SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_5_S6_L002_R1_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; 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 Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_01/20181211_metagenomics_trimmed_fastqc --threads 16 Output file will be GZIP compressed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA Library_Geoduck_MG_5_S6_L002_R1_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 2451.22 s (34 us/read; 1.77 M reads/minute). === Summary === Total reads processed: 72,142,506 Reads with adapters: 31,733,399 (44.0%) Reads written (passing filters): 72,142,506 (100.0%) Total basepairs processed: 10,893,518,406 bp Quality-trimmed: 182,199,295 bp (1.7%) Total written (filtered): 9,783,609,794 bp (89.8%) === Adapter 1 === Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 31733399 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 17.6% C: 32.3% G: 22.3% T: 27.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 9833737 18035626.5 0 9833737 2 2999659 4508906.6 0 2999659 3 844695 1127226.7 0 844695 4 358458 281806.7 0 358458 5 233858 70451.7 0 233858 6 138002 17612.9 0 138002 7 141418 4403.2 0 141418 8 150631 1100.8 0 150631 9 177638 275.2 0 176450 1188 10 126523 68.8 1 121480 5043 11 152994 17.2 1 147475 5519 12 190226 4.3 1 182986 7240 13 206023 4.3 1 199191 6832 14 171362 4.3 1 165850 5512 15 217361 4.3 1 210051 7310 16 189085 4.3 1 181932 7153 17 185794 4.3 1 180385 5409 18 160865 4.3 1 155933 4932 19 108848 4.3 1 105686 3162 20 146247 4.3 1 140767 5480 21 194372 4.3 1 186033 8339 22 192197 4.3 1 186412 5785 23 162000 4.3 1 157253 4747 24 169958 4.3 1 165887 4071 25 198714 4.3 1 193609 5105 26 214676 4.3 1 208712 5964 27 260822 4.3 1 254664 6158 28 100855 4.3 1 97860 2995 29 166673 4.3 1 162076 4597 30 134446 4.3 1 131766 2680 31 117193 4.3 1 114120 3073 32 162194 4.3 1 158800 3394 33 150086 4.3 1 146800 3286 34 169907 4.3 1 166442 3465 35 210457 4.3 1 204885 5572 36 246020 4.3 1 239382 6638 37 182412 4.3 1 179066 3346 38 130670 4.3 1 127768 2902 39 155875 4.3 1 151782 4093 40 169586 4.3 1 164900 4686 41 132785 4.3 1 128879 3906 42 146511 4.3 1 142064 4447 43 284956 4.3 1 277416 7540 44 99308 4.3 1 96832 2476 45 394462 4.3 1 387839 6623 46 36755 4.3 1 35031 1724 47 174118 4.3 1 171161 2957 48 167799 4.3 1 164855 2944 49 167893 4.3 1 164870 3023 50 123538 4.3 1 120717 2821 51 120305 4.3 1 117576 2729 52 112322 4.3 1 110111 2211 53 160808 4.3 1 157183 3625 54 218609 4.3 1 213394 5215 55 292218 4.3 1 286594 5624 56 164816 4.3 1 161751 3065 57 138962 4.3 1 136362 2600 58 178897 4.3 1 175592 3305 59 172817 4.3 1 169923 2894 60 131124 4.3 1 128758 2366 61 115464 4.3 1 113289 2175 62 98925 4.3 1 96912 2013 63 150849 4.3 1 147380 3469 64 175307 4.3 1 171833 3474 65 180494 4.3 1 176840 3654 66 228477 4.3 1 224252 4225 67 202051 4.3 1 198354 3697 68 213709 4.3 1 209582 4127 69 228216 4.3 1 223672 4544 70 246543 4.3 1 241730 4813 71 362823 4.3 1 356208 6615 72 3867212 4.3 1 3845188 22024 73 761150 4.3 1 754576 6574 74 166715 4.3 1 164768 1947 75 64897 4.3 1 63809 1088 76 43443 4.3 1 42471 972 77 43249 4.3 1 42250 999 78 36989 4.3 1 36133 856 79 33052 4.3 1 32237 815 80 29008 4.3 1 28319 689 81 25256 4.3 1 24612 644 82 22598 4.3 1 22015 583 83 24044 4.3 1 23447 597 84 26648 4.3 1 25910 738 85 30827 4.3 1 30159 668 86 31886 4.3 1 31149 737 87 32642 4.3 1 31852 790 88 31909 4.3 1 31205 704 89 29127 4.3 1 28420 707 90 23594 4.3 1 22921 673 91 18651 4.3 1 18107 544 92 15502 4.3 1 15050 452 93 15637 4.3 1 15166 471 94 18011 4.3 1 17438 573 95 23082 4.3 1 22488 594 96 27499 4.3 1 26854 645 97 28133 4.3 1 27449 684 98 26576 4.3 1 25950 626 99 23562 4.3 1 22979 583 100 20601 4.3 1 20056 545 101 17318 4.3 1 16846 472 102 21484 4.3 1 21036 448 103 13333 4.3 1 12948 385 104 13506 4.3 1 13054 452 105 18165 4.3 1 17678 487 106 23200 4.3 1 22574 626 107 25746 4.3 1 25157 589 108 23846 4.3 1 23219 627 109 20651 4.3 1 20039 612 110 16853 4.3 1 16352 501 111 13534 4.3 1 13127 407 112 10621 4.3 1 10266 355 113 9008 4.3 1 8730 278 114 10237 4.3 1 9870 367 115 13508 4.3 1 13106 402 116 15797 4.3 1 15367 430 117 15162 4.3 1 14754 408 118 13440 4.3 1 13070 370 119 10422 4.3 1 10080 342 120 8152 4.3 1 7842 310 121 7333 4.3 1 7020 313 122 6850 4.3 1 6578 272 123 6332 4.3 1 6053 279 124 5153 4.3 1 4902 251 125 1214 4.3 1 1033 181 126 443 4.3 1 278 165 127 367 4.3 1 185 182 128 287 4.3 1 113 174 129 249 4.3 1 61 188 130 297 4.3 1 62 235 131 250 4.3 1 45 205 132 262 4.3 1 47 215 133 212 4.3 1 29 183 134 254 4.3 1 20 234 135 206 4.3 1 7 199 136 189 4.3 1 8 181 137 197 4.3 1 4 193 138 230 4.3 1 6 224 139 207 4.3 1 6 201 140 198 4.3 1 4 194 141 231 4.3 1 7 224 142 343 4.3 1 14 329 143 812 4.3 1 14 798 144 190 4.3 1 1 189 145 207 4.3 1 1 206 146 114 4.3 1 0 114 147 168 4.3 1 0 168 148 401 4.3 1 2 399 149 177 4.3 1 1 176 150 97 4.3 1 0 97 151 48 4.3 1 3 45 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_5_S6_L002_R1_001.fastq.gz ============================================= 72142506 sequences processed in total