SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_26psu_3_S15_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: 474456). 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_3_S15_L002_R2_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 60.28 s (4 us/read; 14.55 M reads/minute). === Summary === Total reads processed: 14,622,552 Reads with adapters: 10,913,941 (74.6%) Reads written (passing filters): 14,622,552 (100.0%) Total basepairs processed: 2,193,382,800 bp Quality-trimmed: 13,012,389 bp (0.6%) Total written (filtered): 1,758,102,450 bp (80.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10913941 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.1% C: 14.2% G: 23.9% T: 33.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2243893 3655638.0 0 2243893 2 361235 913909.5 0 361235 3 221045 228477.4 0 221045 4 102953 57119.3 0 102953 5 80629 14279.8 0 80629 6 70223 3570.0 0 70223 7 53470 892.5 0 53470 8 79479 223.1 0 79479 9 62911 55.8 0 62617 294 10 66925 13.9 1 61688 5237 11 73700 3.5 1 66819 6881 12 72572 0.9 1 65940 6632 13 82700 0.2 1 75488 7212 14 76573 0.2 1 68946 7627 15 61263 0.2 1 55865 5398 16 90146 0.2 1 82109 8037 17 74386 0.2 1 67549 6837 18 67318 0.2 1 61385 5933 19 87145 0.2 1 79499 7646 20 80434 0.2 1 73597 6837 21 71959 0.2 1 65758 6201 22 80520 0.2 1 73704 6816 23 83808 0.2 1 76805 7003 24 83121 0.2 1 75853 7268 25 94721 0.2 1 87319 7402 26 78397 0.2 1 71438 6959 27 87589 0.2 1 79828 7761 28 77436 0.2 1 71759 5677 29 88231 0.2 1 81047 7184 30 81944 0.2 1 75545 6399 31 92581 0.2 1 85292 7289 32 80085 0.2 1 74132 5953 33 91916 0.2 1 84460 7456 34 117300 0.2 1 108202 9098 35 62830 0.2 1 57836 4994 36 92603 0.2 1 85123 7480 37 97494 0.2 1 89682 7812 38 93013 0.2 1 86322 6691 39 86916 0.2 1 80841 6075 40 100050 0.2 1 92533 7517 41 96502 0.2 1 89613 6889 42 98694 0.2 1 91554 7140 43 88091 0.2 1 81948 6143 44 102146 0.2 1 94589 7557 45 106497 0.2 1 98693 7804 46 77918 0.2 1 72391 5527 47 98307 0.2 1 91760 6547 48 96325 0.2 1 89754 6571 49 100699 0.2 1 93521 7178 50 95936 0.2 1 89184 6752 51 117412 0.2 1 109335 8077 52 84318 0.2 1 78674 5644 53 103753 0.2 1 97370 6383 54 76703 0.2 1 71688 5015 55 100303 0.2 1 94078 6225 56 104185 0.2 1 97076 7109 57 98544 0.2 1 92645 5899 58 94450 0.2 1 88927 5523 59 94831 0.2 1 88887 5944 60 99091 0.2 1 92777 6314 61 100905 0.2 1 94656 6249 62 109121 0.2 1 102218 6903 63 142655 0.2 1 134487 8168 64 117121 0.2 1 111484 5637 65 77324 0.2 1 72904 4420 66 84925 0.2 1 79850 5075 67 82998 0.2 1 77768 5230 68 84356 0.2 1 79351 5005 69 83969 0.2 1 78702 5267 70 86991 0.2 1 81734 5257 71 92058 0.2 1 86658 5400 72 87408 0.2 1 82156 5252 73 92562 0.2 1 87094 5468 74 84507 0.2 1 79446 5061 75 80670 0.2 1 75777 4893 76 78563 0.2 1 73818 4745 77 77927 0.2 1 73312 4615 78 73796 0.2 1 69197 4599 79 71841 0.2 1 67592 4249 80 70609 0.2 1 66510 4099 81 69349 0.2 1 65453 3896 82 67523 0.2 1 63514 4009 83 64665 0.2 1 60869 3796 84 63972 0.2 1 60280 3692 85 62543 0.2 1 58851 3692 86 62248 0.2 1 58801 3447 87 61991 0.2 1 58664 3327 88 61620 0.2 1 58173 3447 89 55062 0.2 1 51949 3113 90 52411 0.2 1 49511 2900 91 49315 0.2 1 46549 2766 92 47010 0.2 1 44328 2682 93 44789 0.2 1 42339 2450 94 43445 0.2 1 41012 2433 95 40986 0.2 1 38680 2306 96 39258 0.2 1 37094 2164 97 36644 0.2 1 34643 2001 98 34564 0.2 1 32670 1894 99 32993 0.2 1 31157 1836 100 31055 0.2 1 29316 1739 101 27872 0.2 1 26391 1481 102 25485 0.2 1 24012 1473 103 24164 0.2 1 22767 1397 104 23318 0.2 1 22028 1290 105 20591 0.2 1 19438 1153 106 19078 0.2 1 17973 1105 107 17270 0.2 1 16333 937 108 15786 0.2 1 14877 909 109 14538 0.2 1 13717 821 110 13063 0.2 1 12333 730 111 12532 0.2 1 11819 713 112 10933 0.2 1 10317 616 113 9707 0.2 1 9177 530 114 8352 0.2 1 7861 491 115 7373 0.2 1 6927 446 116 6174 0.2 1 5812 362 117 5508 0.2 1 5151 357 118 4695 0.2 1 4387 308 119 4109 0.2 1 3838 271 120 3479 0.2 1 3278 201 121 3246 0.2 1 3039 207 122 2778 0.2 1 2609 169 123 2432 0.2 1 2288 144 124 2091 0.2 1 1964 127 125 1753 0.2 1 1626 127 126 1569 0.2 1 1461 108 127 1430 0.2 1 1321 109 128 1051 0.2 1 972 79 129 984 0.2 1 936 48 130 686 0.2 1 639 47 131 713 0.2 1 668 45 132 719 0.2 1 681 38 133 1234 0.2 1 1177 57 134 2006 0.2 1 1917 89 135 763 0.2 1 728 35 136 321 0.2 1 299 22 137 192 0.2 1 179 13 138 174 0.2 1 164 10 139 115 0.2 1 111 4 140 101 0.2 1 87 14 141 72 0.2 1 66 6 142 70 0.2 1 63 7 143 96 0.2 1 90 6 144 66 0.2 1 61 5 145 236 0.2 1 225 11 146 987 0.2 1 943 44 147 4949 0.2 1 4744 205 148 3207 0.2 1 3070 137 149 1976 0.2 1 1884 92 150 15929 0.2 1 15207 722 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_26psu_3_S15_L002_R2_001.fastq.gz ============================================= 14622552 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 14622552 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 170305 (1.16%)