SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/CTRL_8C_26psu_2_S18_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: 751160). 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/CTRL_8C_26psu_2_S18_L001_R2_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 57.48 s (3 us/read; 17.73 M reads/minute). === Summary === Total reads processed: 16,982,389 Reads with adapters: 15,175,955 (89.4%) Reads written (passing filters): 16,982,389 (100.0%) Total basepairs processed: 2,547,358,350 bp Quality-trimmed: 14,637,859 bp (0.6%) Total written (filtered): 1,670,081,107 bp (65.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 15175955 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 26.2% C: 14.2% G: 26.5% T: 33.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 988355 4245597.2 0 988355 2 174327 1061399.3 0 174327 3 112326 265349.8 0 112326 4 66944 66337.5 0 66944 5 68049 16584.4 0 68049 6 59622 4146.1 0 59622 7 48077 1036.5 0 48077 8 70632 259.1 0 70632 9 56419 64.8 0 56220 199 10 62892 16.2 1 59906 2986 11 67246 4.0 1 63200 4046 12 67488 1.0 1 63307 4181 13 76798 0.3 1 72553 4245 14 73938 0.3 1 68873 5065 15 59370 0.3 1 55860 3510 16 87943 0.3 1 82783 5160 17 71376 0.3 1 66695 4681 18 68792 0.3 1 64885 3907 19 88616 0.3 1 83090 5526 20 83852 0.3 1 79094 4758 21 75082 0.3 1 70636 4446 22 86387 0.3 1 81609 4778 23 90257 0.3 1 85055 5202 24 90691 0.3 1 85295 5396 25 104055 0.3 1 98264 5791 26 86753 0.3 1 81712 5041 27 96821 0.3 1 90516 6305 28 92589 0.3 1 88280 4309 29 100006 0.3 1 94283 5723 30 100693 0.3 1 95722 4971 31 110238 0.3 1 104335 5903 32 99509 0.3 1 94661 4848 33 112333 0.3 1 106128 6205 34 145441 0.3 1 137472 7969 35 84427 0.3 1 80249 4178 36 119286 0.3 1 112593 6693 37 127293 0.3 1 120329 6964 38 123047 0.3 1 117261 5786 39 119775 0.3 1 114281 5494 40 135696 0.3 1 128262 7434 41 130689 0.3 1 124366 6323 42 135604 0.3 1 129108 6496 43 126835 0.3 1 120741 6094 44 146922 0.3 1 139741 7181 45 154339 0.3 1 146909 7430 46 118308 0.3 1 112832 5476 47 149295 0.3 1 142485 6810 48 148606 0.3 1 142089 6517 49 156890 0.3 1 149693 7197 50 148375 0.3 1 141320 7055 51 190171 0.3 1 181254 8917 52 136804 0.3 1 130968 5836 53 165906 0.3 1 159264 6642 54 128157 0.3 1 122871 5286 55 169343 0.3 1 162704 6639 56 177473 0.3 1 169804 7669 57 169211 0.3 1 162646 6565 58 164197 0.3 1 158052 6145 59 169249 0.3 1 162429 6820 60 177455 0.3 1 170133 7322 61 185762 0.3 1 177933 7829 62 204728 0.3 1 196280 8448 63 277535 0.3 1 267196 10339 64 238674 0.3 1 230905 7769 65 152399 0.3 1 146631 5768 66 166909 0.3 1 160634 6275 67 166804 0.3 1 160075 6729 68 169255 0.3 1 162913 6342 69 169940 0.3 1 163142 6798 70 182641 0.3 1 175571 7070 71 198941 0.3 1 191661 7280 72 188343 0.3 1 181180 7163 73 204850 0.3 1 197436 7414 74 188381 0.3 1 181668 6713 75 180633 0.3 1 173941 6692 76 178500 0.3 1 172078 6422 77 180330 0.3 1 173546 6784 78 173641 0.3 1 167180 6461 79 170287 0.3 1 164090 6197 80 170838 0.3 1 164653 6185 81 172175 0.3 1 165934 6241 82 165553 0.3 1 159555 5998 83 164742 0.3 1 158792 5950 84 160682 0.3 1 154778 5904 85 159281 0.3 1 153367 5914 86 160523 0.3 1 154638 5885 87 163301 0.3 1 157413 5888 88 161676 0.3 1 155871 5805 89 147453 0.3 1 142105 5348 90 143818 0.3 1 138625 5193 91 138225 0.3 1 133103 5122 92 131088 0.3 1 126317 4771 93 128053 0.3 1 123615 4438 94 125505 0.3 1 121074 4431 95 119294 0.3 1 114964 4330 96 116155 0.3 1 112159 3996 97 108812 0.3 1 105094 3718 98 104976 0.3 1 101373 3603 99 105895 0.3 1 102281 3614 100 97778 0.3 1 94611 3167 101 95386 0.3 1 92351 3035 102 88691 0.3 1 85785 2906 103 80552 0.3 1 77853 2699 104 77505 0.3 1 74941 2564 105 70382 0.3 1 68000 2382 106 65184 0.3 1 63051 2133 107 60057 0.3 1 58146 1911 108 55681 0.3 1 53827 1854 109 50629 0.3 1 48896 1733 110 46572 0.3 1 45046 1526 111 44577 0.3 1 43131 1446 112 39344 0.3 1 38114 1230 113 34530 0.3 1 33382 1148 114 30993 0.3 1 30031 962 115 26355 0.3 1 25472 883 116 23180 0.3 1 22328 852 117 19825 0.3 1 19141 684 118 17184 0.3 1 16546 638 119 14938 0.3 1 14436 502 120 12856 0.3 1 12387 469 121 11667 0.3 1 11246 421 122 9613 0.3 1 9258 355 123 8582 0.3 1 8274 308 124 7156 0.3 1 6897 259 125 6130 0.3 1 5897 233 126 5195 0.3 1 5039 156 127 4372 0.3 1 4226 146 128 3397 0.3 1 3245 152 129 2899 0.3 1 2785 114 130 2231 0.3 1 2140 91 131 2005 0.3 1 1925 80 132 1815 0.3 1 1740 75 133 2411 0.3 1 2321 90 134 4708 0.3 1 4577 131 135 1657 0.3 1 1601 56 136 589 0.3 1 574 15 137 406 0.3 1 391 15 138 265 0.3 1 252 13 139 182 0.3 1 175 7 140 132 0.3 1 124 8 141 111 0.3 1 106 5 142 101 0.3 1 96 5 143 63 0.3 1 60 3 144 61 0.3 1 57 4 145 160 0.3 1 154 6 146 146 0.3 1 139 7 147 687 0.3 1 666 21 148 439 0.3 1 426 13 149 260 0.3 1 251 9 150 2448 0.3 1 2325 123 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/CTRL_8C_26psu_2_S18_L001_R2_001.fastq.gz ============================================= 16982389 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 16982389 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 410915 (2.42%)