SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_32psu_4_S8_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: 488601). 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/8C_32psu_4_S8_L002_R1_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 58.84 s (4 us/read; 14.90 M reads/minute). === Summary === Total reads processed: 14,607,942 Reads with adapters: 11,056,021 (75.7%) Reads written (passing filters): 14,607,942 (100.0%) Total basepairs processed: 2,191,191,300 bp Quality-trimmed: 9,138,103 bp (0.4%) Total written (filtered): 1,772,690,067 bp (80.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11056021 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.7% C: 11.8% G: 21.0% T: 36.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2179670 3651985.5 0 2179670 2 288357 912996.4 0 288357 3 156435 228249.1 0 156435 4 98004 57062.3 0 98004 5 83153 14265.6 0 83153 6 80849 3566.4 0 80849 7 66215 891.6 0 66215 8 83652 222.9 0 83652 9 81421 55.7 0 80631 790 10 76420 13.9 1 72069 4351 11 85164 3.5 1 78240 6924 12 81348 0.9 1 75711 5637 13 83598 0.2 1 77773 5825 14 83352 0.2 1 76916 6436 15 87371 0.2 1 80774 6597 16 86829 0.2 1 79522 7307 17 105942 0.2 1 96774 9168 18 88487 0.2 1 82567 5920 19 76290 0.2 1 70996 5294 20 90707 0.2 1 84433 6274 21 101596 0.2 1 93808 7788 22 84911 0.2 1 79523 5388 23 99744 0.2 1 92683 7061 24 90626 0.2 1 82850 7776 25 98474 0.2 1 91331 7143 26 89046 0.2 1 83387 5659 27 100470 0.2 1 92717 7753 28 97480 0.2 1 90362 7118 29 103196 0.2 1 94309 8887 30 114370 0.2 1 107320 7050 31 79392 0.2 1 73939 5453 32 105208 0.2 1 97664 7544 33 95289 0.2 1 88120 7169 34 103964 0.2 1 96266 7698 35 100819 0.2 1 93035 7784 36 104164 0.2 1 96092 8072 37 105927 0.2 1 98240 7687 38 112135 0.2 1 103582 8553 39 96387 0.2 1 90041 6346 40 110619 0.2 1 102036 8583 41 118329 0.2 1 106686 11643 42 106988 0.2 1 97227 9761 43 165097 0.2 1 154382 10715 44 56454 0.2 1 50914 5540 45 117022 0.2 1 106731 10291 46 248165 0.2 1 231776 16389 47 141744 0.2 1 132412 9332 48 71383 0.2 1 63944 7439 49 214966 0.2 1 202098 12868 50 67123 0.2 1 61729 5394 51 84537 0.2 1 77868 6669 52 227448 0.2 1 214969 12479 53 153876 0.2 1 146571 7305 54 58063 0.2 1 53681 4382 55 96470 0.2 1 91390 5080 56 61719 0.2 1 56899 4820 57 135082 0.2 1 128247 6835 58 34302 0.2 1 31774 2528 59 37018 0.2 1 33361 3657 60 120449 0.2 1 114261 6188 61 79440 0.2 1 75334 4106 62 40303 0.2 1 37043 3260 63 92254 0.2 1 86676 5578 64 78944 0.2 1 74628 4316 65 54545 0.2 1 50567 3978 66 92915 0.2 1 86970 5945 67 106337 0.2 1 98786 7551 68 178710 0.2 1 168688 10022 69 108665 0.2 1 102241 6424 70 43742 0.2 1 39918 3824 71 19154 0.2 1 17119 2035 72 62321 0.2 1 58726 3595 73 80997 0.2 1 76319 4678 74 82292 0.2 1 77235 5057 75 80453 0.2 1 75230 5223 76 78946 0.2 1 73647 5299 77 78496 0.2 1 73454 5042 78 73891 0.2 1 68991 4900 79 72359 0.2 1 67790 4569 80 70385 0.2 1 65644 4741 81 70687 0.2 1 66072 4615 82 67765 0.2 1 63360 4405 83 64119 0.2 1 59858 4261 84 61128 0.2 1 56996 4132 85 58834 0.2 1 54971 3863 86 56645 0.2 1 52920 3725 87 53397 0.2 1 50007 3390 88 52020 0.2 1 48563 3457 89 48843 0.2 1 45677 3166 90 48488 0.2 1 45284 3204 91 45775 0.2 1 42701 3074 92 42633 0.2 1 39741 2892 93 39061 0.2 1 36500 2561 94 37084 0.2 1 34707 2377 95 34306 0.2 1 31956 2350 96 31990 0.2 1 29804 2186 97 29916 0.2 1 28016 1900 98 27386 0.2 1 25513 1873 99 26105 0.2 1 24176 1929 100 23728 0.2 1 22014 1714 101 21360 0.2 1 19893 1467 102 19677 0.2 1 18296 1381 103 17691 0.2 1 16474 1217 104 16298 0.2 1 15194 1104 105 14499 0.2 1 13498 1001 106 13016 0.2 1 12109 907 107 11299 0.2 1 10529 770 108 10657 0.2 1 9906 751 109 9041 0.2 1 8358 683 110 8101 0.2 1 7484 617 111 7203 0.2 1 6631 572 112 6115 0.2 1 5677 438 113 5247 0.2 1 4830 417 114 4477 0.2 1 4092 385 115 3837 0.2 1 3499 338 116 3178 0.2 1 2885 293 117 2717 0.2 1 2476 241 118 2308 0.2 1 2079 229 119 1913 0.2 1 1734 179 120 1562 0.2 1 1431 131 121 1324 0.2 1 1204 120 122 1075 0.2 1 965 110 123 859 0.2 1 768 91 124 724 0.2 1 640 84 125 591 0.2 1 519 72 126 475 0.2 1 409 66 127 455 0.2 1 404 51 128 340 0.2 1 294 46 129 243 0.2 1 193 50 130 216 0.2 1 182 34 131 170 0.2 1 146 24 132 150 0.2 1 133 17 133 129 0.2 1 114 15 134 222 0.2 1 199 23 135 80 0.2 1 75 5 136 46 0.2 1 42 4 137 44 0.2 1 37 7 138 28 0.2 1 28 139 21 0.2 1 18 3 140 10 0.2 1 6 4 141 12 0.2 1 8 4 142 16 0.2 1 13 3 143 7 0.2 1 3 4 144 10 0.2 1 10 145 6 0.2 1 4 2 146 6 0.2 1 4 2 147 26 0.2 1 24 2 148 13 0.2 1 11 2 149 11 0.2 1 11 150 141 0.2 1 126 15 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_32psu_4_S8_L002_R1_001.fastq.gz ============================================= 14607942 sequences processed in total