 12 86868 1.0 1 79554 7314 13 99881 0.3 1 91747 8134 14 90834 0.3 1 82543 8291 15 75785 0.3 1 69708 6077 16 109506 0.3 1 100461 9045 17 89706 0.3 1 82164 7542 18 82342 0.3 1 75779 6563 19 105511 0.3 1 97019 8492 20 99413 0.3 1 91913 7500 21 89589 0.3 1 82387 7202 22 99486 0.3 1 91727 7759 23 104499 0.3 1 96352 8147 24 104372 0.3 1 95967 8405 25 118405 0.3 1 110027 8378 26 97628 0.3 1 89447 8181 27 110575 0.3 1 101151 9424 28 97751 0.3 1 91186 6565 29 111505 0.3 1 102881 8624 30 104420 0.3 1 97112 7308 31 118911 0.3 1 110316 8595 32 102066 0.3 1 95076 6990 33 118362 0.3 1 109639 8723 34 152523 0.3 1 141524 10999 35 81147 0.3 1 75248 5899 36 120338 0.3 1 111218 9120 37 127944 0.3 1 118775 9169 38 118773 0.3 1 111107 7666 39 114524 0.3 1 107290 7234 40 130962 0.3 1 121798 9164 41 127042 0.3 1 118718 8324 42 130066 0.3 1 121378 8688 43 114447 0.3 1 107009 7438 44 134439 0.3 1 125115 9324 45 139316 0.3 1 130061 9255 46 105889 0.3 1 98943 6946 47 133294 0.3 1 125179 8115 48 129000 0.3 1 120992 8008 49 134472 0.3 1 125771 8701 50 129511 0.3 1 120901 8610 51 156322 0.3 1 146348 9974 52 115554 0.3 1 108318 7236 53 141127 0.3 1 132995 8132 54 105383 0.3 1 99036 6347 55 137072 0.3 1 129093 7979 56 141674 0.3 1 132689 8985 57 134402 0.3 1 126942 7460 58 130317 0.3 1 123061 7256 59 129827 0.3 1 122170 7657 60 136682 0.3 1 128763 7919 61 138438 0.3 1 130627 7811 62 151584 0.3 1 142493 9091 63 198913 0.3 1 188533 10380 64 165224 0.3 1 157788 7436 65 109943 0.3 1 103886 6057 66 119196 0.3 1 112621 6575 67 118137 0.3 1 111336 6801 68 119874 0.3 1 113325 6549 69 119266 0.3 1 112294 6972 70 126609 0.3 1 119544 7065 71 132620 0.3 1 125297 7323 72 125393 0.3 1 118453 6940 73 132184 0.3 1 124866 7318 74 122169 0.3 1 115334 6835 75 116493 0.3 1 110071 6422 76 113442 0.3 1 106974 6468 77 113685 0.3 1 107141 6544 78 108607 0.3 1 102395 6212 79 104353 0.3 1 98543 5810 80 104020 0.3 1 98279 5741 81 102310 0.3 1 96699 5611 82 98054 0.3 1 92664 5390 83 96480 0.3 1 91293 5187 84 93016 0.3 1 87985 5031 85 91834 0.3 1 86918 4916 86 92118 0.3 1 87322 4796 87 91952 0.3 1 87281 4671 88 89832 0.3 1 85225 4607 89 81915 0.3 1 77620 4295 90 78846 0.3 1 74588 4258 91 74284 0.3 1 70441 3843 92 69858 0.3 1 66293 3565 93 66592 0.3 1 63127 3465 94 65539 0.3 1 62049 3490 95 61188 0.3 1 57883 3305 96 59534 0.3 1 56516 3018 97 56011 0.3 1 53174 2837 98 53355 0.3 1 50647 2708 99 53101 0.3 1 50373 2728 100 48195 0.3 1 45837 2358 101 43522 0.3 1 41188 2334 102 41863 0.3 1 39765 2098 103 39452 0.3 1 37477 1975 104 38339 0.3 1 36409 1930 105 33606 0.3 1 31895 1711 106 30952 0.3 1 29448 1504 107 27675 0.3 1 26330 1345 108 24951 0.3 1 23635 1316 109 22743 0.3 1 21560 1183 110 20811 0.3 1 19684 1127 111 19926 0.3 1 18958 968 112 17187 0.3 1 16283 904 113 15096 0.3 1 14331 765 114 13260 0.3 1 12650 610 115 11435 0.3 1 10854 581 116 9981 0.3 1 9425 556 117 8327 0.3 1 7873 454 118 7364 0.3 1 6994 370 119 6240 0.3 1 5915 325 120 5208 0.3 1 4920 288 121 4741 0.3 1 4467 274 122 4055 0.3 1 3851 204 123 3533 0.3 1 3332 201 124 2985 0.3 1 2813 172 125 2559 0.3 1 2417 142 126 2133 0.3 1 2012 121 127 1706 0.3 1 1579 127 128 1327 0.3 1 1241 86 129 1121 0.3 1 1038 83 130 901 0.3 1 842 59 131 784 0.3 1 738 46 132 657 0.3 1 620 37 133 809 0.3 1 770 39 134 1081 0.3 1 1031 50 135 490 0.3 1 465 25 136 231 0.3 1 213 18 137 165 0.3 1 153 12 138 122 0.3 1 117 5 139 68 0.3 1 64 4 140 60 0.3 1 53 7 141 31 0.3 1 25 6 142 34 0.3 1 30 4 143 37 0.3 1 30 7 144 24 0.3 1 20 4 145 49 0.3 1 45 4 146 39 0.3 1 34 5 147 87 0.3 1 77 10 148 52 0.3 1 48 4 149 25 0.3 1 23 2 150 408 0.3 1 378 30 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_26psu_4_S16_L002_R2_001.fastq.gz ============================================= 17208353 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 17208353 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 195032 (1.13%)