SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_26psu_2_S10_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: 565606). Second best hit was Nextera (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_26psu_2_S10_L002_R2_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 70.33 s (4 us/read; 15.69 M reads/minute). === Summary === Total reads processed: 18,388,474 Reads with adapters: 14,677,085 (79.8%) Reads written (passing filters): 18,388,474 (100.0%) Total basepairs processed: 2,758,271,100 bp Quality-trimmed: 14,282,591 bp (0.5%) Total written (filtered): 2,101,274,280 bp (76.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14677085 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.7% C: 12.6% G: 24.2% T: 34.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2268778 4597118.5 0 2268778 2 320662 1149279.6 0 320662 3 193123 287319.9 0 193123 4 107505 71830.0 0 107505 5 98136 17957.5 0 98136 6 87605 4489.4 0 87605 7 69984 1122.3 0 69984 8 100736 280.6 0 100736 9 80882 70.1 0 80636 246 10 85130 17.5 1 79348 5782 11 93238 4.4 1 85689 7549 12 92545 1.1 1 85062 7483 13 106121 0.3 1 97648 8473 14 98586 0.3 1 90015 8571 15 79603 0.3 1 73456 6147 16 116674 0.3 1 107221 9453 17 98395 0.3 1 90346 8049 18 87513 0.3 1 80658 6855 19 114688 0.3 1 105582 9106 20 107373 0.3 1 99285 8088 21 94108 0.3 1 86828 7280 22 106536 0.3 1 98497 8039 23 113709 0.3 1 104976 8733 24 111940 0.3 1 103269 8671 25 127403 0.3 1 118648 8755 26 106762 0.3 1 98223 8539 27 118132 0.3 1 108645 9487 28 106930 0.3 1 99955 6975 29 120647 0.3 1 111606 9041 30 115537 0.3 1 107678 7859 31 127962 0.3 1 118733 9229 32 110371 0.3 1 102883 7488 33 128535 0.3 1 119135 9400 34 166074 0.3 1 154379 11695 35 88153 0.3 1 82039 6114 36 130243 0.3 1 120604 9639 37 137437 0.3 1 127611 9826 38 129360 0.3 1 121250 8110 39 122871 0.3 1 115373 7498 40 140913 0.3 1 131295 9618 41 137375 0.3 1 128487 8888 42 139853 0.3 1 130785 9068 43 126879 0.3 1 118647 8232 44 149301 0.3 1 139495 9806 45 151738 0.3 1 141722 10016 46 118782 0.3 1 111205 7577 47 144918 0.3 1 136263 8655 48 142402 0.3 1 133845 8557 49 148370 0.3 1 138956 9414 50 143101 0.3 1 133924 9177 51 175097 0.3 1 164092 11005 52 127562 0.3 1 119653 7909 53 156552 0.3 1 147706 8846 54 114039 0.3 1 107283 6756 55 151265 0.3 1 142708 8557 56 156754 0.3 1 146983 9771 57 149767 0.3 1 141656 8111 58 144481 0.3 1 136475 8006 59 145577 0.3 1 137588 7989 60 151210 0.3 1 142573 8637 61 154000 0.3 1 145457 8543 62 169208 0.3 1 159141 10067 63 223876 0.3 1 212453 11423 64 187828 0.3 1 179799 8029 65 121115 0.3 1 114588 6527 66 133231 0.3 1 126151 7080 67 130874 0.3 1 123245 7629 68 134376 0.3 1 127002 7374 69 132637 0.3 1 125114 7523 70 138657 0.3 1 130979 7678 71 148179 0.3 1 140033 8146 72 141424 0.3 1 133547 7877 73 147578 0.3 1 139587 7991 74 136704 0.3 1 129204 7500 75 129081 0.3 1 122024 7057 76 126400 0.3 1 119414 6986 77 125876 0.3 1 118871 7005 78 121079 0.3 1 114302 6777 79 116625 0.3 1 110208 6417 80 115718 0.3 1 109559 6159 81 115429 0.3 1 109090 6339 82 109791 0.3 1 103782 6009 83 107050 0.3 1 101360 5690 84 102872 0.3 1 97327 5545 85 102015 0.3 1 96553 5462 86 101949 0.3 1 96606 5343 87 102660 0.3 1 97419 5241 88 99584 0.3 1 94677 4907 89 90213 0.3 1 85644 4569 90 87335 0.3 1 82845 4490 91 81890 0.3 1 77745 4145 92 77363 0.3 1 73520 3843 93 73690 0.3 1 70013 3677 94 72610 0.3 1 68880 3730 95 68219 0.3 1 64684 3535 96 65235 0.3 1 61847 3388 97 59727 0.3 1 56753 2974 98 56047 0.3 1 53250 2797 99 53654 0.3 1 50884 2770 100 50544 0.3 1 48047 2497 101 46267 0.3 1 43991 2276 102 43012 0.3 1 40866 2146 103 39825 0.3 1 37849 1976 104 37894 0.3 1 35883 2011 105 33884 0.3 1 32215 1669 106 31153 0.3 1 29674 1479 107 28444 0.3 1 27053 1391 108 25994 0.3 1 24692 1302 109 23338 0.3 1 22212 1126 110 21606 0.3 1 20453 1153 111 20243 0.3 1 19234 1009 112 17922 0.3 1 16980 942 113 15507 0.3 1 14731 776 114 13757 0.3 1 13111 646 115 11617 0.3 1 11010 607 116 10230 0.3 1 9713 517 117 8353 0.3 1 7888 465 118 7422 0.3 1 7053 369 119 6284 0.3 1 5939 345 120 5303 0.3 1 5008 295 121 4751 0.3 1 4456 295 122 3933 0.3 1 3679 254 123 3312 0.3 1 3148 164 124 2831 0.3 1 2672 159 125 2374 0.3 1 2211 163 126 2009 0.3 1 1881 128 127 1689 0.3 1 1578 111 128 1328 0.3 1 1253 75 129 1073 0.3 1 1017 56 130 798 0.3 1 754 44 131 632 0.3 1 599 33 132 607 0.3 1 572 35 133 679 0.3 1 639 40 134 1080 0.3 1 1037 43 135 476 0.3 1 455 21 136 209 0.3 1 191 18 137 180 0.3 1 172 8 138 119 0.3 1 105 14 139 64 0.3 1 58 6 140 54 0.3 1 50 4 141 33 0.3 1 30 3 142 22 0.3 1 22 143 32 0.3 1 26 6 144 37 0.3 1 35 2 145 89 0.3 1 87 2 146 113 0.3 1 108 5 147 383 0.3 1 362 21 148 262 0.3 1 256 6 149 189 0.3 1 171 18 150 1406 0.3 1 1326 80 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_26psu_2_S10_L002_R2_001.fastq.gz ============================================= 18388474 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 18388474 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 197607 (1.07%)