SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_32psu_2_S6_L002_R1_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: 561352). 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_32psu_2_S6_L002_R1_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 50.13 s (4 us/read; 15.40 M reads/minute). === Summary === Total reads processed: 12,868,767 Reads with adapters: 10,286,843 (79.9%) Reads written (passing filters): 12,868,767 (100.0%) Total basepairs processed: 1,930,315,050 bp Quality-trimmed: 3,674,826 bp (0.2%) Total written (filtered): 1,483,181,496 bp (76.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10286843 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.8% C: 14.7% G: 20.5% T: 35.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 1541222 3217191.8 0 1541222 2 228030 804297.9 0 228030 3 129528 201074.5 0 129528 4 78688 50268.6 0 78688 5 67124 12567.2 0 67124 6 66330 3141.8 0 66330 7 52508 785.4 0 52508 8 67652 196.4 0 67652 9 67615 49.1 0 66819 796 10 63063 12.3 1 59213 3850 11 71894 3.1 1 65954 5940 12 67897 0.8 1 62829 5068 13 71151 0.2 1 65849 5302 14 69055 0.2 1 63709 5346 15 75069 0.2 1 69302 5767 16 71424 0.2 1 65420 6004 17 86810 0.2 1 79021 7789 18 77955 0.2 1 72600 5355 19 63383 0.2 1 58809 4574 20 78965 0.2 1 73063 5902 21 85485 0.2 1 79014 6471 22 72855 0.2 1 68021 4834 23 85346 0.2 1 78944 6402 24 80318 0.2 1 73301 7017 25 85430 0.2 1 78969 6461 26 78740 0.2 1 73485 5255 27 88451 0.2 1 81474 6977 28 85790 0.2 1 79338 6452 29 91791 0.2 1 83845 7946 30 95449 0.2 1 89482 5967 31 75838 0.2 1 70423 5415 32 92731 0.2 1 85851 6880 33 86762 0.2 1 80055 6707 34 99437 0.2 1 91057 8380 35 85081 0.2 1 79384 5697 36 99297 0.2 1 91300 7997 37 101918 0.2 1 94163 7755 38 96379 0.2 1 88997 7382 39 103865 0.2 1 95226 8639 40 94376 0.2 1 87615 6761 41 104329 0.2 1 95123 9206 42 94892 0.2 1 86892 8000 43 148535 0.2 1 139624 8911 44 48085 0.2 1 43529 4556 45 105311 0.2 1 97887 7424 46 95734 0.2 1 88889 6845 47 101958 0.2 1 94804 7154 48 102091 0.2 1 94808 7283 49 112404 0.2 1 104035 8369 50 93295 0.2 1 87104 6191 51 104120 0.2 1 96595 7525 52 107257 0.2 1 99149 8108 53 113672 0.2 1 105961 7711 54 91213 0.2 1 85172 6041 55 107994 0.2 1 100085 7909 56 133513 0.2 1 124815 8698 57 81884 0.2 1 75254 6630 58 110562 0.2 1 103755 6807 59 98179 0.2 1 91032 7147 60 104453 0.2 1 97116 7337 61 104191 0.2 1 97239 6952 62 114950 0.2 1 107431 7519 63 89541 0.2 1 82900 6641 64 101345 0.2 1 94868 6477 65 113295 0.2 1 105436 7859 66 116379 0.2 1 108386 7993 67 124994 0.2 1 114943 10051 68 229157 0.2 1 217120 12037 69 41354 0.2 1 37561 3793 70 17861 0.2 1 14972 2889 71 66015 0.2 1 61819 4196 72 88699 0.2 1 83225 5474 73 92274 0.2 1 86536 5738 74 90496 0.2 1 84396 6100 75 91072 0.2 1 84946 6126 76 89676 0.2 1 83357 6319 77 89231 0.2 1 83068 6163 78 83699 0.2 1 77980 5719 79 83174 0.2 1 77470 5704 80 80873 0.2 1 75140 5733 81 79905 0.2 1 74411 5494 82 77850 0.2 1 72450 5400 83 75463 0.2 1 70383 5080 84 72909 0.2 1 67760 5149 85 70237 0.2 1 65392 4845 86 67846 0.2 1 63270 4576 87 65212 0.2 1 60837 4375 88 63724 0.2 1 59434 4290 89 60287 0.2 1 56154 4133 90 60221 0.2 1 55941 4280 91 56630 0.2 1 52736 3894 92 53891 0.2 1 50132 3759 93 50029 0.2 1 46571 3458 94 48812 0.2 1 45399 3413 95 45157 0.2 1 41906 3251 96 42860 0.2 1 39861 2999 97 40400 0.2 1 37713 2687 98 37633 0.2 1 34970 2663 99 36386 0.2 1 33717 2669 100 32744 0.2 1 30375 2369 101 30684 0.2 1 28451 2233 102 28336 0.2 1 26275 2061 103 26125 0.2 1 24257 1868 104 24496 0.2 1 22774 1722 105 21603 0.2 1 20114 1489 106 19703 0.2 1 18252 1451 107 18114 0.2 1 16740 1374 108 16491 0.2 1 15275 1216 109 15050 0.2 1 13866 1184 110 13423 0.2 1 12430 993 111 12182 0.2 1 11225 957 112 10547 0.2 1 9689 858 113 9161 0.2 1 8400 761 114 7859 0.2 1 7209 650 115 6948 0.2 1 6344 604 116 6269 0.2 1 5743 526 117 5202 0.2 1 4768 434 118 4673 0.2 1 4242 431 119 3797 0.2 1 3484 313 120 3288 0.2 1 2990 298 121 2786 0.2 1 2513 273 122 2451 0.2 1 2220 231 123 1988 0.2 1 1766 222 124 1684 0.2 1 1506 178 125 1280 0.2 1 1137 143 126 1164 0.2 1 1040 124 127 900 0.2 1 789 111 128 728 0.2 1 654 74 129 628 0.2 1 547 81 130 442 0.2 1 393 49 131 450 0.2 1 380 70 132 321 0.2 1 277 44 133 283 0.2 1 243 40 134 293 0.2 1 262 31 135 181 0.2 1 154 27 136 135 0.2 1 102 33 137 78 0.2 1 61 17 138 63 0.2 1 56 7 139 49 0.2 1 46 3 140 36 0.2 1 28 8 141 27 0.2 1 20 7 142 11 0.2 1 8 3 143 11 0.2 1 10 1 144 9 0.2 1 4 5 145 13 0.2 1 10 3 146 15 0.2 1 11 4 147 27 0.2 1 25 2 148 26 0.2 1 23 3 149 15 0.2 1 15 150 143 0.2 1 117 26 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_32psu_2_S6_L002_R1_001.fastq.gz ============================================= 12868767 sequences processed in total