SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/CTRL_8C_26psu_1_S17_L002_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: 487093). 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/CTRL_8C_26psu_1_S17_L002_R2_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 56.89 s (4 us/read; 14.37 M reads/minute). === Summary === Total reads processed: 13,627,098 Reads with adapters: 10,276,263 (75.4%) Reads written (passing filters): 13,627,098 (100.0%) Total basepairs processed: 2,044,064,700 bp Quality-trimmed: 9,937,551 bp (0.5%) Total written (filtered): 1,630,739,955 bp (79.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10276263 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.9% C: 12.4% G: 23.0% T: 34.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2146357 3406774.5 0 2146357 2 269360 851693.6 0 269360 3 157893 212923.4 0 157893 4 87930 53230.9 0 87930 5 73543 13307.7 0 73543 6 64791 3326.9 0 64791 7 52189 831.7 0 52189 8 74756 207.9 0 74756 9 60599 52.0 0 60366 233 10 63543 13.0 1 59315 4228 11 68667 3.2 1 63268 5399 12 67618 0.8 1 62224 5394 13 77226 0.2 1 71131 6095 14 69709 0.2 1 63900 5809 15 58686 0.2 1 54055 4631 16 84262 0.2 1 77680 6582 17 67924 0.2 1 62515 5409 18 64114 0.2 1 59144 4970 19 80499 0.2 1 74211 6288 20 76034 0.2 1 70274 5760 21 67847 0.2 1 62554 5293 22 74609 0.2 1 68953 5656 23 78584 0.2 1 72661 5923 24 77507 0.2 1 71592 5915 25 87777 0.2 1 81767 6010 26 72611 0.2 1 66753 5858 27 83123 0.2 1 76411 6712 28 73079 0.2 1 68272 4807 29 82291 0.2 1 76291 6000 30 76541 0.2 1 71237 5304 31 89563 0.2 1 83077 6486 32 74346 0.2 1 69371 4975 33 86840 0.2 1 80487 6353 34 112360 0.2 1 104461 7899 35 60619 0.2 1 56337 4282 36 90028 0.2 1 83414 6614 37 96370 0.2 1 89511 6859 38 89130 0.2 1 83444 5686 39 86200 0.2 1 80889 5311 40 97029 0.2 1 90271 6758 41 93202 0.2 1 87114 6088 42 93307 0.2 1 87268 6039 43 83469 0.2 1 77943 5526 44 97590 0.2 1 91014 6576 45 100276 0.2 1 93792 6484 46 75444 0.2 1 70447 4997 47 93307 0.2 1 87603 5704 48 90968 0.2 1 85370 5598 49 95545 0.2 1 89305 6240 50 91141 0.2 1 85291 5850 51 108887 0.2 1 102107 6780 52 80355 0.2 1 75335 5020 53 99048 0.2 1 93311 5737 54 72741 0.2 1 68334 4407 55 95947 0.2 1 90438 5509 56 99513 0.2 1 93368 6145 57 93556 0.2 1 88452 5104 58 90539 0.2 1 85415 5124 59 90467 0.2 1 85091 5376 60 93608 0.2 1 88124 5484 61 95101 0.2 1 89698 5403 62 102226 0.2 1 96046 6180 63 136011 0.2 1 129004 7007 64 112722 0.2 1 107622 5100 65 75623 0.2 1 71479 4144 66 81004 0.2 1 76564 4440 67 79874 0.2 1 75268 4606 68 81531 0.2 1 76952 4579 69 80094 0.2 1 75476 4618 70 85599 0.2 1 80759 4840 71 89528 0.2 1 84657 4871 72 84362 0.2 1 79637 4725 73 87554 0.2 1 82710 4844 74 81739 0.2 1 77139 4600 75 76846 0.2 1 72538 4308 76 75616 0.2 1 71298 4318 77 75671 0.2 1 71375 4296 78 71297 0.2 1 67330 3967 79 68959 0.2 1 65062 3897 80 69385 0.2 1 65444 3941 81 68113 0.2 1 64379 3734 82 65128 0.2 1 61578 3550 83 63398 0.2 1 59890 3508 84 61642 0.2 1 58327 3315 85 61077 0.2 1 57799 3278 86 60708 0.2 1 57467 3241 87 60697 0.2 1 57594 3103 88 59562 0.2 1 56463 3099 89 54239 0.2 1 51398 2841 90 51773 0.2 1 48980 2793 91 49319 0.2 1 46756 2563 92 46223 0.2 1 43736 2487 93 44798 0.2 1 42455 2343 94 43852 0.2 1 41584 2268 95 41908 0.2 1 39647 2261 96 39622 0.2 1 37536 2086 97 36420 0.2 1 34621 1799 98 33185 0.2 1 31489 1696 99 32771 0.2 1 31125 1646 100 29865 0.2 1 28321 1544 101 27753 0.2 1 26308 1445 102 25712 0.2 1 24349 1363 103 23843 0.2 1 22528 1315 104 23330 0.2 1 22084 1246 105 20720 0.2 1 19658 1062 106 19342 0.2 1 18364 978 107 17248 0.2 1 16375 873 108 15847 0.2 1 15052 795 109 14536 0.2 1 13807 729 110 12976 0.2 1 12292 684 111 12529 0.2 1 11885 644 112 10963 0.2 1 10373 590 113 9349 0.2 1 8908 441 114 8548 0.2 1 8120 428 115 7299 0.2 1 6916 383 116 6237 0.2 1 5941 296 117 5243 0.2 1 4920 323 118 4696 0.2 1 4465 231 119 3975 0.2 1 3763 212 120 3508 0.2 1 3309 199 121 3040 0.2 1 2875 165 122 2575 0.2 1 2428 147 123 2186 0.2 1 2073 113 124 1945 0.2 1 1832 113 125 1652 0.2 1 1551 101 126 1464 0.2 1 1388 76 127 1181 0.2 1 1120 61 128 990 0.2 1 926 64 129 867 0.2 1 802 65 130 639 0.2 1 610 29 131 564 0.2 1 532 32 132 517 0.2 1 490 27 133 691 0.2 1 653 38 134 1520 0.2 1 1458 62 135 553 0.2 1 527 26 136 201 0.2 1 194 7 137 155 0.2 1 146 9 138 95 0.2 1 92 3 139 52 0.2 1 49 3 140 44 0.2 1 40 4 141 42 0.2 1 38 4 142 33 0.2 1 31 2 143 49 0.2 1 44 5 144 63 0.2 1 60 3 145 162 0.2 1 155 7 146 237 0.2 1 226 11 147 1276 0.2 1 1212 64 148 739 0.2 1 700 39 149 423 0.2 1 396 27 150 2548 0.2 1 2400 148 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/CTRL_8C_26psu_1_S17_L002_R2_001.fastq.gz ============================================= 13627098 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 13627098 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 134846 (0.99%)