SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_32psu_3_S7_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: 622739). Second best hit was smallRNA (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/8C_32psu_3_S7_L002_R2_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 53.15 s (4 us/read; 15.94 M reads/minute). === Summary === Total reads processed: 14,120,008 Reads with adapters: 11,722,164 (83.0%) Reads written (passing filters): 14,120,008 (100.0%) Total basepairs processed: 2,118,001,200 bp Quality-trimmed: 10,398,441 bp (0.5%) Total written (filtered): 1,557,917,839 bp (73.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11722164 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 27.6% C: 13.3% G: 24.5% T: 34.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 1423484 3530002.0 0 1423484 2 217404 882500.5 0 217404 3 135747 220625.1 0 135747 4 77416 55156.3 0 77416 5 73163 13789.1 0 73163 6 65957 3447.3 0 65957 7 52727 861.8 0 52727 8 75617 215.5 0 75617 9 60824 53.9 0 60611 213 10 64613 13.5 1 60561 4052 11 71071 3.4 1 65663 5408 12 69904 0.8 1 64695 5209 13 80991 0.2 1 75018 5973 14 75627 0.2 1 69287 6340 15 61630 0.2 1 57275 4355 16 89541 0.2 1 82804 6737 17 75362 0.2 1 69553 5809 18 67936 0.2 1 63097 4839 19 88766 0.2 1 82324 6442 20 83180 0.2 1 77328 5852 21 74299 0.2 1 69124 5175 22 83499 0.2 1 77755 5744 23 88403 0.2 1 82296 6107 24 88389 0.2 1 82109 6280 25 100119 0.2 1 93881 6238 26 84031 0.2 1 77871 6160 27 93205 0.2 1 86091 7114 28 83882 0.2 1 78923 4959 29 95544 0.2 1 89031 6513 30 91423 0.2 1 85830 5593 31 102885 0.2 1 96159 6726 32 88346 0.2 1 83048 5298 33 103020 0.2 1 96084 6936 34 134691 0.2 1 125875 8816 35 71511 0.2 1 67043 4468 36 106372 0.2 1 99204 7168 37 111667 0.2 1 104414 7253 38 105292 0.2 1 99304 5988 39 99654 0.2 1 94273 5381 40 115518 0.2 1 108179 7339 41 111214 0.2 1 104737 6477 42 115443 0.2 1 108784 6659 43 104707 0.2 1 98628 6079 44 122428 0.2 1 115040 7388 45 129896 0.2 1 122003 7893 46 92988 0.2 1 87594 5394 47 119950 0.2 1 113634 6316 48 117307 0.2 1 110893 6414 49 123614 0.2 1 116211 7403 50 118595 0.2 1 111825 6770 51 146157 0.2 1 137800 8357 52 108528 0.2 1 102556 5972 53 133051 0.2 1 126144 6907 54 97258 0.2 1 92286 4972 55 128012 0.2 1 121714 6298 56 133239 0.2 1 125868 7371 57 126482 0.2 1 120493 5989 58 123495 0.2 1 117409 6086 59 123171 0.2 1 116902 6269 60 129991 0.2 1 123447 6544 61 132791 0.2 1 126344 6447 62 145203 0.2 1 137595 7608 63 193193 0.2 1 184570 8623 64 164505 0.2 1 158250 6255 65 106154 0.2 1 101191 4963 66 116219 0.2 1 110707 5512 67 115499 0.2 1 109857 5642 68 116592 0.2 1 111069 5523 69 115665 0.2 1 109783 5882 70 124608 0.2 1 118610 5998 71 128211 0.2 1 122084 6127 72 122112 0.2 1 116125 5987 73 126921 0.2 1 120760 6161 74 118790 0.2 1 112963 5827 75 113173 0.2 1 107712 5461 76 111463 0.2 1 105998 5465 77 111662 0.2 1 106140 5522 78 107207 0.2 1 101895 5312 79 104292 0.2 1 99234 5058 80 103845 0.2 1 98916 4929 81 101938 0.2 1 97104 4834 82 97773 0.2 1 93124 4649 83 95971 0.2 1 91487 4484 84 92983 0.2 1 88672 4311 85 91731 0.2 1 87597 4134 86 91538 0.2 1 87240 4298 87 90919 0.2 1 86818 4101 88 89775 0.2 1 85803 3972 89 80478 0.2 1 76988 3490 90 77967 0.2 1 74477 3490 91 73781 0.2 1 70569 3212 92 69447 0.2 1 66340 3107 93 66394 0.2 1 63362 3032 94 63823 0.2 1 61051 2772 95 60418 0.2 1 57617 2801 96 57934 0.2 1 55484 2450 97 54242 0.2 1 51870 2372 98 51153 0.2 1 49011 2142 99 50193 0.2 1 47988 2205 100 43401 0.2 1 41462 1939 101 41188 0.2 1 39459 1729 102 38238 0.2 1 36636 1602 103 35697 0.2 1 34094 1603 104 34260 0.2 1 32771 1489 105 30330 0.2 1 29031 1299 106 27539 0.2 1 26325 1214 107 24680 0.2 1 23635 1045 108 22009 0.2 1 21062 947 109 19974 0.2 1 19117 857 110 18015 0.2 1 17209 806 111 16915 0.2 1 16205 710 112 14332 0.2 1 13689 643 113 12446 0.2 1 11895 551 114 10968 0.2 1 10478 490 115 9016 0.2 1 8590 426 116 7818 0.2 1 7478 340 117 6323 0.2 1 6027 296 118 5766 0.2 1 5518 248 119 4704 0.2 1 4500 204 120 3901 0.2 1 3708 193 121 3388 0.2 1 3195 193 122 2862 0.2 1 2731 131 123 2458 0.2 1 2315 143 124 2060 0.2 1 1986 74 125 1642 0.2 1 1547 95 126 1477 0.2 1 1395 82 127 1193 0.2 1 1127 66 128 861 0.2 1 803 58 129 803 0.2 1 750 53 130 513 0.2 1 479 34 131 475 0.2 1 451 24 132 384 0.2 1 349 35 133 402 0.2 1 380 22 134 430 0.2 1 416 14 135 203 0.2 1 185 18 136 160 0.2 1 156 4 137 84 0.2 1 74 10 138 68 0.2 1 64 4 139 47 0.2 1 44 3 140 21 0.2 1 20 1 141 24 0.2 1 21 3 142 16 0.2 1 13 3 143 16 0.2 1 13 3 144 10 0.2 1 10 145 20 0.2 1 19 1 146 18 0.2 1 18 147 25 0.2 1 23 2 148 19 0.2 1 15 4 149 13 0.2 1 12 1 150 153 0.2 1 145 8 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_32psu_3_S7_L002_R2_001.fastq.gz ============================================= 14120008 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 14120008 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 147363 (1.04%)