SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_26psu_2_S14_L001_R2_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: 522594). Second best hit was smallRNA (count: 1) 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_26psu_2_S14_L001_R2_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 70.09 s (4 us/read; 14.76 M reads/minute). === Summary === Total reads processed: 17,243,447 Reads with adapters: 13,270,528 (77.0%) Reads written (passing filters): 17,243,447 (100.0%) Total basepairs processed: 2,586,517,050 bp Quality-trimmed: 11,661,219 bp (0.5%) Total written (filtered): 2,049,890,632 bp (79.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 13270528 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.6% C: 12.8% G: 23.5% T: 35.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2410570 4310861.8 0 2410570 2 362455 1077715.4 0 362455 3 204625 269428.9 0 204625 4 116204 67357.2 0 116204 5 102265 16839.3 0 102265 6 87780 4209.8 0 87780 7 72496 1052.5 0 72496 8 102751 263.1 0 102751 9 81658 65.8 0 81386 272 10 89121 16.4 1 84631 4490 11 93864 4.1 1 87983 5881 12 94565 1.0 1 88491 6074 13 105522 0.3 1 99372 6150 14 98340 0.3 1 91512 6828 15 80980 0.3 1 75936 5044 16 116316 0.3 1 109001 7315 17 93497 0.3 1 87166 6331 18 89538 0.3 1 84129 5409 19 112544 0.3 1 105239 7305 20 105651 0.3 1 99238 6413 21 93625 0.3 1 87782 5843 22 104844 0.3 1 98723 6121 23 109552 0.3 1 102808 6744 24 108841 0.3 1 101825 7016 25 121233 0.3 1 114032 7201 26 101015 0.3 1 94639 6376 27 112490 0.3 1 104790 7700 28 105074 0.3 1 99527 5547 29 111755 0.3 1 104926 6829 30 110664 0.3 1 104658 6006 31 120328 0.3 1 113206 7122 32 108098 0.3 1 102252 5846 33 119317 0.3 1 112198 7119 34 151071 0.3 1 142232 8839 35 87186 0.3 1 82458 4728 36 120833 0.3 1 113650 7183 37 128643 0.3 1 121059 7584 38 120495 0.3 1 114429 6066 39 117189 0.3 1 111171 6018 40 129860 0.3 1 122333 7527 41 123836 0.3 1 117366 6470 42 127654 0.3 1 120939 6715 43 116428 0.3 1 110085 6343 44 133061 0.3 1 125767 7294 45 139911 0.3 1 132604 7307 46 103489 0.3 1 98069 5420 47 129515 0.3 1 122821 6694 48 126933 0.3 1 120634 6299 49 132432 0.3 1 125535 6897 50 125382 0.3 1 118618 6764 51 155910 0.3 1 147950 7960 52 112001 0.3 1 106554 5447 53 134464 0.3 1 128383 6081 54 103158 0.3 1 98052 5106 55 131983 0.3 1 126024 5959 56 136358 0.3 1 129807 6551 57 127296 0.3 1 121594 5702 58 122071 0.3 1 116674 5397 59 124219 0.3 1 118380 5839 60 128066 0.3 1 121909 6157 61 132129 0.3 1 125705 6424 62 142837 0.3 1 135944 6893 63 190582 0.3 1 182484 8098 64 150467 0.3 1 144624 5843 65 101740 0.3 1 97088 4652 66 109816 0.3 1 104968 4848 67 107749 0.3 1 102613 5136 68 108633 0.3 1 103740 4893 69 107596 0.3 1 102648 4948 70 114794 0.3 1 109576 5218 71 116610 0.3 1 111540 5070 72 110184 0.3 1 105059 5125 73 115749 0.3 1 110692 5057 74 106275 0.3 1 101612 4663 75 101750 0.3 1 97259 4491 76 99053 0.3 1 94705 4348 77 99069 0.3 1 94745 4324 78 94226 0.3 1 90009 4217 79 90763 0.3 1 86805 3958 80 89778 0.3 1 85958 3820 81 88669 0.3 1 84684 3985 82 84401 0.3 1 80642 3759 83 81824 0.3 1 78236 3588 84 78990 0.3 1 75425 3565 85 76455 0.3 1 73024 3431 86 76386 0.3 1 73029 3357 87 75988 0.3 1 72761 3227 88 73818 0.3 1 70558 3260 89 65970 0.3 1 63085 2885 90 63019 0.3 1 60213 2806 91 58914 0.3 1 56366 2548 92 54704 0.3 1 52314 2390 93 52692 0.3 1 50404 2288 94 51139 0.3 1 48941 2198 95 47428 0.3 1 45341 2087 96 45523 0.3 1 43617 1906 97 43074 0.3 1 41264 1810 98 39986 0.3 1 38323 1663 99 40439 0.3 1 38720 1719 100 35462 0.3 1 34051 1411 101 31343 0.3 1 29998 1345 102 28451 0.3 1 27239 1212 103 26443 0.3 1 25307 1136 104 24686 0.3 1 23698 988 105 22319 0.3 1 21394 925 106 20298 0.3 1 19438 860 107 18363 0.3 1 17549 814 108 16498 0.3 1 15775 723 109 15075 0.3 1 14486 589 110 13470 0.3 1 12883 587 111 12724 0.3 1 12179 545 112 10843 0.3 1 10385 458 113 9574 0.3 1 9156 418 114 8065 0.3 1 7698 367 115 6969 0.3 1 6632 337 116 5939 0.3 1 5624 315 117 5106 0.3 1 4872 234 118 4425 0.3 1 4206 219 119 3716 0.3 1 3520 196 120 3161 0.3 1 3007 154 121 2854 0.3 1 2727 127 122 2418 0.3 1 2305 113 123 2039 0.3 1 1907 132 124 1593 0.3 1 1516 77 125 1395 0.3 1 1318 77 126 1136 0.3 1 1075 61 127 1068 0.3 1 1004 64 128 801 0.3 1 764 37 129 660 0.3 1 625 35 130 510 0.3 1 471 39 131 432 0.3 1 407 25 132 400 0.3 1 378 22 133 460 0.3 1 436 24 134 592 0.3 1 573 19 135 262 0.3 1 249 13 136 158 0.3 1 150 8 137 105 0.3 1 102 3 138 83 0.3 1 78 5 139 62 0.3 1 57 5 140 55 0.3 1 49 6 141 58 0.3 1 56 2 142 36 0.3 1 36 143 49 0.3 1 47 2 144 33 0.3 1 30 3 145 52 0.3 1 45 7 146 154 0.3 1 152 2 147 543 0.3 1 532 11 148 399 0.3 1 383 16 149 287 0.3 1 273 14 150 2663 0.3 1 2573 90 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_26psu_2_S14_L001_R2_001.fastq.gz ============================================= 17243447 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 17243447 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 129767 (0.75%)