SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_26psu_3_S11_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: 684443). 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/8C_26psu_3_S11_L001_R2_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 63.44 s (4 us/read; 16.29 M reads/minute). === Summary === Total reads processed: 17,221,011 Reads with adapters: 14,791,093 (85.9%) Reads written (passing filters): 17,221,011 (100.0%) Total basepairs processed: 2,583,151,650 bp Quality-trimmed: 13,446,962 bp (0.5%) Total written (filtered): 1,830,093,875 bp (70.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14791093 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 27.4% C: 12.3% G: 25.7% T: 34.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 1396647 4305252.8 0 1396647 2 233877 1076313.2 0 233877 3 144492 269078.3 0 144492 4 87098 67269.6 0 87098 5 86055 16817.4 0 86055 6 74999 4204.3 0 74999 7 60602 1051.1 0 60602 8 88349 262.8 0 88349 9 70295 65.7 0 70075 220 10 78524 16.4 1 74626 3898 11 82895 4.1 1 77738 5157 12 84476 1.0 1 79233 5243 13 94326 0.3 1 88847 5479 14 89984 0.3 1 83845 6139 15 72879 0.3 1 68520 4359 16 107100 0.3 1 100533 6567 17 87871 0.3 1 82033 5838 18 83139 0.3 1 78397 4742 19 107298 0.3 1 100402 6896 20 100171 0.3 1 94390 5781 21 88114 0.3 1 82713 5401 22 101076 0.3 1 95306 5770 23 105877 0.3 1 99537 6340 24 106645 0.3 1 100049 6596 25 121932 0.3 1 115168 6764 26 100476 0.3 1 94344 6132 27 110166 0.3 1 102758 7408 28 107176 0.3 1 101924 5252 29 114111 0.3 1 107493 6618 30 115359 0.3 1 109345 6014 31 124714 0.3 1 117673 7041 32 113114 0.3 1 107249 5865 33 126653 0.3 1 119283 7370 34 161416 0.3 1 152249 9167 35 95165 0.3 1 90366 4799 36 130060 0.3 1 122395 7665 37 137916 0.3 1 130202 7714 38 132706 0.3 1 126385 6321 39 129385 0.3 1 123068 6317 40 145600 0.3 1 137496 8104 41 141184 0.3 1 134070 7114 42 147655 0.3 1 140213 7442 43 133334 0.3 1 126611 6723 44 155705 0.3 1 147696 8009 45 171369 0.3 1 162810 8559 46 117297 0.3 1 111483 5814 47 154795 0.3 1 147535 7260 48 153124 0.3 1 145909 7215 49 161825 0.3 1 153802 8023 50 152605 0.3 1 145077 7528 51 196303 0.3 1 186610 9693 52 140348 0.3 1 134075 6273 53 169943 0.3 1 162909 7034 54 129681 0.3 1 123901 5780 55 171452 0.3 1 164350 7102 56 175614 0.3 1 167693 7921 57 166121 0.3 1 159314 6807 58 161387 0.3 1 155069 6318 59 166619 0.3 1 159538 7081 60 171867 0.3 1 164363 7504 61 178391 0.3 1 170609 7782 62 196679 0.3 1 188081 8598 63 261274 0.3 1 251029 10245 64 223191 0.3 1 215765 7426 65 140786 0.3 1 135022 5764 66 154538 0.3 1 148311 6227 67 154027 0.3 1 147524 6503 68 155618 0.3 1 149295 6323 69 156069 0.3 1 149599 6470 70 165853 0.3 1 158998 6855 71 174385 0.3 1 167574 6811 72 166867 0.3 1 160011 6856 73 177560 0.3 1 170679 6881 74 163422 0.3 1 157175 6247 75 155704 0.3 1 149734 5970 76 153010 0.3 1 147031 5979 77 153177 0.3 1 146921 6256 78 148366 0.3 1 142418 5948 79 143302 0.3 1 137662 5640 80 143393 0.3 1 137924 5469 81 142595 0.3 1 137094 5501 82 136572 0.3 1 131469 5103 83 132737 0.3 1 127619 5118 84 127991 0.3 1 122783 5208 85 126965 0.3 1 121917 5048 86 125977 0.3 1 120895 5082 87 128246 0.3 1 123231 5015 88 125283 0.3 1 120412 4871 89 112372 0.3 1 108049 4323 90 108791 0.3 1 104559 4232 91 102461 0.3 1 98288 4173 92 96447 0.3 1 92722 3725 93 93869 0.3 1 90286 3583 94 91252 0.3 1 87743 3509 95 86357 0.3 1 83052 3305 96 82971 0.3 1 79818 3153 97 76434 0.3 1 73514 2920 98 72048 0.3 1 69275 2773 99 70150 0.3 1 67632 2518 100 63666 0.3 1 61347 2319 101 59861 0.3 1 57732 2129 102 55598 0.3 1 53622 1976 103 51026 0.3 1 49092 1934 104 48386 0.3 1 46675 1711 105 42639 0.3 1 41080 1559 106 39613 0.3 1 38200 1413 107 35228 0.3 1 33949 1279 108 31897 0.3 1 30649 1248 109 28672 0.3 1 27578 1094 110 25914 0.3 1 24951 963 111 24295 0.3 1 23481 814 112 21304 0.3 1 20453 851 113 18350 0.3 1 17653 697 114 16256 0.3 1 15627 629 115 13357 0.3 1 12793 564 116 11612 0.3 1 11150 462 117 9484 0.3 1 9116 368 118 8205 0.3 1 7826 379 119 6936 0.3 1 6629 307 120 5765 0.3 1 5525 240 121 5231 0.3 1 5015 216 122 4247 0.3 1 4080 167 123 3547 0.3 1 3416 131 124 2936 0.3 1 2808 128 125 2425 0.3 1 2314 111 126 2011 0.3 1 1915 96 127 1702 0.3 1 1617 85 128 1242 0.3 1 1178 64 129 1065 0.3 1 1006 59 130 766 0.3 1 721 45 131 781 0.3 1 739 42 132 668 0.3 1 634 34 133 887 0.3 1 866 21 134 1489 0.3 1 1430 59 135 583 0.3 1 560 23 136 206 0.3 1 191 15 137 151 0.3 1 146 5 138 116 0.3 1 111 5 139 72 0.3 1 65 7 140 56 0.3 1 54 2 141 35 0.3 1 27 8 142 30 0.3 1 26 4 143 21 0.3 1 18 3 144 19 0.3 1 17 2 145 37 0.3 1 35 2 146 25 0.3 1 22 3 147 50 0.3 1 46 4 148 39 0.3 1 37 2 149 45 0.3 1 42 3 150 451 0.3 1 418 33 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_26psu_3_S11_L001_R2_001.fastq.gz ============================================= 17221011 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 17221011 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 215194 (1.25%)