SUMMARISING RUN PARAMETERS ========================== Input filename: Geoduck-NMP-gDNA-2_S5_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: '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-2_S5_L002_R1_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 11570.25 s (31 us/read; 1.96 M reads/minute). === Summary === Total reads processed: 377,072,437 Reads with adapters: 81,687,193 (21.7%) Reads written (passing filters): 377,072,437 (100.0%) Total basepairs processed: 45,779,442,385 bp Quality-trimmed: 1,582,148,221 bp (3.5%) Total written (filtered): 44,038,626,908 bp (96.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 81687193 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 34.4% C: 22.3% G: 13.9% T: 29.3% none/other: 0.2% Overview of removed sequences length count expect max.err error counts 1 61748741 94268109.2 0 61748741 2 13647943 23567027.3 0 13647943 3 3649207 5891756.8 0 3649207 4 1523738 1472939.2 0 1523738 5 288184 368234.8 0 288184 6 36201 92058.7 0 36201 7 17928 23014.7 0 17928 8 9237 5753.7 0 9237 9 3201 1438.4 0 1055 2146 10 12776 359.6 1 3950 8826 11 3231 89.9 1 717 2514 12 6049 22.5 1 3462 2587 13 6707 5.6 1 4038 2669 14 4631 5.6 1 2944 1687 15 6219 5.6 1 3847 2372 16 4777 5.6 1 3116 1661 17 3230 5.6 1 1419 1811 18 10287 5.6 1 6511 3776 19 12285 5.6 1 9157 3128 20 2004 5.6 1 829 1175 21 1516 5.6 1 655 861 22 7405 5.6 1 4683 2722 23 5127 5.6 1 3354 1773 24 7828 5.6 1 5655 2173 25 2924 5.6 1 1440 1484 26 5004 5.6 1 3347 1657 27 5857 5.6 1 3865 1992 28 10568 5.6 1 7259 3309 29 2009 5.6 1 886 1123 30 4302 5.6 1 2524 1778 31 6663 5.6 1 4881 1782 32 5841 5.6 1 3866 1975 33 5482 5.6 1 3695 1787 34 6718 5.6 1 4455 2263 35 5039 5.6 1 2658 2381 36 16294 5.6 1 11080 5214 37 5912 5.6 1 3728 2184 38 3485 5.6 1 2305 1180 39 9356 5.6 1 6775 2581 40 7977 5.6 1 5877 2100 41 6049 5.6 1 4558 1491 42 5994 5.6 1 4040 1954 43 2050 5.6 1 1099 951 44 3741 5.6 1 2611 1130 45 1976 5.6 1 1028 948 46 7799 5.6 1 5485 2314 47 8110 5.6 1 6076 2034 48 2264 5.6 1 1287 977 49 5157 5.6 1 3643 1514 50 9233 5.6 1 6953 2280 51 6518 5.6 1 4694 1824 52 3591 5.6 1 2189 1402 53 13144 5.6 1 9964 3180 54 7954 5.6 1 5990 1964 55 5005 5.6 1 3457 1548 56 4581 5.6 1 3177 1404 57 10323 5.6 1 8315 2008 58 2673 5.6 1 1627 1046 59 1771 5.6 1 1034 737 60 8790 5.6 1 6742 2048 61 4077 5.6 1 2665 1412 62 3532 5.6 1 2365 1167 63 5386 5.6 1 3939 1447 64 12584 5.6 1 9818 2766 65 5910 5.6 1 4504 1406 66 5404 5.6 1 4009 1395 67 5878 5.6 1 4453 1425 68 5853 5.6 1 4401 1452 69 6281 5.6 1 4763 1518 70 6802 5.6 1 5241 1561 71 7174 5.6 1 5486 1688 72 8350 5.6 1 6163 2187 73 36176 5.6 1 8496 27680 74 59933 5.6 1 35492 24441 75 35724 5.6 1 22371 13353 76 19621 5.6 1 11210 8411 77 13076 5.6 1 7680 5396 78 9304 5.6 1 5531 3773 79 7025 5.6 1 4215 2810 80 6051 5.6 1 3736 2315 81 5340 5.6 1 3342 1998 82 4789 5.6 1 3022 1767 83 4765 5.6 1 2946 1819 84 4638 5.6 1 2933 1705 85 4426 5.6 1 2852 1574 86 4428 5.6 1 2863 1565 87 4127 5.6 1 2645 1482 88 4200 5.6 1 2739 1461 89 4029 5.6 1 2609 1420 90 3985 5.6 1 2603 1382 91 3987 5.6 1 2626 1361 92 3741 5.6 1 2468 1273 93 3638 5.6 1 2368 1270 94 3605 5.6 1 2420 1185 95 3546 5.6 1 2378 1168 96 3446 5.6 1 2305 1141 97 3319 5.6 1 2227 1092 98 3342 5.6 1 2193 1149 99 3254 5.6 1 2144 1110 100 3181 5.6 1 2129 1052 101 3274 5.6 1 2166 1108 102 3017 5.6 1 2050 967 103 2999 5.6 1 2037 962 104 2841 5.6 1 1952 889 105 2819 5.6 1 1907 912 106 2722 5.6 1 1866 856 107 2638 5.6 1 1769 869 108 2607 5.6 1 1739 868 109 2485 5.6 1 1690 795 110 2488 5.6 1 1692 796 111 2393 5.6 1 1610 783 112 2358 5.6 1 1599 759 113 2157 5.6 1 1466 691 114 2100 5.6 1 1414 686 115 2037 5.6 1 1351 686 116 1874 5.6 1 1271 603 117 1977 5.6 1 1313 664 118 1758 5.6 1 1227 531 119 1758 5.6 1 1151 607 120 1716 5.6 1 1152 564 121 1536 5.6 1 1046 490 122 1376 5.6 1 907 469 123 1365 5.6 1 904 461 124 1265 5.6 1 845 420 125 1253 5.6 1 856 397 126 1069 5.6 1 697 372 127 984 5.6 1 675 309 128 884 5.6 1 623 261 129 721 5.6 1 489 232 130 629 5.6 1 400 229 131 606 5.6 1 390 216 132 542 5.6 1 357 185 133 537 5.6 1 356 181 134 539 5.6 1 342 197 135 474 5.6 1 280 194 136 400 5.6 1 226 174 137 369 5.6 1 193 176 138 370 5.6 1 194 176 139 359 5.6 1 165 194 140 326 5.6 1 120 206 141 358 5.6 1 137 221 142 361 5.6 1 132 229 143 436 5.6 1 155 281 144 459 5.6 1 190 269 145 537 5.6 1 172 365 146 681 5.6 1 212 469 147 1047 5.6 1 319 728 148 2274 5.6 1 664 1610 149 5755 5.6 1 1708 4047 150 19097 5.6 1 5563 13534 151 10033 5.6 1 2811 7222 RUN STATISTICS FOR INPUT FILE: Geoduck-NMP-gDNA-2_S5_L002_R1_001.fastq.gz ============================================= 377072437 sequences processed in total