SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_26psu_1_S13_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: 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_R1_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 85.79 s (4 us/read; 15.43 M reads/minute). === Summary === Total reads processed: 22,055,675 Reads with adapters: 17,288,884 (78.4%) Reads written (passing filters): 22,055,675 (100.0%) Total basepairs processed: 3,308,351,250 bp Quality-trimmed: 20,473,501 bp (0.6%) Total written (filtered): 2,585,092,173 bp (78.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 17288884 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.9% C: 14.0% G: 20.5% T: 35.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2888739 5513918.8 0 2888739 2 417982 1378479.7 0 417982 3 229648 344619.9 0 229648 4 140558 86155.0 0 140558 5 117330 21538.7 0 117330 6 114463 5384.7 0 114463 7 92119 1346.2 0 92119 8 118305 336.5 0 118305 9 116870 84.1 0 115423 1447 10 109085 21.0 1 102190 6895 11 122273 5.3 1 111534 10739 12 117728 1.3 1 108915 8813 13 119559 0.3 1 110607 8952 14 120718 0.3 1 110803 9915 15 126246 0.3 1 116067 10179 16 124980 0.3 1 114018 10962 17 152992 0.3 1 138965 14027 18 127404 0.3 1 118125 9279 19 110945 0.3 1 102558 8387 20 133534 0.3 1 123405 10129 21 147067 0.3 1 135223 11844 22 124353 0.3 1 115585 8768 23 146038 0.3 1 134941 11097 24 136315 0.3 1 124052 12263 25 144095 0.3 1 132766 11329 26 132325 0.3 1 123014 9311 27 148607 0.3 1 136108 12499 28 145176 0.3 1 133796 11380 29 153982 0.3 1 140231 13751 30 162931 0.3 1 151904 11027 31 127590 0.3 1 117988 9602 32 158563 0.3 1 146202 12361 33 143459 0.3 1 131864 11595 34 158293 0.3 1 145587 12706 35 161600 0.3 1 146632 14968 36 173713 0.3 1 161385 12328 37 138576 0.3 1 128088 10488 38 164914 0.3 1 152362 12552 39 166196 0.3 1 152847 13349 40 174913 0.3 1 159838 15075 41 195923 0.3 1 172793 23130 42 162924 0.3 1 146209 16715 43 267611 0.3 1 248773 18838 44 88981 0.3 1 79036 9945 45 199179 0.3 1 175262 23917 46 690085 0.3 1 650909 39176 47 257754 0.3 1 240653 17101 48 117426 0.3 1 103023 14403 49 402804 0.3 1 380078 22726 50 126965 0.3 1 116321 10644 51 110357 0.3 1 99078 11279 52 376565 0.3 1 356163 20402 53 193192 0.3 1 182832 10360 54 64424 0.3 1 58616 5808 55 110681 0.3 1 104197 6484 56 61759 0.3 1 55308 6451 57 169454 0.3 1 160172 9282 58 37968 0.3 1 34229 3739 59 46940 0.3 1 41198 5742 60 169988 0.3 1 161028 8960 61 86428 0.3 1 81402 5026 62 43888 0.3 1 39006 4882 63 131951 0.3 1 123251 8700 64 119378 0.3 1 112438 6940 65 67995 0.3 1 61783 6212 66 148705 0.3 1 138293 10412 67 175463 0.3 1 161782 13681 68 280115 0.3 1 262817 17298 69 200997 0.3 1 188546 12451 70 91468 0.3 1 84121 7347 71 26418 0.3 1 22702 3716 72 93747 0.3 1 87405 6342 73 136042 0.3 1 127373 8669 74 142888 0.3 1 133128 9760 75 142439 0.3 1 132394 10045 76 141347 0.3 1 131130 10217 77 141016 0.3 1 131311 9705 78 132511 0.3 1 122849 9662 79 132027 0.3 1 122622 9405 80 128769 0.3 1 119387 9382 81 126902 0.3 1 118148 8754 82 123681 0.3 1 114826 8855 83 118947 0.3 1 110667 8280 84 114559 0.3 1 106314 8245 85 111485 0.3 1 103536 7949 86 107436 0.3 1 99695 7741 87 103344 0.3 1 96004 7340 88 100991 0.3 1 93808 7183 89 95415 0.3 1 88771 6644 90 94998 0.3 1 88363 6635 91 89676 0.3 1 83270 6406 92 85299 0.3 1 79247 6052 93 79596 0.3 1 73937 5659 94 76506 0.3 1 71043 5463 95 71120 0.3 1 65893 5227 96 67197 0.3 1 62368 4829 97 63520 0.3 1 59045 4475 98 58336 0.3 1 54045 4291 99 56900 0.3 1 52530 4370 100 51732 0.3 1 47977 3755 101 47750 0.3 1 44264 3486 102 44471 0.3 1 41149 3322 103 40594 0.3 1 37603 2991 104 37603 0.3 1 34872 2731 105 33894 0.3 1 31456 2438 106 30780 0.3 1 28387 2393 107 27659 0.3 1 25538 2121 108 26065 0.3 1 24009 2056 109 23274 0.3 1 21434 1840 110 20689 0.3 1 19111 1578 111 18796 0.3 1 17291 1505 112 16460 0.3 1 15232 1228 113 14306 0.3 1 13173 1133 114 12558 0.3 1 11518 1040 115 10829 0.3 1 9919 910 116 9235 0.3 1 8487 748 117 7908 0.3 1 7205 703 118 6968 0.3 1 6363 605 119 5769 0.3 1 5245 524 120 4920 0.3 1 4475 445 121 4219 0.3 1 3831 388 122 3544 0.3 1 3202 342 123 3058 0.3 1 2744 314 124 2517 0.3 1 2275 242 125 2174 0.3 1 1950 224 126 1777 0.3 1 1603 174 127 1561 0.3 1 1396 165 128 1149 0.3 1 1015 134 129 996 0.3 1 899 97 130 753 0.3 1 670 83 131 665 0.3 1 585 80 132 569 0.3 1 501 68 133 543 0.3 1 476 67 134 671 0.3 1 623 48 135 378 0.3 1 347 31 136 222 0.3 1 190 32 137 159 0.3 1 149 10 138 107 0.3 1 97 10 139 82 0.3 1 68 14 140 62 0.3 1 55 7 141 48 0.3 1 42 6 142 40 0.3 1 35 5 143 27 0.3 1 21 6 144 22 0.3 1 19 3 145 23 0.3 1 21 2 146 31 0.3 1 24 7 147 94 0.3 1 87 7 148 48 0.3 1 41 7 149 39 0.3 1 31 8 150 382 0.3 1 330 52 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_26psu_1_S13_L002_R1_001.fastq.gz ============================================= 22055675 sequences processed in total