SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_26psu_2_S14_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: 513491). 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_26psu_2_S14_L002_R1_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 67.45 s (4 us/read; 15.28 M reads/minute). === Summary === Total reads processed: 17,174,050 Reads with adapters: 13,278,050 (77.3%) Reads written (passing filters): 17,174,050 (100.0%) Total basepairs processed: 2,576,107,500 bp Quality-trimmed: 5,444,792 bp (0.2%) Total written (filtered): 2,038,071,183 bp (79.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 13278050 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.9% C: 14.3% G: 20.5% T: 35.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2359801 4293512.5 0 2359801 2 349363 1073378.1 0 349363 3 195448 268344.5 0 195448 4 112766 67086.1 0 112766 5 92768 16771.5 0 92768 6 90305 4192.9 0 90305 7 71626 1048.2 0 71626 8 92261 262.1 0 92261 9 91976 65.5 0 90926 1050 10 85467 16.4 1 79925 5542 11 96691 4.1 1 88355 8336 12 91713 1.0 1 84839 6874 13 92754 0.3 1 85809 6945 14 95464 0.3 1 87621 7843 15 99277 0.3 1 91369 7908 16 97348 0.3 1 88681 8667 17 119420 0.3 1 108369 11051 18 98719 0.3 1 91552 7167 19 85310 0.3 1 78884 6426 20 103518 0.3 1 95770 7748 21 115588 0.3 1 106188 9400 22 95906 0.3 1 89272 6634 23 115386 0.3 1 106435 8951 24 102949 0.3 1 93582 9367 25 112836 0.3 1 104100 8736 26 100484 0.3 1 93502 6982 27 114811 0.3 1 105307 9504 28 113076 0.3 1 104189 8887 29 118710 0.3 1 108207 10503 30 126214 0.3 1 117742 8472 31 97121 0.3 1 89907 7214 32 120516 0.3 1 111427 9089 33 110848 0.3 1 101943 8905 34 122175 0.3 1 112281 9894 35 122064 0.3 1 111107 10957 36 119580 0.3 1 110830 8750 37 130636 0.3 1 120649 9987 38 115572 0.3 1 106536 9036 39 129905 0.3 1 119211 10694 40 124968 0.3 1 115039 9929 41 145398 0.3 1 132929 12469 42 108151 0.3 1 98831 9320 43 190551 0.3 1 178361 12190 44 58099 0.3 1 52480 5619 45 130794 0.3 1 121367 9427 46 121400 0.3 1 112370 9030 47 129048 0.3 1 119631 9417 48 126222 0.3 1 116730 9492 49 139750 0.3 1 128710 11040 50 117206 0.3 1 109130 8076 51 127012 0.3 1 117729 9283 52 132886 0.3 1 122231 10655 53 141918 0.3 1 132027 9891 54 110897 0.3 1 103000 7897 55 132094 0.3 1 122452 9642 56 162870 0.3 1 151676 11194 57 103170 0.3 1 94887 8283 58 132668 0.3 1 124347 8321 59 116116 0.3 1 107462 8654 60 129021 0.3 1 119747 9274 61 124026 0.3 1 115604 8422 62 137460 0.3 1 128199 9261 63 110698 0.3 1 102173 8525 64 120813 0.3 1 112906 7907 65 134938 0.3 1 125626 9312 66 138037 0.3 1 128352 9685 67 146504 0.3 1 134535 11969 68 277060 0.3 1 261442 15618 69 59870 0.3 1 54647 5223 70 22664 0.3 1 19044 3620 71 71972 0.3 1 67240 4732 72 103041 0.3 1 96552 6489 73 110046 0.3 1 102755 7291 74 107843 0.3 1 100538 7305 75 106162 0.3 1 98772 7390 76 105323 0.3 1 97926 7397 77 104408 0.3 1 97267 7141 78 97073 0.3 1 90169 6904 79 96839 0.3 1 89879 6960 80 93988 0.3 1 87339 6649 81 93546 0.3 1 86918 6628 82 90241 0.3 1 83957 6284 83 86944 0.3 1 80903 6041 84 83168 0.3 1 77255 5913 85 80437 0.3 1 74815 5622 86 77338 0.3 1 71860 5478 87 73439 0.3 1 68315 5124 88 73001 0.3 1 67818 5183 89 68544 0.3 1 63628 4916 90 68084 0.3 1 63234 4850 91 64534 0.3 1 60016 4518 92 61115 0.3 1 56823 4292 93 56566 0.3 1 52542 4024 94 55074 0.3 1 51146 3928 95 50909 0.3 1 47255 3654 96 48357 0.3 1 44862 3495 97 45610 0.3 1 42541 3069 98 41384 0.3 1 38355 3029 99 39655 0.3 1 36624 3031 100 36325 0.3 1 33739 2586 101 33659 0.3 1 31212 2447 102 31157 0.3 1 28883 2274 103 28746 0.3 1 26792 1954 104 26425 0.3 1 24518 1907 105 23705 0.3 1 22021 1684 106 21201 0.3 1 19619 1582 107 19613 0.3 1 18232 1381 108 17790 0.3 1 16434 1356 109 16006 0.3 1 14830 1176 110 14326 0.3 1 13263 1063 111 12771 0.3 1 11779 992 112 11222 0.3 1 10318 904 113 9534 0.3 1 8824 710 114 8358 0.3 1 7698 660 115 7285 0.3 1 6692 593 116 6411 0.3 1 5816 595 117 5570 0.3 1 5108 462 118 4832 0.3 1 4420 412 119 3906 0.3 1 3549 357 120 3397 0.3 1 3108 289 121 2929 0.3 1 2664 265 122 2444 0.3 1 2212 232 123 2198 0.3 1 1992 206 124 1767 0.3 1 1602 165 125 1386 0.3 1 1230 156 126 1228 0.3 1 1089 139 127 1105 0.3 1 989 116 128 786 0.3 1 705 81 129 664 0.3 1 591 73 130 581 0.3 1 508 73 131 479 0.3 1 435 44 132 414 0.3 1 361 53 133 450 0.3 1 408 42 134 646 0.3 1 602 44 135 289 0.3 1 262 27 136 173 0.3 1 154 19 137 125 0.3 1 108 17 138 98 0.3 1 88 10 139 90 0.3 1 77 13 140 54 0.3 1 46 8 141 52 0.3 1 45 7 142 38 0.3 1 35 3 143 50 0.3 1 43 7 144 42 0.3 1 37 5 145 46 0.3 1 45 1 146 125 0.3 1 116 9 147 651 0.3 1 623 28 148 442 0.3 1 421 21 149 216 0.3 1 204 12 150 2921 0.3 1 2713 208 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_26psu_2_S14_L002_R1_001.fastq.gz ============================================= 17174050 sequences processed in total