SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_32psu_2_S2_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: 617121). 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_2_S2_L002_R2_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 68.57 s (4 us/read; 15.47 M reads/minute). === Summary === Total reads processed: 17,682,252 Reads with adapters: 14,653,341 (82.9%) Reads written (passing filters): 17,682,252 (100.0%) Total basepairs processed: 2,652,337,800 bp Quality-trimmed: 13,059,983 bp (0.5%) Total written (filtered): 1,958,600,443 bp (73.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14653341 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.0% C: 12.0% G: 24.7% T: 34.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 1817135 4420563.0 0 1817135 2 279096 1105140.8 0 279096 3 175846 276285.2 0 175846 4 97770 69071.3 0 97770 5 91322 17267.8 0 91322 6 82979 4317.0 0 82979 7 65452 1079.2 0 65452 8 95994 269.8 0 95994 9 76273 67.5 0 76051 222 10 81686 16.9 1 76699 4987 11 88683 4.2 1 82075 6608 12 88254 1.1 1 81734 6520 13 102186 0.3 1 94885 7301 14 94341 0.3 1 86650 7691 15 77377 0.3 1 72050 5327 16 111829 0.3 1 103609 8220 17 95099 0.3 1 87974 7125 18 85068 0.3 1 79390 5678 19 110655 0.3 1 102928 7727 20 104031 0.3 1 97040 6991 21 92000 0.3 1 85864 6136 22 104100 0.3 1 97146 6954 23 109645 0.3 1 102128 7517 24 108307 0.3 1 100742 7565 25 123264 0.3 1 115703 7561 26 104401 0.3 1 96855 7546 27 119574 0.3 1 110821 8753 28 105530 0.3 1 99453 6077 29 120646 0.3 1 112687 7959 30 114291 0.3 1 107348 6943 31 129583 0.3 1 121518 8065 32 112118 0.3 1 105486 6632 33 129638 0.3 1 121053 8585 34 165788 0.3 1 155262 10526 35 90769 0.3 1 85358 5411 36 134484 0.3 1 125338 9146 37 141040 0.3 1 132135 8905 38 130890 0.3 1 123508 7382 39 125992 0.3 1 119419 6573 40 143114 0.3 1 134816 8298 41 141161 0.3 1 133004 8157 42 150560 0.3 1 142032 8528 43 126059 0.3 1 119274 6785 44 153119 0.3 1 144163 8956 45 156350 0.3 1 146944 9406 46 124535 0.3 1 117729 6806 47 151106 0.3 1 143277 7829 48 145709 0.3 1 138077 7632 49 153645 0.3 1 144717 8928 50 152443 0.3 1 143810 8633 51 186444 0.3 1 176105 10339 52 135339 0.3 1 128275 7064 53 167309 0.3 1 158978 8331 54 122506 0.3 1 116488 6018 55 159881 0.3 1 152187 7694 56 166549 0.3 1 157620 8929 57 159405 0.3 1 152142 7263 58 154742 0.3 1 147569 7173 59 154815 0.3 1 147039 7776 60 162353 0.3 1 154259 8094 61 164751 0.3 1 156984 7767 62 181848 0.3 1 172769 9079 63 243575 0.3 1 232900 10675 64 204233 0.3 1 196775 7458 65 131464 0.3 1 125558 5906 66 143870 0.3 1 137254 6616 67 143305 0.3 1 136348 6957 68 146020 0.3 1 139340 6680 69 145720 0.3 1 138556 7164 70 152388 0.3 1 145229 7159 71 160483 0.3 1 152923 7560 72 153910 0.3 1 146668 7242 73 161080 0.3 1 153734 7346 74 148742 0.3 1 141577 7165 75 142283 0.3 1 135459 6824 76 139212 0.3 1 132662 6550 77 138672 0.3 1 132174 6498 78 134120 0.3 1 127702 6418 79 128493 0.3 1 122569 5924 80 128817 0.3 1 123042 5775 81 126667 0.3 1 120859 5808 82 120873 0.3 1 115386 5487 83 118191 0.3 1 112948 5243 84 114338 0.3 1 109255 5083 85 112679 0.3 1 107691 4988 86 112861 0.3 1 107936 4925 87 113253 0.3 1 108504 4749 88 112053 0.3 1 107404 4649 89 99896 0.3 1 95509 4387 90 94224 0.3 1 90152 4072 91 88708 0.3 1 84909 3799 92 84091 0.3 1 80464 3627 93 80972 0.3 1 77474 3498 94 78965 0.3 1 75719 3246 95 74676 0.3 1 71434 3242 96 70973 0.3 1 67917 3056 97 64791 0.3 1 62029 2762 98 59852 0.3 1 57281 2571 99 56272 0.3 1 53840 2432 100 50916 0.3 1 48630 2286 101 48192 0.3 1 46113 2079 102 45225 0.3 1 43338 1887 103 42981 0.3 1 41068 1913 104 41627 0.3 1 39818 1809 105 36524 0.3 1 34997 1527 106 32960 0.3 1 31559 1401 107 28968 0.3 1 27743 1225 108 25878 0.3 1 24765 1113 109 23275 0.3 1 22256 1019 110 21045 0.3 1 20178 867 111 19919 0.3 1 19038 881 112 16987 0.3 1 16274 713 113 14633 0.3 1 14022 611 114 12693 0.3 1 12155 538 115 10546 0.3 1 10065 481 116 8985 0.3 1 8625 360 117 7253 0.3 1 6908 345 118 6254 0.3 1 5971 283 119 5291 0.3 1 5043 248 120 4411 0.3 1 4200 211 121 3756 0.3 1 3560 196 122 3023 0.3 1 2867 156 123 2649 0.3 1 2500 149 124 2061 0.3 1 1951 110 125 1723 0.3 1 1623 100 126 1447 0.3 1 1342 105 127 1137 0.3 1 1082 55 128 888 0.3 1 830 58 129 801 0.3 1 760 41 130 520 0.3 1 487 33 131 493 0.3 1 458 35 132 407 0.3 1 377 30 133 444 0.3 1 414 30 134 445 0.3 1 433 12 135 251 0.3 1 241 10 136 140 0.3 1 129 11 137 98 0.3 1 90 8 138 74 0.3 1 66 8 139 51 0.3 1 50 1 140 46 0.3 1 45 1 141 23 0.3 1 22 1 142 21 0.3 1 19 2 143 18 0.3 1 16 2 144 19 0.3 1 19 145 44 0.3 1 42 2 146 27 0.3 1 26 1 147 73 0.3 1 69 4 148 42 0.3 1 38 4 149 58 0.3 1 55 3 150 398 0.3 1 372 26 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_32psu_2_S2_L002_R2_001.fastq.gz ============================================= 17682252 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 17682252 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 169414 (0.96%)