SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_26psu_2_S10_L002_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: 565606). Second best hit was Nextera (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_26psu_2_S10_L002_R1_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 68.88 s (4 us/read; 16.02 M reads/minute). === Summary === Total reads processed: 18,388,474 Reads with adapters: 14,774,548 (80.3%) Reads written (passing filters): 18,388,474 (100.0%) Total basepairs processed: 2,758,271,100 bp Quality-trimmed: 5,422,014 bp (0.2%) Total written (filtered): 2,096,179,695 bp (76.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14774548 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.0% C: 14.7% G: 20.4% T: 34.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2179283 4597118.5 0 2179283 2 319389 1149279.6 0 319389 3 179573 287319.9 0 179573 4 108126 71830.0 0 108126 5 90944 17957.5 0 90944 6 89410 4489.4 0 89410 7 72797 1122.3 0 72797 8 91422 280.6 0 91422 9 93678 70.1 0 92415 1263 10 84673 17.5 1 79267 5406 11 97249 4.4 1 88769 8480 12 93054 1.1 1 86160 6894 13 93570 0.3 1 86447 7123 14 97334 0.3 1 89025 8309 15 99065 0.3 1 91404 7661 16 99365 0.3 1 90487 8878 17 122566 0.3 1 111250 11316 18 102597 0.3 1 95121 7476 19 88093 0.3 1 81291 6802 20 107045 0.3 1 98814 8231 21 119128 0.3 1 109388 9740 22 98363 0.3 1 91503 6860 23 118120 0.3 1 108869 9251 24 109512 0.3 1 99530 9982 25 117620 0.3 1 108476 9144 26 107233 0.3 1 99745 7488 27 121679 0.3 1 111586 10093 28 118815 0.3 1 109364 9451 29 129909 0.3 1 118061 11848 30 136643 0.3 1 127560 9083 31 99248 0.3 1 91716 7532 32 129461 0.3 1 119254 10207 33 120389 0.3 1 110237 10152 34 133674 0.3 1 122112 11562 35 135326 0.3 1 125969 9357 36 125558 0.3 1 113748 11810 37 131811 0.3 1 122131 9680 38 134596 0.3 1 124192 10404 39 144370 0.3 1 133180 11190 40 130508 0.3 1 120297 10211 41 146230 0.3 1 133678 12552 42 134185 0.3 1 121889 12296 43 205437 0.3 1 192857 12580 44 71406 0.3 1 64241 7165 45 146811 0.3 1 136113 10698 46 133431 0.3 1 123482 9949 47 146963 0.3 1 136319 10644 48 142772 0.3 1 132090 10682 49 156871 0.3 1 144261 12610 50 134522 0.3 1 125136 9386 51 145234 0.3 1 134471 10763 52 151741 0.3 1 139780 11961 53 160323 0.3 1 148993 11330 54 129391 0.3 1 119763 9628 55 153504 0.3 1 142065 11439 56 189438 0.3 1 176473 12965 57 121885 0.3 1 111816 10069 58 156277 0.3 1 146133 10144 59 138166 0.3 1 127798 10368 60 151809 0.3 1 140696 11113 61 148378 0.3 1 138229 10149 62 164350 0.3 1 153017 11333 63 132176 0.3 1 121776 10400 64 146283 0.3 1 136343 9940 65 162567 0.3 1 150970 11597 66 169475 0.3 1 157430 12045 67 180215 0.3 1 164843 15372 68 335801 0.3 1 317089 18712 69 66723 0.3 1 60845 5878 70 26090 0.3 1 21811 4279 71 91663 0.3 1 85518 6145 72 129140 0.3 1 120846 8294 73 135992 0.3 1 126800 9192 74 136581 0.3 1 127154 9427 75 134341 0.3 1 124926 9415 76 133080 0.3 1 123316 9764 77 133409 0.3 1 123959 9450 78 126607 0.3 1 117538 9069 79 125070 0.3 1 116034 9036 80 121818 0.3 1 113223 8595 81 121825 0.3 1 113140 8685 82 118244 0.3 1 109604 8640 83 114640 0.3 1 106502 8138 84 109963 0.3 1 101985 7978 85 107204 0.3 1 99478 7726 86 104741 0.3 1 97192 7549 87 100621 0.3 1 93543 7078 88 98776 0.3 1 91675 7101 89 94677 0.3 1 87957 6720 90 94332 0.3 1 87620 6712 91 89612 0.3 1 83296 6316 92 85598 0.3 1 79627 5971 93 79579 0.3 1 73824 5755 94 77934 0.3 1 72425 5509 95 72110 0.3 1 66875 5235 96 68840 0.3 1 63845 4995 97 64799 0.3 1 60100 4699 98 60773 0.3 1 56257 4516 99 58381 0.3 1 53874 4507 100 53848 0.3 1 49904 3944 101 49943 0.3 1 46245 3698 102 46241 0.3 1 42732 3509 103 43196 0.3 1 39990 3206 104 40167 0.3 1 37244 2923 105 35834 0.3 1 33163 2671 106 33023 0.3 1 30489 2534 107 30207 0.3 1 27948 2259 108 28472 0.3 1 26245 2227 109 25094 0.3 1 23102 1992 110 22988 0.3 1 21194 1794 111 20538 0.3 1 18949 1589 112 18521 0.3 1 17080 1441 113 15947 0.3 1 14645 1302 114 14330 0.3 1 13057 1273 115 12384 0.3 1 11329 1055 116 11096 0.3 1 10163 933 117 9114 0.3 1 8363 751 118 8187 0.3 1 7390 797 119 6803 0.3 1 6183 620 120 5832 0.3 1 5301 531 121 5072 0.3 1 4620 452 122 4206 0.3 1 3803 403 123 3440 0.3 1 3104 336 124 3042 0.3 1 2726 316 125 2501 0.3 1 2242 259 126 2111 0.3 1 1904 207 127 1791 0.3 1 1610 181 128 1444 0.3 1 1292 152 129 1148 0.3 1 1034 114 130 877 0.3 1 785 92 131 693 0.3 1 607 86 132 646 0.3 1 559 87 133 689 0.3 1 596 93 134 1090 0.3 1 1005 85 135 492 0.3 1 440 52 136 216 0.3 1 190 26 137 184 0.3 1 157 27 138 124 0.3 1 103 21 139 70 0.3 1 60 10 140 61 0.3 1 49 12 141 35 0.3 1 30 5 142 23 0.3 1 21 2 143 27 0.3 1 25 2 144 40 0.3 1 34 6 145 86 0.3 1 71 15 146 101 0.3 1 97 4 147 403 0.3 1 365 38 148 275 0.3 1 252 23 149 182 0.3 1 169 13 150 1714 0.3 1 1347 367 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_26psu_2_S10_L002_R1_001.fastq.gz ============================================= 18388474 sequences processed in total