SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_32psu_1_S1_L001_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: 635901). 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/16C_32psu_1_S1_L001_R2_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 73.11 s (4 us/read; 16.11 M reads/minute). === Summary === Total reads processed: 19,624,894 Reads with adapters: 16,339,161 (83.3%) Reads written (passing filters): 19,624,894 (100.0%) Total basepairs processed: 2,943,734,100 bp Quality-trimmed: 15,599,605 bp (0.5%) Total written (filtered): 2,144,342,165 bp (72.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 16339161 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.5% C: 12.6% G: 25.0% T: 33.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 1942196 4906223.5 0 1942196 2 299564 1226555.9 0 299564 3 177742 306639.0 0 177742 4 105333 76659.7 0 105333 5 100538 19164.9 0 100538 6 87955 4791.2 0 87955 7 71440 1197.8 0 71440 8 102524 299.5 0 102524 9 81367 74.9 0 81047 320 10 89669 18.7 1 85117 4552 11 95729 4.7 1 89915 5814 12 95768 1.2 1 89687 6081 13 108234 0.3 1 101948 6286 14 103335 0.3 1 96341 6994 15 82616 0.3 1 77316 5300 16 121595 0.3 1 114016 7579 17 98896 0.3 1 92218 6678 18 93415 0.3 1 87589 5826 19 120547 0.3 1 112557 7990 20 113077 0.3 1 106404 6673 21 99743 0.3 1 93549 6194 22 113380 0.3 1 106586 6794 23 116836 0.3 1 109692 7144 24 119139 0.3 1 111646 7493 25 135500 0.3 1 127577 7923 26 112154 0.3 1 104938 7216 27 122636 0.3 1 114199 8437 28 117975 0.3 1 111836 6139 29 125073 0.3 1 117359 7714 30 127096 0.3 1 120402 6694 31 137659 0.3 1 129729 7930 32 123762 0.3 1 117342 6420 33 138965 0.3 1 130590 8375 34 180950 0.3 1 170447 10503 35 102752 0.3 1 97235 5517 36 141525 0.3 1 133105 8420 37 151296 0.3 1 142475 8821 38 141804 0.3 1 134802 7002 39 139699 0.3 1 132682 7017 40 156245 0.3 1 147123 9122 41 150848 0.3 1 143057 7791 42 156523 0.3 1 148491 8032 43 142855 0.3 1 135344 7511 44 166066 0.3 1 157102 8964 45 178466 0.3 1 169227 9239 46 128203 0.3 1 121604 6599 47 163666 0.3 1 155525 8141 48 161229 0.3 1 153502 7727 49 169595 0.3 1 161041 8554 50 162191 0.3 1 153908 8283 51 204248 0.3 1 193780 10468 52 147164 0.3 1 140471 6693 53 177383 0.3 1 169465 7918 54 135474 0.3 1 129206 6268 55 177540 0.3 1 169636 7904 56 183270 0.3 1 174617 8653 57 175273 0.3 1 167802 7471 58 168130 0.3 1 160997 7133 59 172563 0.3 1 164868 7695 60 179506 0.3 1 171470 8036 61 186851 0.3 1 178181 8670 62 203675 0.3 1 194173 9502 63 273998 0.3 1 262527 11471 64 226808 0.3 1 218491 8317 65 147108 0.3 1 140746 6362 66 160644 0.3 1 153693 6951 67 159286 0.3 1 152193 7093 68 161933 0.3 1 155050 6883 69 160655 0.3 1 153681 6974 70 170416 0.3 1 162996 7420 71 179225 0.3 1 171910 7315 72 171231 0.3 1 163925 7306 73 181424 0.3 1 173901 7523 74 167534 0.3 1 160668 6866 75 160295 0.3 1 153643 6652 76 157715 0.3 1 151296 6419 77 157679 0.3 1 150903 6776 78 152483 0.3 1 146130 6353 79 147737 0.3 1 141492 6245 80 146667 0.3 1 140666 6001 81 145920 0.3 1 140003 5917 82 140689 0.3 1 134853 5836 83 136034 0.3 1 130439 5595 84 133908 0.3 1 128250 5658 85 131675 0.3 1 126012 5663 86 131672 0.3 1 126197 5475 87 133848 0.3 1 128384 5464 88 129850 0.3 1 124580 5270 89 116878 0.3 1 112187 4691 90 113165 0.3 1 108451 4714 91 107851 0.3 1 103636 4215 92 101212 0.3 1 97187 4025 93 98995 0.3 1 94995 4000 94 95394 0.3 1 91542 3852 95 90020 0.3 1 86380 3640 96 85913 0.3 1 82550 3363 97 80493 0.3 1 77312 3181 98 75879 0.3 1 72925 2954 99 77605 0.3 1 74598 3007 100 70637 0.3 1 67912 2725 101 67043 0.3 1 64475 2568 102 62076 0.3 1 59759 2317 103 56002 0.3 1 53869 2133 104 53213 0.3 1 51172 2041 105 47322 0.3 1 45493 1829 106 43803 0.3 1 42161 1642 107 39428 0.3 1 37938 1490 108 36024 0.3 1 34621 1403 109 33005 0.3 1 31801 1204 110 30413 0.3 1 29223 1190 111 28718 0.3 1 27704 1014 112 24826 0.3 1 23909 917 113 22246 0.3 1 21395 851 114 19255 0.3 1 18504 751 115 16125 0.3 1 15460 665 116 14013 0.3 1 13452 561 117 11755 0.3 1 11314 441 118 10504 0.3 1 10075 429 119 8740 0.3 1 8381 359 120 7099 0.3 1 6789 310 121 6395 0.3 1 6127 268 122 5283 0.3 1 5086 197 123 4656 0.3 1 4456 200 124 3824 0.3 1 3672 152 125 3323 0.3 1 3181 142 126 2821 0.3 1 2694 127 127 2334 0.3 1 2219 115 128 1727 0.3 1 1654 73 129 1502 0.3 1 1423 79 130 1215 0.3 1 1157 58 131 1055 0.3 1 1002 53 132 1009 0.3 1 967 42 133 1312 0.3 1 1260 52 134 1503 0.3 1 1462 41 135 647 0.3 1 618 29 136 354 0.3 1 338 16 137 216 0.3 1 209 7 138 150 0.3 1 140 10 139 114 0.3 1 110 4 140 64 0.3 1 60 4 141 66 0.3 1 61 5 142 51 0.3 1 49 2 143 40 0.3 1 37 3 144 27 0.3 1 25 2 145 50 0.3 1 45 5 146 38 0.3 1 37 1 147 120 0.3 1 112 8 148 74 0.3 1 68 6 149 76 0.3 1 73 3 150 581 0.3 1 559 22 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_32psu_1_S1_L001_R2_001.fastq.gz ============================================= 19624894 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 19624894 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 262575 (1.34%)