SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/CTRL_8C_26psu_2_S18_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: 743143). 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/CTRL_8C_26psu_2_S18_L002_R2_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 54.15 s (3 us/read; 18.81 M reads/minute). === Summary === Total reads processed: 16,972,486 Reads with adapters: 15,133,409 (89.2%) Reads written (passing filters): 16,972,486 (100.0%) Total basepairs processed: 2,545,872,900 bp Quality-trimmed: 14,118,915 bp (0.6%) Total written (filtered): 1,669,911,692 bp (65.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 15133409 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 991330 4243121.5 0 991330 2 172347 1060780.4 0 172347 3 115382 265195.1 0 115382 4 65389 66298.8 0 65389 5 65284 16574.7 0 65284 6 59675 4143.7 0 59675 7 47228 1035.9 0 47228 8 69329 259.0 0 69329 9 55587 64.7 0 55396 191 10 60044 16.2 1 55911 4133 11 66669 4.0 1 61266 5403 12 66198 1.0 1 60904 5294 13 76711 0.3 1 70697 6014 14 72459 0.3 1 66111 6348 15 58334 0.3 1 54019 4315 16 86573 0.3 1 79901 6672 17 73457 0.3 1 67527 5930 18 65883 0.3 1 60982 4901 19 88155 0.3 1 81417 6738 20 82480 0.3 1 76391 6089 21 74222 0.3 1 68897 5325 22 85010 0.3 1 78866 6144 23 89940 0.3 1 83333 6607 24 90783 0.3 1 83898 6885 25 103545 0.3 1 96553 6992 26 86049 0.3 1 79414 6635 27 97578 0.3 1 89843 7735 28 88487 0.3 1 82899 5588 29 101443 0.3 1 94374 7069 30 98065 0.3 1 91540 6525 31 110927 0.3 1 103494 7433 32 96042 0.3 1 90040 6002 33 113007 0.3 1 105053 7954 34 146678 0.3 1 136868 9810 35 80284 0.3 1 75023 5261 36 119636 0.3 1 111148 8488 37 126797 0.3 1 118353 8444 38 121741 0.3 1 114473 7268 39 116427 0.3 1 109798 6629 40 134566 0.3 1 125810 8756 41 132132 0.3 1 124200 7932 42 135345 0.3 1 127009 8336 43 125343 0.3 1 118018 7325 44 147397 0.3 1 138044 9353 45 153169 0.3 1 143585 9584 46 116858 0.3 1 110003 6855 47 148662 0.3 1 140422 8240 48 146456 0.3 1 138141 8315 49 155663 0.3 1 146241 9422 50 150144 0.3 1 140998 9146 51 186605 0.3 1 175426 11179 52 135487 0.3 1 127796 7691 53 169781 0.3 1 161047 8734 54 125345 0.3 1 118710 6635 55 168692 0.3 1 160003 8689 56 176257 0.3 1 166258 9999 57 169891 0.3 1 161571 8320 58 164276 0.3 1 156000 8276 59 168462 0.3 1 159572 8890 60 177599 0.3 1 168506 9093 61 183440 0.3 1 174203 9237 62 202372 0.3 1 191386 10986 63 270936 0.3 1 258181 12755 64 234996 0.3 1 225774 9222 65 151631 0.3 1 144050 7581 66 166302 0.3 1 157972 8330 67 167833 0.3 1 159201 8632 68 170330 0.3 1 161782 8548 69 171332 0.3 1 162512 8820 70 183649 0.3 1 174535 9114 71 199117 0.3 1 189420 9697 72 190292 0.3 1 180708 9584 73 205025 0.3 1 195024 10001 74 188852 0.3 1 179445 9407 75 181257 0.3 1 172280 8977 76 178734 0.3 1 169881 8853 77 180452 0.3 1 171277 9175 78 172679 0.3 1 164051 8628 79 170532 0.3 1 162087 8445 80 171521 0.3 1 163340 8181 81 171140 0.3 1 162630 8510 82 165207 0.3 1 157233 7974 83 163608 0.3 1 155825 7783 84 160013 0.3 1 152625 7388 85 159454 0.3 1 151925 7529 86 161481 0.3 1 153907 7574 87 162581 0.3 1 155126 7455 88 162054 0.3 1 154673 7381 89 147788 0.3 1 141132 6656 90 145172 0.3 1 138698 6474 91 139015 0.3 1 132745 6270 92 132299 0.3 1 126316 5983 93 128552 0.3 1 122735 5817 94 126711 0.3 1 120900 5811 95 119947 0.3 1 114454 5493 96 117162 0.3 1 111939 5223 97 108989 0.3 1 104182 4807 98 105848 0.3 1 101282 4566 99 105989 0.3 1 101349 4640 100 98144 0.3 1 93908 4236 101 94920 0.3 1 90864 4056 102 89211 0.3 1 85259 3952 103 81188 0.3 1 77654 3534 104 77565 0.3 1 74081 3484 105 70248 0.3 1 67249 2999 106 65288 0.3 1 62604 2684 107 60022 0.3 1 57428 2594 108 55515 0.3 1 53019 2496 109 50990 0.3 1 48728 2262 110 46869 0.3 1 44831 2038 111 44489 0.3 1 42630 1859 112 39619 0.3 1 37888 1731 113 34543 0.3 1 33015 1528 114 31368 0.3 1 30023 1345 115 26935 0.3 1 25774 1161 116 23611 0.3 1 22614 997 117 19912 0.3 1 18993 919 118 17572 0.3 1 16789 783 119 14871 0.3 1 14194 677 120 12844 0.3 1 12244 600 121 11858 0.3 1 11313 545 122 9930 0.3 1 9463 467 123 8753 0.3 1 8342 411 124 7126 0.3 1 6812 314 125 6158 0.3 1 5890 268 126 5177 0.3 1 4954 223 127 4434 0.3 1 4233 201 128 3338 0.3 1 3185 153 129 2850 0.3 1 2742 108 130 2111 0.3 1 2001 110 131 1887 0.3 1 1807 80 132 1727 0.3 1 1658 69 133 2467 0.3 1 2378 89 134 4553 0.3 1 4401 152 135 1770 0.3 1 1714 56 136 598 0.3 1 559 39 137 389 0.3 1 374 15 138 283 0.3 1 271 12 139 188 0.3 1 181 7 140 133 0.3 1 124 9 141 75 0.3 1 73 2 142 64 0.3 1 61 3 143 64 0.3 1 59 5 144 68 0.3 1 66 2 145 139 0.3 1 132 7 146 159 0.3 1 151 8 147 678 0.3 1 647 31 148 467 0.3 1 450 17 149 278 0.3 1 263 15 150 2366 0.3 1 2224 142 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/CTRL_8C_26psu_2_S18_L002_R2_001.fastq.gz ============================================= 16972486 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 16972486 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 410938 (2.42%)