SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_32psu_3_S3_L001_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: 664838). Second best hit was smallRNA (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_3_S3_L001_R1_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 46.27 s (3 us/read; 17.75 M reads/minute). === Summary === Total reads processed: 13,688,650 Reads with adapters: 11,692,195 (85.4%) Reads written (passing filters): 13,688,650 (100.0%) Total basepairs processed: 2,053,297,500 bp Quality-trimmed: 4,119,462 bp (0.2%) Total written (filtered): 1,465,023,732 bp (71.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11692195 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.2% C: 13.5% G: 21.8% T: 35.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 1153280 3422162.5 0 1153280 2 188115 855540.6 0 188115 3 111422 213885.2 0 111422 4 69723 53471.3 0 69723 5 62088 13367.8 0 62088 6 60662 3342.0 0 60662 7 51512 835.5 0 51512 8 64264 208.9 0 64264 9 63671 52.2 0 62836 835 10 60542 13.1 1 57278 3264 11 67613 3.3 1 62345 5268 12 65175 0.8 1 60838 4337 13 67473 0.2 1 62952 4521 14 68261 0.2 1 63487 4774 15 72178 0.2 1 67286 4892 16 70299 0.2 1 65086 5213 17 86060 0.2 1 78938 7122 18 74650 0.2 1 70063 4587 19 65040 0.2 1 60840 4200 20 78366 0.2 1 73149 5217 21 84846 0.2 1 78850 5996 22 74487 0.2 1 70107 4380 23 86083 0.2 1 80316 5767 24 80721 0.2 1 73972 6749 25 87753 0.2 1 81677 6076 26 80514 0.2 1 75647 4867 27 90438 0.2 1 83662 6776 28 90174 0.2 1 83716 6458 29 93389 0.2 1 85784 7605 30 100786 0.2 1 94960 5826 31 81881 0.2 1 76679 5202 32 98375 0.2 1 91951 6424 33 93955 0.2 1 87212 6743 34 99759 0.2 1 92551 7208 35 105302 0.2 1 98208 7094 36 99885 0.2 1 93387 6498 37 106334 0.2 1 98270 8064 38 113806 0.2 1 106308 7498 39 98325 0.2 1 92047 6278 40 111911 0.2 1 104331 7580 41 123334 0.2 1 114370 8964 42 99813 0.2 1 92381 7432 43 174315 0.2 1 165200 9115 44 51463 0.2 1 46797 4666 45 117571 0.2 1 110330 7241 46 111696 0.2 1 104449 7247 47 119263 0.2 1 111850 7413 48 117185 0.2 1 109504 7681 49 129249 0.2 1 119912 9337 50 113265 0.2 1 106460 6805 51 123578 0.2 1 115577 8001 52 126860 0.2 1 117703 9157 53 136778 0.2 1 128183 8595 54 111542 0.2 1 104628 6914 55 130509 0.2 1 122033 8476 56 160806 0.2 1 151398 9408 57 105238 0.2 1 97627 7611 58 136703 0.2 1 129347 7356 59 118654 0.2 1 110900 7754 60 133349 0.2 1 124657 8692 61 131151 0.2 1 123141 8010 62 146081 0.2 1 137646 8435 63 116527 0.2 1 108569 7958 64 131388 0.2 1 123568 7820 65 146211 0.2 1 137343 8868 66 153623 0.2 1 144098 9525 67 163622 0.2 1 150969 12653 68 316517 0.2 1 301519 14998 69 50118 0.2 1 45752 4366 70 19043 0.2 1 15441 3602 71 86203 0.2 1 80944 5259 72 120080 0.2 1 113140 6940 73 127657 0.2 1 119892 7765 74 126886 0.2 1 119284 7602 75 126438 0.2 1 118691 7747 76 124650 0.2 1 117103 7547 77 126032 0.2 1 118426 7606 78 119720 0.2 1 112423 7297 79 118994 0.2 1 111880 7114 80 116560 0.2 1 109502 7058 81 114889 0.2 1 107938 6951 82 112663 0.2 1 105830 6833 83 109839 0.2 1 103073 6766 84 105779 0.2 1 99490 6289 85 104543 0.2 1 98380 6163 86 100937 0.2 1 94813 6124 87 97367 0.2 1 91433 5934 88 96957 0.2 1 90929 6028 89 91739 0.2 1 86072 5667 90 91064 0.2 1 85580 5484 91 86291 0.2 1 80995 5296 92 83034 0.2 1 77959 5075 93 78558 0.2 1 73687 4871 94 75965 0.2 1 71248 4717 95 70608 0.2 1 66214 4394 96 66613 0.2 1 62491 4122 97 63167 0.2 1 59156 4011 98 59278 0.2 1 55535 3743 99 58315 0.2 1 54380 3935 100 52512 0.2 1 49178 3334 101 49162 0.2 1 45965 3197 102 45067 0.2 1 42105 2962 103 41984 0.2 1 39185 2799 104 39240 0.2 1 36628 2612 105 34957 0.2 1 32577 2380 106 31819 0.2 1 29724 2095 107 29159 0.2 1 27051 2108 108 27128 0.2 1 25184 1944 109 24322 0.2 1 22614 1708 110 21994 0.2 1 20354 1640 111 19565 0.2 1 18156 1409 112 17167 0.2 1 15854 1313 113 14819 0.2 1 13686 1133 114 13381 0.2 1 12379 1002 115 11437 0.2 1 10576 861 116 9792 0.2 1 9003 789 117 8262 0.2 1 7551 711 118 7359 0.2 1 6738 621 119 6022 0.2 1 5480 542 120 5103 0.2 1 4650 453 121 4422 0.2 1 4023 399 122 3603 0.2 1 3261 342 123 3138 0.2 1 2830 308 124 2526 0.2 1 2281 245 125 2064 0.2 1 1886 178 126 1770 0.2 1 1574 196 127 1476 0.2 1 1324 152 128 1074 0.2 1 953 121 129 984 0.2 1 870 114 130 708 0.2 1 638 70 131 577 0.2 1 522 55 132 547 0.2 1 477 70 133 519 0.2 1 468 51 134 567 0.2 1 518 49 135 307 0.2 1 275 32 136 217 0.2 1 195 22 137 172 0.2 1 148 24 138 111 0.2 1 95 16 139 77 0.2 1 67 10 140 52 0.2 1 47 5 141 43 0.2 1 38 5 142 44 0.2 1 33 11 143 50 0.2 1 44 6 144 49 0.2 1 46 3 145 55 0.2 1 44 11 146 89 0.2 1 78 11 147 261 0.2 1 233 28 148 216 0.2 1 199 17 149 67 0.2 1 64 3 150 763 0.2 1 633 130 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_32psu_3_S3_L001_R1_001.fastq.gz ============================================= 13688650 sequences processed in total