SUMMARISING RUN PARAMETERS ========================== Input filename: Geoduck-NMP-gDNA-2to4kb-4_S14_L004_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: '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 Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/20180328_fastqc_trimmed_hiseq_geoduck --threads 28 Output file will be GZIP compressed This is cutadapt 1.16 with Python 2.7.14 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC Geoduck-NMP-gDNA-2to4kb-4_S14_L004_R1_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 11149.52 s (31 us/read; 1.94 M reads/minute). === Summary === Total reads processed: 360,317,079 Reads with adapters: 80,220,248 (22.3%) Reads written (passing filters): 360,317,079 (100.0%) Total basepairs processed: 43,967,642,352 bp Quality-trimmed: 1,560,685,314 bp (3.5%) Total written (filtered): 42,238,637,269 bp (96.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 80220248 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 32.7% C: 23.8% G: 13.9% T: 29.5% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 60338788 90079269.8 0 60338788 2 13605218 22519817.4 0 13605218 3 3509248 5629954.4 0 3509248 4 1388109 1407488.6 0 1388109 5 269107 351872.1 0 269107 6 38516 87968.0 0 38516 7 24597 21992.0 0 24597 8 13084 5498.0 0 13084 9 3788 1374.5 0 1722 2066 10 15707 343.6 1 5942 9765 11 4631 85.9 1 1305 3326 12 9306 21.5 1 5226 4080 13 10308 5.4 1 6011 4297 14 7214 5.4 1 4454 2760 15 9487 5.4 1 5666 3821 16 7360 5.4 1 4595 2765 17 5695 5.4 1 2558 3137 18 17902 5.4 1 11159 6743 19 16909 5.4 1 12269 4640 20 3927 5.4 1 1688 2239 21 2448 5.4 1 1009 1439 22 11394 5.4 1 7038 4356 23 8390 5.4 1 5384 3006 24 11059 5.4 1 7864 3195 25 5527 5.4 1 2843 2684 26 7450 5.4 1 4873 2577 27 9300 5.4 1 5970 3330 28 16610 5.4 1 11225 5385 29 3060 5.4 1 1401 1659 30 8133 5.4 1 4772 3361 31 11251 5.4 1 7831 3420 32 11086 5.4 1 7279 3807 33 7409 5.4 1 4966 2443 34 18112 5.4 1 12473 5639 35 3598 5.4 1 1708 1890 36 10948 5.4 1 6916 4032 37 9972 5.4 1 6855 3117 38 12068 5.4 1 8008 4060 39 10475 5.4 1 7070 3405 40 7730 5.4 1 5298 2432 41 15577 5.4 1 10426 5151 42 14206 5.4 1 9693 4513 43 13143 5.4 1 9768 3375 44 9748 5.4 1 6353 3395 45 3463 5.4 1 1943 1520 46 5989 5.4 1 4121 1868 47 3489 5.4 1 1874 1615 48 12721 5.4 1 8917 3804 49 12876 5.4 1 9453 3423 50 4344 5.4 1 2587 1757 51 8241 5.4 1 5807 2434 52 14678 5.4 1 10804 3874 53 10691 5.4 1 7559 3132 54 6585 5.4 1 4001 2584 55 22691 5.4 1 17087 5604 56 12588 5.4 1 9530 3058 57 8760 5.4 1 6001 2759 58 7707 5.4 1 5513 2194 59 16258 5.4 1 12946 3312 60 4532 5.4 1 2802 1730 61 2863 5.4 1 1719 1144 62 14085 5.4 1 10944 3141 63 7437 5.4 1 4926 2511 64 6375 5.4 1 4354 2021 65 8460 5.4 1 6271 2189 66 22175 5.4 1 17281 4894 67 10442 5.4 1 7941 2501 68 9244 5.4 1 6990 2254 69 10026 5.4 1 7687 2339 70 9896 5.4 1 7644 2252 71 10434 5.4 1 8167 2267 72 11523 5.4 1 8923 2600 73 12491 5.4 1 9955 2536 74 13421 5.4 1 10746 2675 75 23025 5.4 1 15119 7906 76 58275 5.4 1 51215 7060 77 34068 5.4 1 29418 4650 78 19389 5.4 1 15709 3680 79 12783 5.4 1 9957 2826 80 9794 5.4 1 7282 2512 81 7950 5.4 1 5779 2171 82 7225 5.4 1 5102 2123 83 6698 5.4 1 4721 1977 84 6438 5.4 1 4485 1953 85 6426 5.4 1 4408 2018 86 6221 5.4 1 4277 1944 87 6176 5.4 1 4261 1915 88 6119 5.4 1 4198 1921 89 5828 5.4 1 3925 1903 90 5873 5.4 1 4054 1819 91 5786 5.4 1 3959 1827 92 5637 5.4 1 3802 1835 93 5482 5.4 1 3764 1718 94 5299 5.4 1 3668 1631 95 5376 5.4 1 3657 1719 96 5158 5.4 1 3560 1598 97 5088 5.4 1 3510 1578 98 5111 5.4 1 3454 1657 99 4842 5.4 1 3330 1512 100 4810 5.4 1 3333 1477 101 4645 5.4 1 3175 1470 102 4645 5.4 1 3210 1435 103 4531 5.4 1 3152 1379 104 4251 5.4 1 2924 1327 105 4186 5.4 1 2897 1289 106 4246 5.4 1 3014 1232 107 4096 5.4 1 2835 1261 108 3968 5.4 1 2782 1186 109 3865 5.4 1 2738 1127 110 3704 5.4 1 2601 1103 111 3388 5.4 1 2329 1059 112 3440 5.4 1 2398 1042 113 3310 5.4 1 2321 989 114 3078 5.4 1 2196 882 115 3117 5.4 1 2226 891 116 2949 5.4 1 2077 872 117 2757 5.4 1 1966 791 118 2541 5.4 1 1804 737 119 2416 5.4 1 1735 681 120 2306 5.4 1 1624 682 121 2288 5.4 1 1583 705 122 2058 5.4 1 1438 620 123 1907 5.4 1 1317 590 124 1907 5.4 1 1342 565 125 1725 5.4 1 1237 488 126 1458 5.4 1 1056 402 127 1372 5.4 1 1025 347 128 1171 5.4 1 916 255 129 937 5.4 1 713 224 130 782 5.4 1 614 168 131 646 5.4 1 506 140 132 565 5.4 1 430 135 133 517 5.4 1 413 104 134 485 5.4 1 356 129 135 428 5.4 1 307 121 136 362 5.4 1 247 115 137 298 5.4 1 193 105 138 277 5.4 1 187 90 139 274 5.4 1 167 107 140 271 5.4 1 147 124 141 283 5.4 1 136 147 142 200 5.4 1 95 105 143 223 5.4 1 126 97 144 255 5.4 1 128 127 145 269 5.4 1 130 139 146 341 5.4 1 178 163 147 424 5.4 1 224 200 148 731 5.4 1 408 323 149 1575 5.4 1 862 713 150 5215 5.4 1 2875 2340 151 2608 5.4 1 1396 1212 RUN STATISTICS FOR INPUT FILE: Geoduck-NMP-gDNA-2to4kb-4_S14_L004_R1_001.fastq.gz ============================================= 360317079 sequences processed in total