SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_32psu_4_S4_L002_R1_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.6.4_dev Cutadapt version: 2.4 Python version: could not detect Number of cores used for trimming: 8 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Using Illumina adapter for trimming (count: 426581). Second best hit was Nextera (count: 0) 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 All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /gscratch/scrubbed/strigg/analyses/20200427/TG_PE_FASTQS/FastQC --threads 28 Output file will be GZIP compressed This is cutadapt 2.4 with Python 3.7.6 Command line parameters: -j 8 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_32psu_4_S4_L002_R1_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 64.35 s (4 us/read; 14.54 M reads/minute). === Summary === Total reads processed: 15,591,852 Reads with adapters: 11,241,936 (72.1%) Reads written (passing filters): 15,591,852 (100.0%) Total basepairs processed: 2,338,777,800 bp Quality-trimmed: 7,762,195 bp (0.3%) Total written (filtered): 1,950,418,217 bp (83.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11241936 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 31.8% C: 13.2% G: 19.5% T: 35.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2728314 3897963.0 0 2728314 2 352949 974490.8 0 352949 3 189042 243622.7 0 189042 4 110295 60905.7 0 110295 5 86754 15226.4 0 86754 6 84318 3806.6 0 84318 7 67898 951.7 0 67898 8 84774 237.9 0 84774 9 86162 59.5 0 85323 839 10 77737 14.9 1 73221 4516 11 88459 3.7 1 81353 7106 12 84258 0.9 1 78502 5756 13 83829 0.2 1 77646 6183 14 87427 0.2 1 80554 6873 15 88669 0.2 1 82188 6481 16 87155 0.2 1 79865 7290 17 108105 0.2 1 98581 9524 18 88189 0.2 1 82109 6080 19 75841 0.2 1 70534 5307 20 90690 0.2 1 84354 6336 21 100155 0.2 1 92424 7731 22 84109 0.2 1 78568 5541 23 100437 0.2 1 93211 7226 24 89008 0.2 1 81375 7633 25 97433 0.2 1 90437 6996 26 86900 0.2 1 81328 5572 27 98051 0.2 1 90237 7814 28 106220 0.2 1 97819 8401 29 94302 0.2 1 86322 7980 30 107823 0.2 1 101345 6478 31 77079 0.2 1 71662 5417 32 102558 0.2 1 95070 7488 33 91366 0.2 1 84409 6957 34 99532 0.2 1 91471 8061 35 107666 0.2 1 99772 7894 36 89079 0.2 1 83528 5551 37 100059 0.2 1 92531 7528 38 104683 0.2 1 96200 8483 39 105342 0.2 1 97340 8002 40 103603 0.2 1 95197 8406 41 116472 0.2 1 105109 11363 42 91799 0.2 1 84082 7717 43 151482 0.2 1 141550 9932 44 48893 0.2 1 44323 4570 45 107330 0.2 1 98158 9172 46 169588 0.2 1 157239 12349 47 115292 0.2 1 107496 7796 48 81237 0.2 1 73490 7747 49 158364 0.2 1 148089 10275 50 62839 0.2 1 58050 4789 51 90568 0.2 1 83874 6694 52 192734 0.2 1 181187 11547 53 137640 0.2 1 130713 6927 54 59884 0.2 1 55438 4446 55 102380 0.2 1 96895 5485 56 71739 0.2 1 66587 5152 57 121813 0.2 1 115448 6365 58 43981 0.2 1 41008 2973 59 41261 0.2 1 37490 3771 60 111430 0.2 1 105252 6178 61 87063 0.2 1 82619 4444 62 47900 0.2 1 44309 3591 63 85477 0.2 1 80258 5219 64 72824 0.2 1 68588 4236 65 60641 0.2 1 56399 4242 66 87315 0.2 1 81607 5708 67 100034 0.2 1 92897 7137 68 160033 0.2 1 150907 9126 69 87754 0.2 1 82192 5562 70 34259 0.2 1 30999 3260 71 22148 0.2 1 20058 2090 72 59270 0.2 1 55764 3506 73 72359 0.2 1 68127 4232 74 73545 0.2 1 68961 4584 75 72172 0.2 1 67396 4776 76 70342 0.2 1 65617 4725 77 69830 0.2 1 65084 4746 78 66115 0.2 1 61597 4518 79 64360 0.2 1 60010 4350 80 63230 0.2 1 58997 4233 81 61274 0.2 1 57172 4102 82 59014 0.2 1 55084 3930 83 57125 0.2 1 53358 3767 84 54574 0.2 1 50808 3766 85 52527 0.2 1 48940 3587 86 50257 0.2 1 46911 3346 87 48208 0.2 1 45026 3182 88 45866 0.2 1 42781 3085 89 44045 0.2 1 41050 2995 90 43438 0.2 1 40512 2926 91 40328 0.2 1 37640 2688 92 38164 0.2 1 35615 2549 93 35352 0.2 1 32983 2369 94 33785 0.2 1 31458 2327 95 31871 0.2 1 29668 2203 96 29463 0.2 1 27470 1993 97 27711 0.2 1 25891 1820 98 25451 0.2 1 23610 1841 99 24415 0.2 1 22590 1825 100 21725 0.2 1 20167 1558 101 20433 0.2 1 19008 1425 102 18660 0.2 1 17274 1386 103 16794 0.2 1 15616 1178 104 15844 0.2 1 14677 1167 105 14021 0.2 1 13036 985 106 12448 0.2 1 11562 886 107 11573 0.2 1 10706 867 108 10412 0.2 1 9602 810 109 8989 0.2 1 8297 692 110 8150 0.2 1 7523 627 111 7254 0.2 1 6680 574 112 6183 0.2 1 5709 474 113 5353 0.2 1 4937 416 114 4766 0.2 1 4364 402 115 4132 0.2 1 3707 425 116 3477 0.2 1 3165 312 117 3036 0.2 1 2738 298 118 2618 0.2 1 2398 220 119 2115 0.2 1 1918 197 120 1769 0.2 1 1599 170 121 1495 0.2 1 1327 168 122 1258 0.2 1 1133 125 123 1079 0.2 1 967 112 124 920 0.2 1 808 112 125 777 0.2 1 674 103 126 681 0.2 1 592 89 127 553 0.2 1 494 59 128 387 0.2 1 336 51 129 401 0.2 1 353 48 130 291 0.2 1 256 35 131 270 0.2 1 235 35 132 242 0.2 1 222 20 133 268 0.2 1 225 43 134 327 0.2 1 297 30 135 148 0.2 1 131 17 136 79 0.2 1 65 14 137 63 0.2 1 55 8 138 35 0.2 1 28 7 139 28 0.2 1 22 6 140 22 0.2 1 20 2 141 16 0.2 1 14 2 142 13 0.2 1 11 2 143 16 0.2 1 11 5 144 10 0.2 1 5 5 145 13 0.2 1 8 5 146 16 0.2 1 12 4 147 29 0.2 1 25 4 148 26 0.2 1 23 3 149 19 0.2 1 18 1 150 167 0.2 1 150 17 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_32psu_4_S4_L002_R1_001.fastq.gz ============================================= 15591852 sequences processed in total