SUMMARISING RUN PARAMETERS ========================== Input filename: A-N4371-2.end2.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4 Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; 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 sequences will be trimmed by 1 bp on their 3' end to avoid problems with invalid paired-end alignments with Bowtie 1 Output file will be GZIP compressed This is cutadapt 1.16 with Python 2.7.13 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA A-N4371-2.end2.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 2017.94 s (35 us/read; 1.73 M reads/minute). === Summary === Total reads processed: 58,348,234 Reads with adapters: 22,731,761 (39.0%) Reads written (passing filters): 58,348,234 (100.0%) Total basepairs processed: 3,745,062,539 bp Quality-trimmed: 258,840 bp (0.0%) Total written (filtered): 3,706,486,363 bp (99.0%) === Adapter 1 === Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 22731761 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 27.6% C: 27.3% G: 23.0% T: 22.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 17791011 14587058.5 0 17791011 2 3390353 3646764.6 0 3390353 3 914840 911691.2 0 914840 4 201825 227922.8 0 201825 5 52313 56980.7 0 52313 6 28318 14245.2 0 28318 7 10037 3561.3 0 10037 8 7691 890.3 0 7691 9 8007 222.6 0 6144 1863 10 8062 55.6 1 5189 2873 11 9433 13.9 1 5716 3717 12 8093 3.5 1 6008 2085 13 7493 3.5 1 5930 1563 14 8702 3.5 1 5273 3429 15 7969 3.5 1 4919 3050 16 6324 3.5 1 4572 1752 17 6136 3.5 1 4707 1429 18 5951 3.5 1 5324 627 19 7465 3.5 1 6298 1167 20 7721 3.5 1 6572 1149 21 8467 3.5 1 7681 786 22 11557 3.5 1 8768 2789 23 11319 3.5 1 10341 978 24 11562 3.5 1 10512 1050 25 8766 3.5 1 8057 709 26 7412 3.5 1 6676 736 27 7340 3.5 1 6312 1028 28 8359 3.5 1 7369 990 29 9252 3.5 1 8337 915 30 10285 3.5 1 9539 746 31 11209 3.5 1 10317 892 32 11966 3.5 1 11047 919 33 21131 3.5 1 19826 1305 34 9482 3.5 1 8692 790 35 16679 3.5 1 15753 926 36 8792 3.5 1 8009 783 37 8114 3.5 1 7528 586 38 13330 3.5 1 12375 955 39 4187 3.5 1 3592 595 40 5986 3.5 1 5301 685 41 2641 3.5 1 2112 529 42 1885 3.5 1 1453 432 43 2158 3.5 1 974 1184 44 1253 3.5 1 781 472 45 1840 3.5 1 824 1016 46 1567 3.5 1 915 652 47 1243 3.5 1 722 521 48 2037 3.5 1 1173 864 49 2148 3.5 1 1619 529 50 4134 3.5 1 206 3928 51 873 3.5 1 44 829 52 600 3.5 1 18 582 53 1172 3.5 1 10 1162 54 364 3.5 1 13 351 55 1028 3.5 1 7 1021 56 543 3.5 1 4 539 57 387 3.5 1 8 379 58 1052 3.5 1 6 1046 59 683 3.5 1 1 682 60 2569 3.5 1 5 2564 61 430 3.5 1 5 425 62 533 3.5 1 29 504 63 919 3.5 1 8 911 64 240 3.5 1 9 231 65 324 3.5 1 5 319 66 366 3.5 1 5 361 67 571 3.5 1 15 556 68 983 3.5 1 11 972 69 194 3.5 1 6 188 70 204 3.5 1 11 193 71 143 3.5 1 4 139 72 234 3.5 1 12 222 73 942 3.5 1 23 919 74 307 3.5 1 55 252 75 2116 3.5 1 1654 462 76 139 3.5 1 8 131 RUN STATISTICS FOR INPUT FILE: A-N4371-2.end2.fastq.gz ============================================= 58348234 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 58348234 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 47307 (0.08%)