SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_32psu_3_S7_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: 631984). 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/8C_32psu_3_S7_L001_R1_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 49.24 s (3 us/read; 17.26 M reads/minute). === Summary === Total reads processed: 14,166,205 Reads with adapters: 11,846,180 (83.6%) Reads written (passing filters): 14,166,205 (100.0%) Total basepairs processed: 2,124,930,750 bp Quality-trimmed: 4,298,957 bp (0.2%) Total written (filtered): 1,559,729,002 bp (73.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11846180 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.1% C: 15.1% G: 21.0% T: 34.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 1373757 3541551.2 0 1373757 2 216270 885387.8 0 216270 3 129588 221347.0 0 129588 4 80077 55336.7 0 80077 5 69163 13834.2 0 69163 6 67518 3458.5 0 67518 7 56035 864.6 0 56035 8 70267 216.2 0 70267 9 70629 54.0 0 69702 927 10 66297 13.5 1 62862 3435 11 73903 3.4 1 68283 5620 12 71104 0.8 1 66580 4524 13 72370 0.2 1 67647 4723 14 73869 0.2 1 68608 5261 15 77649 0.2 1 72603 5046 16 76835 0.2 1 71293 5542 17 93103 0.2 1 85654 7449 18 80962 0.2 1 76131 4831 19 69251 0.2 1 64739 4512 20 83140 0.2 1 77746 5394 21 91983 0.2 1 85635 6348 22 78972 0.2 1 74340 4632 23 91741 0.2 1 85612 6129 24 86730 0.2 1 79637 7093 25 93905 0.2 1 87575 6330 26 84785 0.2 1 79850 4935 27 95659 0.2 1 88641 7018 28 93289 0.2 1 86777 6512 29 102324 0.2 1 94020 8304 30 106573 0.2 1 100735 5838 31 82302 0.2 1 76920 5382 32 102146 0.2 1 95503 6643 33 96707 0.2 1 90380 6327 34 106974 0.2 1 99423 7551 35 107836 0.2 1 100264 7572 36 113175 0.2 1 105186 7989 37 100704 0.2 1 95019 5685 38 121468 0.2 1 112012 9456 39 103157 0.2 1 96822 6335 40 115108 0.2 1 108010 7098 41 129750 0.2 1 120171 9579 42 102179 0.2 1 94823 7356 43 171532 0.2 1 162826 8706 44 55606 0.2 1 50892 4714 45 120800 0.2 1 113289 7511 46 113431 0.2 1 106413 7018 47 120541 0.2 1 113256 7285 48 119747 0.2 1 111882 7865 49 130730 0.2 1 121756 8974 50 111508 0.2 1 104914 6594 51 122095 0.2 1 114233 7862 52 127642 0.2 1 118613 9029 53 137409 0.2 1 129309 8100 54 108827 0.2 1 102141 6686 55 130904 0.2 1 122687 8217 56 157783 0.2 1 148768 9015 57 104771 0.2 1 97389 7382 58 132433 0.2 1 125333 7100 59 115612 0.2 1 108308 7304 60 130650 0.2 1 122277 8373 61 128910 0.2 1 121303 7607 62 139690 0.2 1 131489 8201 63 114068 0.2 1 106664 7404 64 125901 0.2 1 118809 7092 65 141358 0.2 1 132756 8602 66 146823 0.2 1 137956 8867 67 159981 0.2 1 148074 11907 68 301471 0.2 1 287602 13869 69 51550 0.2 1 47181 4369 70 21339 0.2 1 17862 3477 71 81265 0.2 1 76296 4969 72 113463 0.2 1 106973 6490 73 120176 0.2 1 113199 6977 74 119128 0.2 1 112036 7092 75 118829 0.2 1 111689 7140 76 117859 0.2 1 110976 6883 77 119047 0.2 1 112165 6882 78 111406 0.2 1 104659 6747 79 110628 0.2 1 103829 6799 80 108577 0.2 1 102197 6380 81 107611 0.2 1 101254 6357 82 104685 0.2 1 98322 6363 83 101689 0.2 1 95553 6136 84 99042 0.2 1 93220 5822 85 96588 0.2 1 90890 5698 86 93102 0.2 1 87585 5517 87 89497 0.2 1 84148 5349 88 88681 0.2 1 83310 5371 89 83884 0.2 1 78862 5022 90 83820 0.2 1 78644 5176 91 79519 0.2 1 74630 4889 92 75751 0.2 1 71312 4439 93 71060 0.2 1 66734 4326 94 68805 0.2 1 64395 4410 95 63794 0.2 1 59908 3886 96 60732 0.2 1 57025 3707 97 57614 0.2 1 54075 3539 98 53272 0.2 1 49912 3360 99 52704 0.2 1 49079 3625 100 47213 0.2 1 44245 2968 101 43905 0.2 1 41069 2836 102 40757 0.2 1 38090 2667 103 36990 0.2 1 34581 2409 104 34678 0.2 1 32449 2229 105 30517 0.2 1 28453 2064 106 28231 0.2 1 26371 1860 107 25422 0.2 1 23676 1746 108 24129 0.2 1 22480 1649 109 20909 0.2 1 19298 1611 110 19145 0.2 1 17778 1367 111 17228 0.2 1 15946 1282 112 14959 0.2 1 13818 1141 113 12878 0.2 1 11894 984 114 11383 0.2 1 10467 916 115 9899 0.2 1 9096 803 116 8618 0.2 1 7872 746 117 7168 0.2 1 6561 607 118 6256 0.2 1 5711 545 119 5200 0.2 1 4764 436 120 4401 0.2 1 4012 389 121 3754 0.2 1 3388 366 122 3023 0.2 1 2711 312 123 2648 0.2 1 2374 274 124 2210 0.2 1 1991 219 125 1851 0.2 1 1661 190 126 1538 0.2 1 1379 159 127 1281 0.2 1 1146 135 128 1028 0.2 1 906 122 129 844 0.2 1 750 94 130 578 0.2 1 506 72 131 477 0.2 1 408 69 132 403 0.2 1 349 54 133 425 0.2 1 364 61 134 500 0.2 1 457 43 135 253 0.2 1 229 24 136 154 0.2 1 133 21 137 116 0.2 1 99 17 138 91 0.2 1 74 17 139 63 0.2 1 48 15 140 40 0.2 1 34 6 141 25 0.2 1 20 5 142 20 0.2 1 12 8 143 19 0.2 1 15 4 144 21 0.2 1 17 4 145 20 0.2 1 16 4 146 14 0.2 1 12 2 147 31 0.2 1 27 4 148 15 0.2 1 13 2 149 18 0.2 1 14 4 150 240 0.2 1 195 45 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_32psu_3_S7_L001_R1_001.fastq.gz ============================================= 14166205 sequences processed in total