SUMMARISING RUN PARAMETERS ========================== Input filename: Geoduck-NMP-gDNA-2to4kb-3_S10_L003_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-2to4kb-3_S10_L003_R2_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 11944.54 s (34 us/read; 1.79 M reads/minute). === Summary === Total reads processed: 355,466,683 Reads with adapters: 87,792,091 (24.7%) Reads written (passing filters): 355,466,683 (100.0%) Total basepairs processed: 44,550,696,710 bp Quality-trimmed: 3,599,479,756 bp (8.1%) Total written (filtered): 40,651,166,533 bp (91.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 87792091 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 31.7% C: 25.5% G: 14.1% T: 28.5% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 64078764 88866670.8 0 64078764 2 14923642 22216667.7 0 14923642 3 3682921 5554166.9 0 3682921 4 1291006 1388541.7 0 1291006 5 279128 347135.4 0 279128 6 66199 86783.9 0 66199 7 75229 21696.0 0 75229 8 41159 5424.0 0 41159 9 10758 1356.0 0 7896 2862 10 45248 339.0 1 22852 22396 11 16906 84.7 1 6712 10194 12 34689 21.2 1 19362 15327 13 18824 5.3 1 9127 9697 14 78209 5.3 1 50301 27908 15 19623 5.3 1 11660 7963 16 13639 5.3 1 7164 6475 17 46412 5.3 1 30477 15935 18 7329 5.3 1 3587 3742 19 37076 5.3 1 24716 12360 20 24264 5.3 1 15777 8487 21 3829 5.3 1 1472 2357 22 6866 5.3 1 3066 3800 23 30775 5.3 1 18949 11826 24 90660 5.3 1 59176 31484 25 31622 5.3 1 20548 11074 26 36912 5.3 1 26064 10848 27 5139 5.3 1 2480 2659 28 35810 5.3 1 23572 12238 29 6880 5.3 1 3377 3503 30 43337 5.3 1 28840 14497 31 8677 5.3 1 4820 3857 32 48625 5.3 1 33493 15132 33 63118 5.3 1 47066 16052 34 6125 5.3 1 3004 3121 35 22130 5.3 1 12368 9762 36 21874 5.3 1 13264 8610 37 35345 5.3 1 25768 9577 38 19950 5.3 1 12158 7792 39 20417 5.3 1 14266 6151 40 9236 5.3 1 5165 4071 41 37033 5.3 1 25164 11869 42 73083 5.3 1 51256 21827 43 9847 5.3 1 6041 3806 44 39673 5.3 1 27486 12187 45 80374 5.3 1 56800 23574 46 27604 5.3 1 18970 8634 47 9432 5.3 1 5650 3782 48 76424 5.3 1 55491 20933 49 40499 5.3 1 29089 11410 50 20532 5.3 1 13290 7242 51 164629 5.3 1 123228 41401 52 31635 5.3 1 21269 10366 53 23913 5.3 1 16745 7168 54 23961 5.3 1 17767 6194 55 45427 5.3 1 33255 12172 56 28357 5.3 1 20081 8276 57 37627 5.3 1 28557 9070 58 46873 5.3 1 36119 10754 59 33581 5.3 1 25569 8012 60 33588 5.3 1 25684 7904 61 35038 5.3 1 27102 7936 62 39024 5.3 1 30111 8913 63 49081 5.3 1 38457 10624 64 55419 5.3 1 43950 11469 65 60451 5.3 1 48730 11721 66 65618 5.3 1 53678 11940 67 98489 5.3 1 77551 20938 68 345375 5.3 1 314032 31343 69 154747 5.3 1 139923 14824 70 53520 5.3 1 44552 8968 71 32944 5.3 1 26511 6433 72 21067 5.3 1 15914 5153 73 18576 5.3 1 13666 4910 74 15816 5.3 1 11395 4421 75 15769 5.3 1 11103 4666 76 15095 5.3 1 10546 4549 77 14371 5.3 1 9853 4518 78 13542 5.3 1 9409 4133 79 13707 5.3 1 9230 4477 80 13900 5.3 1 9516 4384 81 14165 5.3 1 9489 4676 82 13732 5.3 1 9122 4610 83 13559 5.3 1 9059 4500 84 13247 5.3 1 8844 4403 85 13096 5.3 1 8642 4454 86 12572 5.3 1 8384 4188 87 11844 5.3 1 7806 4038 88 11934 5.3 1 7874 4060 89 11495 5.3 1 7585 3910 90 11441 5.3 1 7640 3801 91 11154 5.3 1 7434 3720 92 10485 5.3 1 6806 3679 93 10116 5.3 1 6716 3400 94 10562 5.3 1 6958 3604 95 9612 5.3 1 6354 3258 96 10091 5.3 1 6644 3447 97 10001 5.3 1 6618 3383 98 9704 5.3 1 6423 3281 99 9745 5.3 1 6358 3387 100 10152 5.3 1 6817 3335 101 9939 5.3 1 6720 3219 102 9854 5.3 1 6597 3257 103 10042 5.3 1 6803 3239 104 9737 5.3 1 6574 3163 105 9511 5.3 1 6365 3146 106 9287 5.3 1 6263 3024 107 8914 5.3 1 6068 2846 108 8557 5.3 1 5785 2772 109 8447 5.3 1 5733 2714 110 8098 5.3 1 5504 2594 111 8075 5.3 1 5503 2572 112 7756 5.3 1 5264 2492 113 7572 5.3 1 5208 2364 114 7358 5.3 1 4978 2380 115 7022 5.3 1 4746 2276 116 6628 5.3 1 4533 2095 117 6561 5.3 1 4374 2187 118 6279 5.3 1 4271 2008 119 6078 5.3 1 4145 1933 120 5607 5.3 1 3858 1749 121 5247 5.3 1 3524 1723 122 5119 5.3 1 3459 1660 123 4655 5.3 1 3156 1499 124 4339 5.3 1 2930 1409 125 3917 5.3 1 2649 1268 126 3691 5.3 1 2445 1246 127 2957 5.3 1 1874 1083 128 2546 5.3 1 1606 940 129 2074 5.3 1 1273 801 130 1729 5.3 1 1024 705 131 1292 5.3 1 749 543 132 1126 5.3 1 645 481 133 961 5.3 1 523 438 134 787 5.3 1 437 350 135 618 5.3 1 324 294 136 463 5.3 1 229 234 137 432 5.3 1 199 233 138 281 5.3 1 128 153 139 244 5.3 1 112 132 140 173 5.3 1 60 113 141 139 5.3 1 45 94 142 117 5.3 1 40 77 143 129 5.3 1 36 93 144 132 5.3 1 41 91 145 109 5.3 1 31 78 146 114 5.3 1 36 78 147 142 5.3 1 49 93 148 278 5.3 1 127 151 149 685 5.3 1 334 351 150 2763 5.3 1 1481 1282 151 810 5.3 1 409 401 RUN STATISTICS FOR INPUT FILE: Geoduck-NMP-gDNA-2to4kb-3_S10_L003_R2_001.fastq.gz ============================================= 355466683 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 355466683 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 71185899 (20.03%)