SUMMARISING RUN PARAMETERS ========================== Input filename: Geoduck-NMP-gDNA-8to10kb-7_S28_L007_R2_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-8to10kb-7_S28_L007_R2_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 11519.76 s (31 us/read; 1.94 M reads/minute). === Summary === Total reads processed: 372,443,998 Reads with adapters: 86,031,637 (23.1%) Reads written (passing filters): 372,443,998 (100.0%) Total basepairs processed: 44,070,726,638 bp Quality-trimmed: 3,699,118,639 bp (8.4%) Total written (filtered): 40,140,473,061 bp (91.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 86031637 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 31.1% C: 25.7% G: 14.0% T: 28.7% none/other: 0.5% Overview of removed sequences length count expect max.err error counts 1 62932164 93110999.5 0 62932164 2 15763308 23277749.9 0 15763308 3 3630638 5819437.5 0 3630638 4 1390758 1454859.4 0 1390758 5 285910 363714.8 0 285910 6 44754 90928.7 0 44754 7 38813 22732.2 0 38813 8 20281 5683.0 0 20281 9 5803 1420.8 0 3248 2555 10 22842 355.2 1 10314 12528 11 7097 88.8 1 2587 4510 12 14537 22.2 1 8636 5901 13 8112 5.5 1 4006 4106 14 35258 5.5 1 23275 11983 15 8916 5.5 1 5616 3300 16 6571 5.5 1 3537 3034 17 22095 5.5 1 14704 7391 18 3434 5.5 1 1658 1776 19 17657 5.5 1 12293 5364 20 12174 5.5 1 8567 3607 21 1629 5.5 1 616 1013 22 2961 5.5 1 1350 1611 23 14038 5.5 1 9036 5002 24 39182 5.5 1 26291 12891 25 13711 5.5 1 9272 4439 26 17342 5.5 1 13161 4181 27 2021 5.5 1 943 1078 28 14623 5.5 1 9946 4677 29 2640 5.5 1 1295 1345 30 16676 5.5 1 11583 5093 31 3602 5.5 1 2029 1573 32 20314 5.5 1 14546 5768 33 30288 5.5 1 23871 6417 34 2494 5.5 1 1245 1249 35 8521 5.5 1 4770 3751 36 7839 5.5 1 4752 3087 37 15842 5.5 1 12063 3779 38 7963 5.5 1 4752 3211 39 9215 5.5 1 6785 2430 40 4028 5.5 1 2223 1805 41 15873 5.5 1 11121 4752 42 30172 5.5 1 21809 8363 43 4209 5.5 1 2597 1612 44 16612 5.5 1 11943 4669 45 31129 5.5 1 22916 8213 46 11543 5.5 1 8571 2972 47 4055 5.5 1 2446 1609 48 31668 5.5 1 23729 7939 49 17189 5.5 1 12774 4415 50 9119 5.5 1 5772 3347 51 65138 5.5 1 49833 15305 52 12546 5.5 1 8644 3902 53 9251 5.5 1 6606 2645 54 10466 5.5 1 8114 2352 55 18862 5.5 1 13995 4867 56 10545 5.5 1 7471 3074 57 15133 5.5 1 11674 3459 58 19812 5.5 1 15859 3953 59 13552 5.5 1 10570 2982 60 13377 5.5 1 10567 2810 61 13586 5.5 1 10694 2892 62 14919 5.5 1 11768 3151 63 18785 5.5 1 14930 3855 64 20603 5.5 1 16613 3990 65 22385 5.5 1 17978 4407 66 25310 5.5 1 19734 5576 67 122545 5.5 1 28400 94145 68 306243 5.5 1 220245 85998 69 170620 5.5 1 139154 31466 70 66147 5.5 1 41059 25088 71 39597 5.5 1 28654 10943 72 18236 5.5 1 12191 6045 73 12676 5.5 1 8334 4342 74 9031 5.5 1 5780 3251 75 8608 5.5 1 5441 3167 76 7710 5.5 1 4997 2713 77 7287 5.5 1 4520 2767 78 6991 5.5 1 4328 2663 79 6914 5.5 1 4285 2629 80 6958 5.5 1 4412 2546 81 6817 5.5 1 4218 2599 82 6801 5.5 1 4263 2538 83 6287 5.5 1 3921 2366 84 6764 5.5 1 4198 2566 85 6262 5.5 1 3900 2362 86 5621 5.5 1 3578 2043 87 5397 5.5 1 3301 2096 88 5517 5.5 1 3420 2097 89 5380 5.5 1 3324 2056 90 5498 5.5 1 3396 2102 91 5416 5.5 1 3352 2064 92 6135 5.5 1 3546 2589 93 5226 5.5 1 3157 2069 94 5214 5.5 1 3170 2044 95 4910 5.5 1 2896 2014 96 5787 5.5 1 3301 2486 97 4658 5.5 1 2861 1797 98 4423 5.5 1 2775 1648 99 4421 5.5 1 2733 1688 100 4728 5.5 1 3005 1723 101 4696 5.5 1 2980 1716 102 4631 5.5 1 2884 1747 103 4627 5.5 1 2978 1649 104 4455 5.5 1 2900 1555 105 4440 5.5 1 2915 1525 106 4348 5.5 1 2809 1539 107 4158 5.5 1 2724 1434 108 4226 5.5 1 2759 1467 109 4061 5.5 1 2764 1297 110 3891 5.5 1 2614 1277 111 3704 5.5 1 2459 1245 112 3625 5.5 1 2402 1223 113 3421 5.5 1 2240 1181 114 3391 5.5 1 2198 1193 115 3243 5.5 1 2162 1081 116 3133 5.5 1 2094 1039 117 3019 5.5 1 1990 1029 118 3016 5.5 1 2046 970 119 2881 5.5 1 1921 960 120 2800 5.5 1 1868 932 121 2480 5.5 1 1659 821 122 2424 5.5 1 1627 797 123 2289 5.5 1 1471 818 124 2268 5.5 1 1465 803 125 2002 5.5 1 1317 685 126 1918 5.5 1 1288 630 127 1741 5.5 1 1176 565 128 1688 5.5 1 1184 504 129 1359 5.5 1 866 493 130 1280 5.5 1 897 383 131 995 5.5 1 651 344 132 906 5.5 1 595 311 133 807 5.5 1 505 302 134 775 5.5 1 513 262 135 707 5.5 1 449 258 136 706 5.5 1 460 246 137 590 5.5 1 364 226 138 545 5.5 1 347 198 139 553 5.5 1 330 223 140 500 5.5 1 294 206 141 463 5.5 1 260 203 142 455 5.5 1 232 223 143 475 5.5 1 214 261 144 497 5.5 1 200 297 145 487 5.5 1 195 292 146 554 5.5 1 218 336 147 759 5.5 1 277 482 148 2280 5.5 1 798 1482 149 6141 5.5 1 2138 4003 150 28266 5.5 1 10082 18184 151 6246 5.5 1 2158 4088 RUN STATISTICS FOR INPUT FILE: Geoduck-NMP-gDNA-8to10kb-7_S28_L007_R2_001.fastq.gz ============================================= 372443998 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 372443998 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 90957756 (24.42%)