SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_26psu_1_S13_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: 530467). 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_1_S13_L002_R2_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 90.34 s (4 us/read; 14.65 M reads/minute). === Summary === Total reads processed: 22,055,675 Reads with adapters: 17,164,009 (77.8%) Reads written (passing filters): 22,055,675 (100.0%) Total basepairs processed: 3,308,351,250 bp Quality-trimmed: 16,172,247 bp (0.5%) Total written (filtered): 2,590,121,341 bp (78.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 17164009 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.6% C: 12.4% G: 23.7% T: 35.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2956348 5513918.8 0 2956348 2 421838 1378479.7 0 421838 3 248359 344619.9 0 248359 4 140787 86155.0 0 140787 5 125775 21538.7 0 125775 6 111856 5384.7 0 111856 7 89214 1346.2 0 89214 8 128837 336.5 0 128837 9 101494 84.1 0 101161 333 10 109255 21.0 1 101714 7541 11 118195 5.3 1 108364 9831 12 117038 1.3 1 107170 9868 13 134296 0.3 1 123167 11129 14 123942 0.3 1 112784 11158 15 100887 0.3 1 92534 8353 16 146698 0.3 1 134607 12091 17 124219 0.3 1 113532 10687 18 108678 0.3 1 99668 9010 19 144281 0.3 1 132500 11781 20 133615 0.3 1 123129 10486 21 116612 0.3 1 107459 9153 22 133618 0.3 1 123290 10328 23 141009 0.3 1 130007 11002 24 139397 0.3 1 128279 11118 25 156124 0.3 1 144895 11229 26 130436 0.3 1 119727 10709 27 145243 0.3 1 132821 12422 28 129948 0.3 1 120966 8982 29 147371 0.3 1 136169 11202 30 140000 0.3 1 130086 9914 31 156053 0.3 1 144716 11337 32 135242 0.3 1 125682 9560 33 156256 0.3 1 144163 12093 34 200062 0.3 1 185381 14681 35 108741 0.3 1 100819 7922 36 156564 0.3 1 144598 11966 37 165143 0.3 1 153098 12045 38 153915 0.3 1 143649 10266 39 147077 0.3 1 137848 9229 40 167810 0.3 1 155933 11877 41 163682 0.3 1 152622 11060 42 166228 0.3 1 154981 11247 43 150608 0.3 1 140711 9897 44 176387 0.3 1 164024 12363 45 185146 0.3 1 172572 12574 46 132758 0.3 1 123550 9208 47 167253 0.3 1 156952 10301 48 165177 0.3 1 154705 10472 49 173975 0.3 1 162376 11599 50 166191 0.3 1 155002 11189 51 203241 0.3 1 190158 13083 52 146701 0.3 1 137201 9500 53 181035 0.3 1 170415 10620 54 130972 0.3 1 122872 8100 55 173160 0.3 1 163051 10109 56 176881 0.3 1 165551 11330 57 169136 0.3 1 159682 9454 58 163469 0.3 1 154161 9308 59 163465 0.3 1 153708 9757 60 171325 0.3 1 161169 10156 61 174265 0.3 1 164163 10102 62 189943 0.3 1 178404 11539 63 247557 0.3 1 234468 13089 64 202460 0.3 1 193222 9238 65 135184 0.3 1 127502 7682 66 146610 0.3 1 138357 8253 67 145979 0.3 1 137259 8720 68 147766 0.3 1 139368 8398 69 145296 0.3 1 136585 8711 70 155955 0.3 1 146888 9067 71 158414 0.3 1 149557 8857 72 151267 0.3 1 142345 8922 73 157245 0.3 1 148240 9005 74 144510 0.3 1 136069 8441 75 137730 0.3 1 129832 7898 76 133886 0.3 1 125901 7985 77 133306 0.3 1 125623 7683 78 127271 0.3 1 119937 7334 79 123387 0.3 1 116350 7037 80 122486 0.3 1 115616 6870 81 120050 0.3 1 113299 6751 82 115066 0.3 1 108580 6486 83 111130 0.3 1 104980 6150 84 106741 0.3 1 100726 6015 85 105619 0.3 1 99800 5819 86 104981 0.3 1 99314 5667 87 105156 0.3 1 99595 5561 88 102130 0.3 1 96657 5473 89 91200 0.3 1 86213 4987 90 88189 0.3 1 83375 4814 91 82519 0.3 1 77931 4588 92 77564 0.3 1 73377 4187 93 74406 0.3 1 70415 3991 94 71559 0.3 1 67703 3856 95 67768 0.3 1 64110 3658 96 64417 0.3 1 60976 3441 97 59309 0.3 1 56218 3091 98 54600 0.3 1 51799 2801 99 53526 0.3 1 50607 2919 100 48940 0.3 1 46308 2632 101 44993 0.3 1 42581 2412 102 41335 0.3 1 39097 2238 103 37548 0.3 1 35551 1997 104 35714 0.3 1 33829 1885 105 32156 0.3 1 30392 1764 106 29290 0.3 1 27775 1515 107 26004 0.3 1 24590 1414 108 24018 0.3 1 22665 1353 109 21637 0.3 1 20542 1095 110 19578 0.3 1 18483 1095 111 18464 0.3 1 17459 1005 112 15937 0.3 1 15101 836 113 14018 0.3 1 13272 746 114 12104 0.3 1 11450 654 115 10138 0.3 1 9597 541 116 8616 0.3 1 8197 419 117 7239 0.3 1 6863 376 118 6371 0.3 1 6012 359 119 5403 0.3 1 5093 310 120 4535 0.3 1 4258 277 121 3911 0.3 1 3687 224 122 3351 0.3 1 3130 221 123 2870 0.3 1 2695 175 124 2400 0.3 1 2272 128 125 2105 0.3 1 1957 148 126 1712 0.3 1 1597 115 127 1490 0.3 1 1401 89 128 1075 0.3 1 998 77 129 923 0.3 1 859 64 130 711 0.3 1 666 45 131 624 0.3 1 582 42 132 524 0.3 1 489 35 133 507 0.3 1 469 38 134 649 0.3 1 623 26 135 367 0.3 1 349 18 136 204 0.3 1 188 16 137 158 0.3 1 144 14 138 102 0.3 1 92 10 139 75 0.3 1 67 8 140 58 0.3 1 57 1 141 47 0.3 1 40 7 142 38 0.3 1 34 4 143 23 0.3 1 20 3 144 21 0.3 1 20 1 145 27 0.3 1 23 4 146 22 0.3 1 20 2 147 86 0.3 1 82 4 148 43 0.3 1 41 2 149 33 0.3 1 32 1 150 345 0.3 1 321 24 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_26psu_1_S13_L002_R2_001.fastq.gz ============================================= 22055675 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 22055675 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 180605 (0.82%)