SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_32psu_2_S2_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: 626101). 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_32psu_2_S2_L001_R2_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 66.42 s (4 us/read; 16.02 M reads/minute). === Summary === Total reads processed: 17,734,461 Reads with adapters: 14,708,042 (82.9%) Reads written (passing filters): 17,734,461 (100.0%) Total basepairs processed: 2,660,169,150 bp Quality-trimmed: 13,508,119 bp (0.5%) Total written (filtered): 1,965,332,665 bp (73.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14708042 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.9% C: 12.0% G: 24.7% T: 34.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 1823726 4433615.2 0 1823726 2 284755 1108403.8 0 284755 3 172034 277101.0 0 172034 4 100056 69275.2 0 100056 5 94653 17318.8 0 94653 6 82500 4329.7 0 82500 7 67622 1082.4 0 67622 8 96831 270.6 0 96831 9 76935 67.7 0 76693 242 10 84917 16.9 1 81330 3587 11 89902 4.2 1 84914 4988 12 90846 1.1 1 85794 5052 13 101679 0.3 1 96540 5139 14 96092 0.3 1 90143 5949 15 77319 0.3 1 73208 4111 16 114151 0.3 1 107904 6247 17 91752 0.3 1 86386 5366 18 88174 0.3 1 83679 4495 19 112277 0.3 1 105925 6352 20 105306 0.3 1 99944 5362 21 93914 0.3 1 89017 4897 22 106559 0.3 1 101114 5445 23 110793 0.3 1 104912 5881 24 108885 0.3 1 102936 5949 25 124131 0.3 1 117742 6389 26 104655 0.3 1 98869 5786 27 118794 0.3 1 111576 7218 28 109018 0.3 1 104356 4662 29 118362 0.3 1 112044 6318 30 117104 0.3 1 111822 5282 31 127211 0.3 1 120779 6432 32 116001 0.3 1 110611 5390 33 128546 0.3 1 121947 6599 34 164203 0.3 1 155704 8499 35 96279 0.3 1 92057 4222 36 133909 0.3 1 126861 7048 37 140147 0.3 1 132941 7206 38 132076 0.3 1 126615 5461 39 129476 0.3 1 124081 5395 40 145043 0.3 1 137854 7189 41 140152 0.3 1 133933 6219 42 149889 0.3 1 143207 6682 43 127335 0.3 1 121774 5561 44 151174 0.3 1 144187 6987 45 157069 0.3 1 149770 7299 46 127123 0.3 1 121787 5336 47 151889 0.3 1 145363 6526 48 148136 0.3 1 142156 5980 49 155657 0.3 1 148850 6807 50 151455 0.3 1 144647 6808 51 188717 0.3 1 180540 8177 52 134588 0.3 1 129312 5276 53 165157 0.3 1 158982 6175 54 125197 0.3 1 120399 4798 55 161733 0.3 1 155845 5888 56 166592 0.3 1 159894 6698 57 159442 0.3 1 153722 5720 58 155066 0.3 1 149532 5534 59 156693 0.3 1 150794 5899 60 162642 0.3 1 156571 6071 61 166749 0.3 1 160204 6545 62 183711 0.3 1 176590 7121 63 247983 0.3 1 239379 8604 64 207871 0.3 1 201612 6259 65 131895 0.3 1 127166 4729 66 143535 0.3 1 138546 4989 67 143350 0.3 1 137946 5404 68 144808 0.3 1 139662 5146 69 143872 0.3 1 138552 5320 70 149770 0.3 1 144363 5407 71 159740 0.3 1 154143 5597 72 151950 0.3 1 146385 5565 73 160797 0.3 1 155248 5549 74 148028 0.3 1 142917 5111 75 141398 0.3 1 136490 4908 76 138432 0.3 1 133692 4740 77 138578 0.3 1 133680 4898 78 133953 0.3 1 129214 4739 79 129618 0.3 1 125018 4600 80 128335 0.3 1 124016 4319 81 126134 0.3 1 121892 4242 82 121190 0.3 1 117136 4054 83 117273 0.3 1 113373 3900 84 113306 0.3 1 109397 3909 85 112548 0.3 1 108604 3944 86 113235 0.3 1 109296 3939 87 114063 0.3 1 110237 3826 88 110699 0.3 1 106931 3768 89 99019 0.3 1 95692 3327 90 94514 0.3 1 91234 3280 91 89156 0.3 1 86055 3101 92 83513 0.3 1 80693 2820 93 80899 0.3 1 78065 2834 94 78488 0.3 1 75830 2658 95 74185 0.3 1 71733 2452 96 70096 0.3 1 67821 2275 97 63309 0.3 1 61201 2108 98 59315 0.3 1 57291 2024 99 56316 0.3 1 54360 1956 100 50955 0.3 1 49217 1738 101 47839 0.3 1 46277 1562 102 45011 0.3 1 43553 1458 103 42598 0.3 1 41263 1335 104 41495 0.3 1 40193 1302 105 36516 0.3 1 35305 1211 106 32285 0.3 1 31286 999 107 28907 0.3 1 27939 968 108 26521 0.3 1 25551 970 109 23377 0.3 1 22637 740 110 20921 0.3 1 20208 713 111 19648 0.3 1 19007 641 112 16880 0.3 1 16303 577 113 14733 0.3 1 14236 497 114 12634 0.3 1 12219 415 115 10616 0.3 1 10211 405 116 8792 0.3 1 8474 318 117 7302 0.3 1 7031 271 118 6324 0.3 1 6071 253 119 5278 0.3 1 5066 212 120 4245 0.3 1 4065 180 121 3766 0.3 1 3593 173 122 3122 0.3 1 2986 136 123 2579 0.3 1 2463 116 124 2054 0.3 1 1977 77 125 1702 0.3 1 1630 72 126 1444 0.3 1 1379 65 127 1157 0.3 1 1113 44 128 945 0.3 1 906 39 129 732 0.3 1 690 42 130 636 0.3 1 596 40 131 486 0.3 1 462 24 132 421 0.3 1 393 28 133 391 0.3 1 380 11 134 460 0.3 1 437 23 135 244 0.3 1 230 14 136 145 0.3 1 134 11 137 97 0.3 1 92 5 138 61 0.3 1 60 1 139 51 0.3 1 44 7 140 41 0.3 1 36 5 141 18 0.3 1 15 3 142 19 0.3 1 18 1 143 6 0.3 1 6 144 18 0.3 1 16 2 145 49 0.3 1 42 7 146 32 0.3 1 31 1 147 61 0.3 1 61 148 55 0.3 1 53 2 149 39 0.3 1 37 2 150 364 0.3 1 342 22 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_32psu_2_S2_L001_R2_001.fastq.gz ============================================= 17734461 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 17734461 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 171071 (0.96%)