SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/CTRL_16C_26psu_2_S21_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: 698110). 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/CTRL_16C_26psu_2_S21_L001_R2_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 50.01 s (4 us/read; 16.12 M reads/minute). === Summary === Total reads processed: 13,433,110 Reads with adapters: 11,642,556 (86.7%) Reads written (passing filters): 13,433,110 (100.0%) Total basepairs processed: 2,014,966,500 bp Quality-trimmed: 8,709,221 bp (0.4%) Total written (filtered): 1,432,856,177 bp (71.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11642556 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.1% C: 11.7% G: 26.2% T: 34.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 1015848 3358277.5 0 1015848 2 179924 839569.4 0 179924 3 110740 209892.3 0 110740 4 68288 52473.1 0 68288 5 68265 13118.3 0 68265 6 61219 3279.6 0 61219 7 51190 819.9 0 51190 8 71859 205.0 0 71859 9 56699 51.2 0 56454 245 10 63956 12.8 1 61051 2905 11 67245 3.2 1 63190 4055 12 68588 0.8 1 64563 4025 13 77409 0.2 1 73173 4236 14 74943 0.2 1 70185 4758 15 61575 0.2 1 58112 3463 16 87672 0.2 1 82660 5012 17 73552 0.2 1 68954 4598 18 68802 0.2 1 65063 3739 19 88259 0.2 1 82939 5320 20 82556 0.2 1 78141 4415 21 73225 0.2 1 69045 4180 22 83863 0.2 1 79245 4618 23 87811 0.2 1 82813 4998 24 89014 0.2 1 83968 5046 25 100238 0.2 1 94973 5265 26 83574 0.2 1 78786 4788 27 93033 0.2 1 87412 5621 28 89387 0.2 1 85387 4000 29 95696 0.2 1 90729 4967 30 94787 0.2 1 90441 4346 31 102169 0.2 1 97061 5108 32 94007 0.2 1 89720 4287 33 105833 0.2 1 100418 5415 34 134739 0.2 1 127847 6892 35 80075 0.2 1 76383 3692 36 104516 0.2 1 98895 5621 37 113410 0.2 1 107671 5739 38 107520 0.2 1 102889 4631 39 105637 0.2 1 101025 4612 40 118785 0.2 1 112992 5793 41 115631 0.2 1 110394 5237 42 122110 0.2 1 116550 5560 43 111230 0.2 1 106271 4959 44 128541 0.2 1 122788 5753 45 137963 0.2 1 131813 6150 46 99340 0.2 1 94897 4443 47 125922 0.2 1 120367 5555 48 125595 0.2 1 120423 5172 49 132842 0.2 1 126935 5907 50 127676 0.2 1 122004 5672 51 163515 0.2 1 156244 7271 52 117884 0.2 1 113079 4805 53 142736 0.2 1 137315 5421 54 107101 0.2 1 102800 4301 55 139222 0.2 1 133903 5319 56 143656 0.2 1 137859 5797 57 140073 0.2 1 134871 5202 58 134625 0.2 1 129700 4925 59 134950 0.2 1 129802 5148 60 140295 0.2 1 134781 5514 61 144854 0.2 1 139165 5689 62 159948 0.2 1 153492 6456 63 215119 0.2 1 207339 7780 64 166765 0.2 1 161464 5301 65 114876 0.2 1 110601 4275 66 125878 0.2 1 121273 4605 67 126455 0.2 1 121514 4941 68 128071 0.2 1 123304 4767 69 126908 0.2 1 122039 4869 70 132340 0.2 1 127378 4962 71 137419 0.2 1 132563 4856 72 133254 0.2 1 128394 4860 73 140768 0.2 1 135639 5129 74 130186 0.2 1 125634 4552 75 123476 0.2 1 119176 4300 76 121581 0.2 1 117266 4315 77 120182 0.2 1 115605 4577 78 115742 0.2 1 111521 4221 79 111421 0.2 1 107330 4091 80 110726 0.2 1 106773 3953 81 109599 0.2 1 105677 3922 82 103036 0.2 1 99365 3671 83 100716 0.2 1 97173 3543 84 98439 0.2 1 94811 3628 85 96847 0.2 1 93310 3537 86 96817 0.2 1 93338 3479 87 95905 0.2 1 92582 3323 88 93526 0.2 1 90163 3363 89 83831 0.2 1 80785 3046 90 80158 0.2 1 77319 2839 91 74964 0.2 1 72203 2761 92 70024 0.2 1 67553 2471 93 68027 0.2 1 65623 2404 94 64372 0.2 1 62143 2229 95 61456 0.2 1 59284 2172 96 57585 0.2 1 55560 2025 97 53463 0.2 1 51605 1858 98 50229 0.2 1 48488 1741 99 48358 0.2 1 46710 1648 100 43743 0.2 1 42301 1442 101 39334 0.2 1 37976 1358 102 35681 0.2 1 34444 1237 103 32169 0.2 1 31042 1127 104 30344 0.2 1 29354 990 105 26673 0.2 1 25747 926 106 24610 0.2 1 23753 857 107 21493 0.2 1 20733 760 108 19129 0.2 1 18449 680 109 17216 0.2 1 16604 612 110 15680 0.2 1 15121 559 111 14422 0.2 1 13916 506 112 12048 0.2 1 11652 396 113 10682 0.2 1 10293 389 114 9191 0.2 1 8830 361 115 7355 0.2 1 7077 278 116 6245 0.2 1 6016 229 117 5167 0.2 1 4936 231 118 4511 0.2 1 4330 181 119 3552 0.2 1 3385 167 120 3201 0.2 1 3062 139 121 2450 0.2 1 2343 107 122 2029 0.2 1 1935 94 123 1814 0.2 1 1715 99 124 1524 0.2 1 1436 88 125 1206 0.2 1 1139 67 126 1198 0.2 1 1135 63 127 925 0.2 1 875 50 128 706 0.2 1 663 43 129 633 0.2 1 590 43 130 698 0.2 1 666 32 131 844 0.2 1 815 29 132 910 0.2 1 876 34 133 1412 0.2 1 1368 44 134 1698 0.2 1 1641 57 135 718 0.2 1 696 22 136 190 0.2 1 177 13 137 107 0.2 1 98 9 138 70 0.2 1 67 3 139 53 0.2 1 50 3 140 53 0.2 1 52 1 141 26 0.2 1 26 142 26 0.2 1 24 2 143 21 0.2 1 20 1 144 18 0.2 1 16 2 145 35 0.2 1 32 3 146 39 0.2 1 35 4 147 177 0.2 1 169 8 148 82 0.2 1 76 6 149 45 0.2 1 43 2 150 267 0.2 1 241 26 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/CTRL_16C_26psu_2_S21_L001_R2_001.fastq.gz ============================================= 13433110 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 13433110 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 134210 (1.00%)