No quality encoding type selected. Assuming that the data provided uses Sanger encoded Phred scores (default) Path to Cutadapt set as: 'cutadapt' (default) Cutadapt seems to be working fine (tested command 'cutadapt --version') AUTO-DETECTING ADAPTER TYPE =========================== Attempting to auto-detect adapter type from the first 1 million sequences of the first file (>> 1_ATCACG_L001_R1_001.fastq.gz <<) Found perfect matches for the following adapter sequences: Adapter type Count Sequence Sequences analysed Percentage Illumina 9112 AGATCGGAAGAGC 1000000 0.91 Nextera 0 CTGTCTCTTATA 1000000 0.00 smallRNA 0 TGGAATTCTCGG 1000000 0.00 Using Illumina adapter for trimming (count: 9112). Second best hit was Nextera (count: 0) gzip: stdout: Broken pipe Writing report to '/home/sam/analyses/20180503_trimgalore/1_ATCACG_L001_R1_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: 1_ATCACG_L001_R1_001.fastq.gz Trimming mode: single-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 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 before a sequence 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 1 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 /home/sam/analyses/20180503_trimgalore/20180503_trim_fastqc --threads 16' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to 1_ATCACG_L001_R1_001_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file 1_ATCACG_L001_R1_001.fastq.gz <<< This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC 1_ATCACG_L001_R1_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 178.25 s (19 us/read; 3.16 M reads/minute). === Summary === Total reads processed: 9,402,890 Reads with adapters: 3,614,450 (38.4%) Reads written (passing filters): 9,402,890 (100.0%) Total basepairs processed: 479,547,390 bp Quality-trimmed: 1,696,655 bp (0.4%) Total written (filtered): 470,451,893 bp (98.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 3614450 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 31.4% C: 1.4% G: 20.7% T: 46.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2534817 2350722.5 0 2534817 2 588836 587680.6 0 588836 3 204258 146920.2 0 204258 4 88103 36730.0 0 88103 5 17429 9182.5 0 17429 6 15373 2295.6 0 15373 7 13444 573.9 0 13444 8 12820 143.5 0 12820 9 12758 35.9 0 12524 234 10 11538 9.0 1 10942 596 11 10792 2.2 1 10254 538 12 10254 0.6 1 9851 403 13 8731 0.1 1 8342 389 14 9191 0.1 1 8738 453 15 8084 0.1 1 7583 501 16 7876 0.1 1 7481 395 17 6938 0.1 1 6639 299 18 6454 0.1 1 6171 283 19 5903 0.1 1 5610 293 20 5383 0.1 1 5103 280 21 5083 0.1 1 4790 293 22 4643 0.1 1 4397 246 23 4171 0.1 1 3933 238 24 3683 0.1 1 3464 219 25 3166 0.1 1 2987 179 26 2610 0.1 1 2451 159 27 2135 0.1 1 1984 151 28 1995 0.1 1 1857 138 29 1717 0.1 1 1614 103 30 1262 0.1 1 1188 74 31 987 0.1 1 907 80 32 773 0.1 1 723 50 33 587 0.1 1 556 31 34 338 0.1 1 315 23 35 167 0.1 1 159 8 36 102 0.1 1 95 7 37 53 0.1 1 50 3 38 53 0.1 1 51 2 39 33 0.1 1 31 2 40 32 0.1 1 28 4 41 41 0.1 1 37 4 42 100 0.1 1 90 10 43 111 0.1 1 107 4 44 262 0.1 1 252 10 45 411 0.1 1 399 12 46 385 0.1 1 361 24 47 255 0.1 1 228 27 48 45 0.1 1 42 3 49 27 0.1 1 20 7 50 17 0.1 1 16 1 51 224 0.1 1 183 41 RUN STATISTICS FOR INPUT FILE: 1_ATCACG_L001_R1_001.fastq.gz ============================================= 9402890 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 156572 (1.7%) >>> Now running FastQC on the data <<< Can't exec "fastqc": No such file or directory at /home/shared/TrimGalore-0.4.5/trim_galore line 785. Writing report to '/home/sam/analyses/20180503_trimgalore/2_CGATGT_L001_R1_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: 2_CGATGT_L001_R1_001.fastq.gz Trimming mode: single-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 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 before a sequence 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 1 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 /home/sam/analyses/20180503_trimgalore/20180503_trim_fastqc --threads 16' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to 2_CGATGT_L001_R1_001_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file 2_CGATGT_L001_R1_001.fastq.gz <<< 10000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC 2_CGATGT_L001_R1_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 229.58 s (19 us/read; 3.12 M reads/minute). === Summary === Total reads processed: 11,954,873 Reads with adapters: 4,759,817 (39.8%) Reads written (passing filters): 11,954,873 (100.0%) Total basepairs processed: 609,698,523 bp Quality-trimmed: 1,934,183 bp (0.3%) Total written (filtered): 595,521,684 bp (97.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4759817 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.6% C: 2.2% G: 21.7% T: 45.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 3158682 2988718.2 0 3158682 2 762522 747179.6 0 762522 3 283079 186794.9 0 283079 4 123149 46698.7 0 123149 5 33918 11674.7 0 33918 6 29520 2918.7 0 29520 7 26966 729.7 0 26966 8 26048 182.4 0 26048 9 26083 45.6 0 25757 326 10 23691 11.4 1 22611 1080 11 22687 2.9 1 21775 912 12 21992 0.7 1 21251 741 13 18838 0.2 1 18122 716 14 19991 0.2 1 19139 852 15 18228 0.2 1 17261 967 16 17515 0.2 1 16720 795 17 15543 0.2 1 14889 654 18 14803 0.2 1 14230 573 19 13744 0.2 1 13084 660 20 13268 0.2 1 12580 688 21 12071 0.2 1 11465 606 22 11254 0.2 1 10660 594 23 10146 0.2 1 9659 487 24 9365 0.2 1 8841 524 25 8059 0.2 1 7635 424 26 6645 0.2 1 6261 384 27 5757 0.2 1 5367 390 28 5293 0.2 1 4964 329 29 4478 0.2 1 4163 315 30 3459 0.2 1 3247 212 31 2708 0.2 1 2539 169 32 2250 0.2 1 2116 134 33 1610 0.2 1 1520 90 34 928 0.2 1 877 51 35 581 0.2 1 549 32 36 282 0.2 1 264 18 37 181 0.2 1 171 10 38 146 0.2 1 128 18 39 111 0.2 1 103 8 40 90 0.2 1 79 11 41 136 0.2 1 133 3 42 230 0.2 1 218 12 43 275 0.2 1 260 15 44 517 0.2 1 497 20 45 700 0.2 1 669 31 46 841 0.2 1 800 41 47 561 0.2 1 499 62 48 119 0.2 1 109 10 49 54 0.2 1 47 7 50 67 0.2 1 59 8 51 636 0.2 1 513 123 RUN STATISTICS FOR INPUT FILE: 2_CGATGT_L001_R1_001.fastq.gz ============================================= 11954873 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 300406 (2.5%) >>> Now running FastQC on the data <<< Can't exec "fastqc": No such file or directory at /home/shared/TrimGalore-0.4.5/trim_galore line 785. Writing report to '/home/sam/analyses/20180503_trimgalore/3_TTAGGC_L001_R1_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: 3_TTAGGC_L001_R1_001.fastq.gz Trimming mode: single-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 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 before a sequence 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 1 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 /home/sam/analyses/20180503_trimgalore/20180503_trim_fastqc --threads 16' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to 3_TTAGGC_L001_R1_001_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file 3_TTAGGC_L001_R1_001.fastq.gz <<< 10000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC 3_TTAGGC_L001_R1_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 221.23 s (19 us/read; 3.20 M reads/minute). === Summary === Total reads processed: 11,817,358 Reads with adapters: 4,606,953 (39.0%) Reads written (passing filters): 11,817,358 (100.0%) Total basepairs processed: 602,685,258 bp Quality-trimmed: 2,616,062 bp (0.4%) Total written (filtered): 589,618,988 bp (97.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4606953 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 31.2% C: 1.7% G: 21.0% T: 46.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 3144638 2954339.5 0 3144638 2 749606 738584.9 0 749606 3 263293 184646.2 0 263293 4 117830 46161.6 0 117830 5 28890 11540.4 0 28890 6 25409 2885.1 0 25409 7 22726 721.3 0 22726 8 21766 180.3 0 21766 9 21567 45.1 0 21262 305 10 19726 11.3 1 18729 997 11 18046 2.8 1 17214 832 12 17149 0.7 1 16487 662 13 14709 0.2 1 14113 596 14 15359 0.2 1 14673 686 15 13107 0.2 1 12401 706 16 12953 0.2 1 12295 658 17 11724 0.2 1 11250 474 18 10539 0.2 1 10137 402 19 9528 0.2 1 9077 451 20 9185 0.2 1 8752 433 21 8416 0.2 1 7963 453 22 7405 0.2 1 7045 360 23 6672 0.2 1 6351 321 24 6253 0.2 1 5904 349 25 5200 0.2 1 4911 289 26 4304 0.2 1 4071 233 27 3663 0.2 1 3406 257 28 3422 0.2 1 3191 231 29 2902 0.2 1 2712 190 30 2295 0.2 1 2160 135 31 1760 0.2 1 1652 108 32 1385 0.2 1 1320 65 33 1043 0.2 1 995 48 34 669 0.2 1 641 28 35 389 0.2 1 368 21 36 250 0.2 1 229 21 37 108 0.2 1 101 7 38 87 0.2 1 79 8 39 65 0.2 1 59 6 40 52 0.2 1 49 3 41 64 0.2 1 64 42 127 0.2 1 125 2 43 180 0.2 1 169 11 44 330 0.2 1 313 17 45 541 0.2 1 525 16 46 591 0.2 1 568 23 47 434 0.2 1 382 52 48 87 0.2 1 83 4 49 36 0.2 1 30 6 50 40 0.2 1 33 7 51 433 0.2 1 349 84 RUN STATISTICS FOR INPUT FILE: 3_TTAGGC_L001_R1_001.fastq.gz ============================================= 11817358 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 262037 (2.2%) >>> Now running FastQC on the data <<< Can't exec "fastqc": No such file or directory at /home/shared/TrimGalore-0.4.5/trim_galore line 785. Writing report to '/home/sam/analyses/20180503_trimgalore/4_TGACCA_L001_R1_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: 4_TGACCA_L001_R1_001.fastq.gz Trimming mode: single-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 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 before a sequence 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 1 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 /home/sam/analyses/20180503_trimgalore/20180503_trim_fastqc --threads 16' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to 4_TGACCA_L001_R1_001_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file 4_TGACCA_L001_R1_001.fastq.gz <<< 10000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC 4_TGACCA_L001_R1_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 215.97 s (19 us/read; 3.22 M reads/minute). === Summary === Total reads processed: 11,606,618 Reads with adapters: 4,470,755 (38.5%) Reads written (passing filters): 11,606,618 (100.0%) Total basepairs processed: 591,937,518 bp Quality-trimmed: 2,245,132 bp (0.4%) Total written (filtered): 580,602,143 bp (98.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4470755 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 31.7% C: 1.3% G: 20.3% T: 46.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 3147149 2901654.5 0 3147149 2 722625 725413.6 0 722625 3 250384 181353.4 0 250384 4 108481 45338.4 0 108481 5 21488 11334.6 0 21488 6 18853 2833.6 0 18853 7 16764 708.4 0 16764 8 16269 177.1 0 16269 9 15639 44.3 0 15347 292 10 14359 11.1 1 13593 766 11 13170 2.8 1 12541 629 12 12907 0.7 1 12430 477 13 10766 0.2 1 10328 438 14 11214 0.2 1 10771 443 15 9452 0.2 1 8948 504 16 9996 0.2 1 9523 473 17 8102 0.2 1 7741 361 18 7676 0.2 1 7357 319 19 7168 0.2 1 6807 361 20 6596 0.2 1 6255 341 21 5906 0.2 1 5567 339 22 5435 0.2 1 5122 313 23 4813 0.2 1 4560 253 24 4375 0.2 1 4118 257 25 3610 0.2 1 3432 178 26 2846 0.2 1 2668 178 27 2352 0.2 1 2171 181 28 2192 0.2 1 2045 147 29 1735 0.2 1 1628 107 30 1468 0.2 1 1364 104 31 1005 0.2 1 928 77 32 875 0.2 1 815 60 33 579 0.2 1 549 30 34 335 0.2 1 313 22 35 233 0.2 1 216 17 36 127 0.2 1 119 8 37 91 0.2 1 88 3 38 74 0.2 1 71 3 39 71 0.2 1 66 5 40 71 0.2 1 64 7 41 89 0.2 1 86 3 42 186 0.2 1 170 16 43 201 0.2 1 187 14 44 449 0.2 1 421 28 45 732 0.2 1 699 33 46 739 0.2 1 702 37 47 468 0.2 1 412 56 48 102 0.2 1 95 7 49 41 0.2 1 39 2 50 54 0.2 1 47 7 51 443 0.2 1 360 83 RUN STATISTICS FOR INPUT FILE: 4_TGACCA_L001_R1_001.fastq.gz ============================================= 11606618 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 197762 (1.7%) >>> Now running FastQC on the data <<< Can't exec "fastqc": No such file or directory at /home/shared/TrimGalore-0.4.5/trim_galore line 785. Writing report to '/home/sam/analyses/20180503_trimgalore/5_ACAGTG_L001_R1_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: 5_ACAGTG_L001_R1_001.fastq.gz Trimming mode: single-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 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 before a sequence 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 1 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 /home/sam/analyses/20180503_trimgalore/20180503_trim_fastqc --threads 16' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to 5_ACAGTG_L001_R1_001_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file 5_ACAGTG_L001_R1_001.fastq.gz <<< 10000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC 5_ACAGTG_L001_R1_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 241.78 s (19 us/read; 3.12 M reads/minute). === Summary === Total reads processed: 12,589,609 Reads with adapters: 5,003,685 (39.7%) Reads written (passing filters): 12,589,609 (100.0%) Total basepairs processed: 642,070,059 bp Quality-trimmed: 2,594,232 bp (0.4%) Total written (filtered): 626,202,947 bp (97.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 5003685 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.4% C: 2.0% G: 21.9% T: 45.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 3295604 3147402.2 0 3295604 2 802076 786850.6 0 802076 3 289174 196712.6 0 289174 4 132748 49178.2 0 132748 5 37772 12294.5 0 37772 6 33518 3073.6 0 33518 7 30685 768.4 0 30685 8 29675 192.1 0 29675 9 29294 48.0 0 28914 380 10 26932 12.0 1 25771 1161 11 25424 3.0 1 24438 986 12 24576 0.8 1 23687 889 13 21216 0.2 1 20361 855 14 22921 0.2 1 21965 956 15 18687 0.2 1 17712 975 16 19766 0.2 1 18777 989 17 16813 0.2 1 16133 680 18 16135 0.2 1 15502 633 19 15003 0.2 1 14260 743 20 13995 0.2 1 13335 660 21 12979 0.2 1 12295 684 22 12172 0.2 1 11539 633 23 11217 0.2 1 10663 554 24 10242 0.2 1 9608 634 25 8811 0.2 1 8346 465 26 7468 0.2 1 7010 458 27 6717 0.2 1 6246 471 28 6216 0.2 1 5834 382 29 5562 0.2 1 5215 347 30 4179 0.2 1 3933 246 31 3458 0.2 1 3263 195 32 2742 0.2 1 2590 152 33 2233 0.2 1 2128 105 34 1264 0.2 1 1197 67 35 813 0.2 1 766 47 36 417 0.2 1 393 24 37 250 0.2 1 236 14 38 182 0.2 1 174 8 39 98 0.2 1 94 4 40 96 0.2 1 94 2 41 112 0.2 1 107 5 42 235 0.2 1 225 10 43 281 0.2 1 265 16 44 521 0.2 1 505 16 45 769 0.2 1 747 22 46 900 0.2 1 865 35 47 653 0.2 1 593 60 48 123 0.2 1 117 6 49 71 0.2 1 63 8 50 66 0.2 1 62 4 51 824 0.2 1 707 117 RUN STATISTICS FOR INPUT FILE: 5_ACAGTG_L001_R1_001.fastq.gz ============================================= 12589609 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 358290 (2.8%) >>> Now running FastQC on the data <<< Can't exec "fastqc": No such file or directory at /home/shared/TrimGalore-0.4.5/trim_galore line 785. Writing report to '/home/sam/analyses/20180503_trimgalore/6_GCCAAT_L001_R1_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: 6_GCCAAT_L001_R1_001.fastq.gz Trimming mode: single-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 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 before a sequence 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 1 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 /home/sam/analyses/20180503_trimgalore/20180503_trim_fastqc --threads 16' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to 6_GCCAAT_L001_R1_001_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file 6_GCCAAT_L001_R1_001.fastq.gz <<< 10000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC 6_GCCAAT_L001_R1_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 233.41 s (19 us/read; 3.21 M reads/minute). === Summary === Total reads processed: 12,489,766 Reads with adapters: 4,926,737 (39.4%) Reads written (passing filters): 12,489,766 (100.0%) Total basepairs processed: 636,978,066 bp Quality-trimmed: 2,185,070 bp (0.3%) Total written (filtered): 622,210,082 bp (97.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4926737 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.5% C: 2.0% G: 21.7% T: 45.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 3276852 3122441.5 0 3276852 2 794601 780610.4 0 794601 3 285283 195152.6 0 285283 4 128704 48788.1 0 128704 5 34517 12197.0 0 34517 6 30844 3049.3 0 30844 7 27794 762.3 0 27794 8 26986 190.6 0 26986 9 26705 47.6 0 26364 341 10 24540 11.9 1 23408 1132 11 22952 3.0 1 21953 999 12 22249 0.7 1 21427 822 13 19064 0.2 1 18363 701 14 20118 0.2 1 19165 953 15 18116 0.2 1 17196 920 16 17610 0.2 1 16786 824 17 15552 0.2 1 14920 632 18 14792 0.2 1 14184 608 19 13580 0.2 1 12901 679 20 13017 0.2 1 12408 609 21 12046 0.2 1 11420 626 22 11133 0.2 1 10543 590 23 10274 0.2 1 9720 554 24 9512 0.2 1 8930 582 25 8110 0.2 1 7681 429 26 7068 0.2 1 6648 420 27 6240 0.2 1 5852 388 28 5751 0.2 1 5401 350 29 5135 0.2 1 4807 328 30 3946 0.2 1 3711 235 31 2969 0.2 1 2764 205 32 2533 0.2 1 2391 142 33 1882 0.2 1 1783 99 34 1129 0.2 1 1075 54 35 677 0.2 1 633 44 36 417 0.2 1 393 24 37 181 0.2 1 171 10 38 147 0.2 1 140 7 39 94 0.2 1 87 7 40 78 0.2 1 73 5 41 108 0.2 1 97 11 42 189 0.2 1 173 16 43 214 0.2 1 201 13 44 419 0.2 1 390 29 45 541 0.2 1 524 17 46 683 0.2 1 649 34 47 542 0.2 1 494 48 48 110 0.2 1 96 14 49 49 0.2 1 37 12 50 61 0.2 1 59 2 51 623 0.2 1 514 109 RUN STATISTICS FOR INPUT FILE: 6_GCCAAT_L001_R1_001.fastq.gz ============================================= 12489766 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 314182 (2.5%) >>> Now running FastQC on the data <<< Can't exec "fastqc": No such file or directory at /home/shared/TrimGalore-0.4.5/trim_galore line 785. Writing report to '/home/sam/analyses/20180503_trimgalore/7_CAGATC_L001_R1_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: 7_CAGATC_L001_R1_001.fastq.gz Trimming mode: single-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 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 before a sequence 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 1 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 /home/sam/analyses/20180503_trimgalore/20180503_trim_fastqc --threads 16' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to 7_CAGATC_L001_R1_001_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file 7_CAGATC_L001_R1_001.fastq.gz <<< 10000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC 7_CAGATC_L001_R1_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 196.93 s (19 us/read; 3.14 M reads/minute). === Summary === Total reads processed: 10,295,293 Reads with adapters: 4,013,389 (39.0%) Reads written (passing filters): 10,295,293 (100.0%) Total basepairs processed: 525,059,943 bp Quality-trimmed: 1,586,339 bp (0.3%) Total written (filtered): 514,717,887 bp (98.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4013389 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 31.0% C: 1.5% G: 21.0% T: 46.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2753314 2573823.2 0 2753314 2 652174 643455.8 0 652174 3 234852 160864.0 0 234852 4 103251 40216.0 0 103251 5 24247 10054.0 0 24247 6 21578 2513.5 0 21578 7 19539 628.4 0 19539 8 18333 157.1 0 18333 9 18085 39.3 0 17813 272 10 16281 9.8 1 15449 832 11 15275 2.5 1 14558 717 12 14364 0.6 1 13780 584 13 12550 0.2 1 12015 535 14 12626 0.2 1 12023 603 15 11002 0.2 1 10360 642 16 10624 0.2 1 10072 552 17 9315 0.2 1 8892 423 18 8494 0.2 1 8140 354 19 7724 0.2 1 7315 409 20 6985 0.2 1 6624 361 21 6391 0.2 1 6101 290 22 5631 0.2 1 5324 307 23 5161 0.2 1 4876 285 24 4535 0.2 1 4266 269 25 3712 0.2 1 3500 212 26 3101 0.2 1 2926 175 27 2667 0.2 1 2470 197 28 2496 0.2 1 2324 172 29 2116 0.2 1 1986 130 30 1597 0.2 1 1488 109 31 1151 0.2 1 1078 73 32 928 0.2 1 863 65 33 646 0.2 1 616 30 34 388 0.2 1 362 26 35 261 0.2 1 247 14 36 164 0.2 1 147 17 37 73 0.2 1 61 12 38 53 0.2 1 49 4 39 55 0.2 1 50 5 40 49 0.2 1 47 2 41 44 0.2 1 41 3 42 89 0.2 1 82 7 43 89 0.2 1 81 8 44 185 0.2 1 169 16 45 288 0.2 1 271 17 46 364 0.2 1 350 14 47 232 0.2 1 213 19 48 33 0.2 1 28 5 49 15 0.2 1 14 1 50 21 0.2 1 15 6 51 241 0.2 1 199 42 RUN STATISTICS FOR INPUT FILE: 7_CAGATC_L001_R1_001.fastq.gz ============================================= 10295293 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 181439 (1.8%) >>> Now running FastQC on the data <<< Can't exec "fastqc": No such file or directory at /home/shared/TrimGalore-0.4.5/trim_galore line 785. Writing report to '/home/sam/analyses/20180503_trimgalore/8_ACTTGA_L001_R1_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: 8_ACTTGA_L001_R1_001.fastq.gz Trimming mode: single-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 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 before a sequence 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 1 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 /home/sam/analyses/20180503_trimgalore/20180503_trim_fastqc --threads 16' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to 8_ACTTGA_L001_R1_001_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file 8_ACTTGA_L001_R1_001.fastq.gz <<< 10000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC 8_ACTTGA_L001_R1_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 274.83 s (19 us/read; 3.14 M reads/minute). === Summary === Total reads processed: 14,374,642 Reads with adapters: 5,792,989 (40.3%) Reads written (passing filters): 14,374,642 (100.0%) Total basepairs processed: 733,106,742 bp Quality-trimmed: 2,401,819 bp (0.3%) Total written (filtered): 714,442,682 bp (97.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 5792989 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.1% C: 2.3% G: 22.1% T: 45.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 3740046 3593660.5 0 3740046 2 922606 898415.1 0 922606 3 342031 224603.8 0 342031 4 157961 56150.9 0 157961 5 48861 14037.7 0 48861 6 44020 3509.4 0 44020 7 40037 877.4 0 40037 8 38573 219.3 0 38573 9 38207 54.8 0 37685 522 10 35360 13.7 1 33447 1913 11 33552 3.4 1 31628 1924 12 32274 0.9 1 30595 1679 13 28017 0.2 1 26496 1521 14 29576 0.2 1 27967 1609 15 25117 0.2 1 23397 1720 16 25847 0.2 1 24279 1568 17 22709 0.2 1 21479 1230 18 21119 0.2 1 19963 1156 19 19532 0.2 1 18352 1180 20 18269 0.2 1 17071 1198 21 17315 0.2 1 16162 1153 22 15979 0.2 1 14921 1058 23 14546 0.2 1 13663 883 24 13240 0.2 1 12241 999 25 11561 0.2 1 10799 762 26 9646 0.2 1 8948 698 27 8479 0.2 1 7790 689 28 7753 0.2 1 7178 575 29 6730 0.2 1 6150 580 30 5312 0.2 1 4936 376 31 3881 0.2 1 3564 317 32 3272 0.2 1 3032 240 33 2433 0.2 1 2259 174 34 1382 0.2 1 1284 98 35 876 0.2 1 817 59 36 469 0.2 1 440 29 37 258 0.2 1 234 24 38 153 0.2 1 138 15 39 149 0.2 1 141 8 40 159 0.2 1 146 13 41 199 0.2 1 182 17 42 282 0.2 1 255 27 43 357 0.2 1 330 27 44 764 0.2 1 718 46 45 1062 0.2 1 1014 48 46 1048 0.2 1 988 60 47 823 0.2 1 733 90 48 158 0.2 1 137 21 49 60 0.2 1 52 8 50 78 0.2 1 73 5 51 851 0.2 1 679 172 RUN STATISTICS FOR INPUT FILE: 8_ACTTGA_L001_R1_001.fastq.gz ============================================= 14374642 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 425429 (3.0%) >>> Now running FastQC on the data <<< Can't exec "fastqc": No such file or directory at /home/shared/TrimGalore-0.4.5/trim_galore line 785. Writing report to '/home/sam/analyses/20180503_trimgalore/zr1394_10_s456.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: zr1394_10_s456.fastq.gz Trimming mode: single-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 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 before a sequence 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 1 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 /home/sam/analyses/20180503_trimgalore/20180503_trim_fastqc --threads 16' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr1394_10_s456_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file zr1394_10_s456.fastq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC zr1394_10_s456.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 1484.68 s (19 us/read; 3.20 M reads/minute). === Summary === Total reads processed: 79,264,583 Reads with adapters: 30,297,063 (38.2%) Reads written (passing filters): 79,264,583 (100.0%) Total basepairs processed: 3,978,999,570 bp Quality-trimmed: 5,235,908 bp (0.1%) Total written (filtered): 3,941,256,193 bp (99.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 30297063 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 44.6% C: 10.4% G: 4.9% T: 39.4% none/other: 0.7% Overview of removed sequences length count expect max.err error counts 1 28762957 19816145.8 0 28762957 2 1012763 4954036.4 0 1012763 3 417959 1238509.1 0 417959 4 81634 309627.3 0 81634 5 12134 77406.8 0 12134 6 1255 19351.7 0 1255 7 4142 4837.9 0 4142 8 1302 1209.5 0 1302 9 671 302.4 0 46 625 10 1592 75.6 1 5 1587 11 253 18.9 1 16 237 12 147 4.7 1 0 147 13 36 1.2 1 0 36 14 23 1.2 1 0 23 15 10 1.2 1 0 10 16 27 1.2 1 0 27 17 77 1.2 1 0 77 18 36 1.2 1 0 36 19 11 1.2 1 0 11 20 3 1.2 1 0 3 22 1 1.2 1 0 1 23 3 1.2 1 0 3 25 1 1.2 1 0 1 26 2 1.2 1 0 2 27 5 1.2 1 0 5 28 4 1.2 1 0 4 29 11 1.2 1 0 11 30 1 1.2 1 0 1 31 2 1.2 1 0 2 33 1 1.2 1 0 1 RUN STATISTICS FOR INPUT FILE: zr1394_10_s456.fastq.gz ============================================= 79264583 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 1043126 (1.3%) >>> Now running FastQC on the data <<< Can't exec "fastqc": No such file or directory at /home/shared/TrimGalore-0.4.5/trim_galore line 785. Writing report to '/home/sam/analyses/20180503_trimgalore/zr1394_11_s456.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: zr1394_11_s456.fastq.gz Trimming mode: single-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 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 before a sequence 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 1 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 /home/sam/analyses/20180503_trimgalore/20180503_trim_fastqc --threads 16' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr1394_11_s456_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file zr1394_11_s456.fastq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC zr1394_11_s456.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 1032.71 s (19 us/read; 3.20 M reads/minute). === Summary === Total reads processed: 55,109,528 Reads with adapters: 21,238,441 (38.5%) Reads written (passing filters): 55,109,528 (100.0%) Total basepairs processed: 2,769,826,173 bp Quality-trimmed: 3,100,652 bp (0.1%) Total written (filtered): 2,744,305,038 bp (99.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 21238441 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 46.1% C: 10.8% G: 3.8% T: 38.6% none/other: 0.7% Overview of removed sequences length count expect max.err error counts 1 20439811 13777382.0 0 20439811 2 513654 3444345.5 0 513654 3 226149 861086.4 0 226149 4 45757 215271.6 0 45757 5 7219 53817.9 0 7219 6 683 13454.5 0 683 7 1872 3363.6 0 1872 8 730 840.9 0 730 9 346 210.2 0 39 307 10 807 52.6 1 7 800 11 265 13.1 1 28 237 12 147 3.3 1 0 147 13 59 0.8 1 0 59 14 45 0.8 1 0 45 15 67 0.8 1 0 67 16 182 0.8 1 0 182 17 371 0.8 1 0 371 18 222 0.8 1 0 222 19 24 0.8 1 0 24 20 3 0.8 1 0 3 21 3 0.8 1 0 3 22 2 0.8 1 0 2 23 3 0.8 1 0 3 24 1 0.8 1 0 1 25 3 0.8 1 0 3 26 2 0.8 1 0 2 27 3 0.8 1 0 3 28 3 0.8 1 0 3 29 2 0.8 1 0 2 30 1 0.8 1 0 1 31 1 0.8 1 0 1 34 1 0.8 1 0 1 36 1 0.8 1 0 1 37 1 0.8 1 0 1 38 1 0.8 1 0 1 RUN STATISTICS FOR INPUT FILE: zr1394_11_s456.fastq.gz ============================================= 55109528 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 650956 (1.2%) >>> Now running FastQC on the data <<< Can't exec "fastqc": No such file or directory at /home/shared/TrimGalore-0.4.5/trim_galore line 785. Writing report to '/home/sam/analyses/20180503_trimgalore/zr1394_12_s456.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: zr1394_12_s456.fastq.gz Trimming mode: single-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 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 before a sequence 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 1 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 /home/sam/analyses/20180503_trimgalore/20180503_trim_fastqc --threads 16' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr1394_12_s456_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file zr1394_12_s456.fastq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC zr1394_12_s456.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 1139.67 s (19 us/read; 3.17 M reads/minute). === Summary === Total reads processed: 60,153,246 Reads with adapters: 24,436,298 (40.6%) Reads written (passing filters): 60,153,246 (100.0%) Total basepairs processed: 3,025,392,455 bp Quality-trimmed: 3,405,348 bp (0.1%) Total written (filtered): 2,996,148,248 bp (99.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 24436298 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 46.7% C: 10.8% G: 3.4% T: 38.4% none/other: 0.7% Overview of removed sequences length count expect max.err error counts 1 23481319 15038311.5 0 23481319 2 618279 3759577.9 0 618279 3 262540 939894.5 0 262540 4 61274 234973.6 0 61274 5 6867 58743.4 0 6867 6 674 14685.9 0 674 7 2226 3671.5 0 2226 8 854 917.9 0 854 9 404 229.5 0 34 370 10 865 57.4 1 10 855 11 211 14.3 1 23 188 12 105 3.6 1 3 102 13 36 0.9 1 0 36 14 27 0.9 1 0 27 15 33 0.9 1 0 33 16 112 0.9 1 0 112 17 273 0.9 1 0 273 18 148 0.9 1 0 148 19 21 0.9 1 0 21 20 5 0.9 1 0 5 21 1 0.9 1 0 1 22 3 0.9 1 0 3 23 2 0.9 1 0 2 24 1 0.9 1 0 1 25 5 0.9 1 0 5 26 2 0.9 1 0 2 27 3 0.9 1 0 3 28 1 0.9 1 0 1 29 1 0.9 1 0 1 30 1 0.9 1 0 1 31 1 0.9 1 0 1 32 1 0.9 1 0 1 34 2 0.9 1 0 2 36 1 0.9 1 0 1 RUN STATISTICS FOR INPUT FILE: zr1394_12_s456.fastq.gz ============================================= 60153246 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 693815 (1.2%) >>> Now running FastQC on the data <<< Can't exec "fastqc": No such file or directory at /home/shared/TrimGalore-0.4.5/trim_galore line 785. Writing report to '/home/sam/analyses/20180503_trimgalore/zr1394_13_s456.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: zr1394_13_s456.fastq.gz Trimming mode: single-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 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 before a sequence 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 1 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 /home/sam/analyses/20180503_trimgalore/20180503_trim_fastqc --threads 16' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr1394_13_s456_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file zr1394_13_s456.fastq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC zr1394_13_s456.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 1223.51 s (19 us/read; 3.19 M reads/minute). === Summary === Total reads processed: 65,081,682 Reads with adapters: 25,664,309 (39.4%) Reads written (passing filters): 65,081,682 (100.0%) Total basepairs processed: 3,272,837,182 bp Quality-trimmed: 3,459,477 bp (0.1%) Total written (filtered): 3,242,234,024 bp (99.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 25664309 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 46.6% C: 10.8% G: 3.7% T: 38.2% none/other: 0.7% Overview of removed sequences length count expect max.err error counts 1 24665742 16270420.5 0 24665742 2 643781 4067605.1 0 643781 3 280330 1016901.3 0 280330 4 58268 254225.3 0 58268 5 8366 63556.3 0 8366 6 798 15889.1 0 798 7 2561 3972.3 0 2561 8 1035 993.1 0 1035 9 508 248.3 0 36 472 10 1126 62.1 1 2 1124 11 347 15.5 1 36 311 12 174 3.9 1 1 173 13 64 1.0 1 0 64 14 56 1.0 1 0 56 15 81 1.0 1 0 81 16 200 1.0 1 0 200 17 428 1.0 1 0 428 18 365 1.0 1 0 365 19 29 1.0 1 0 29 20 6 1.0 1 0 6 21 1 1.0 1 0 1 22 1 1.0 1 0 1 23 6 1.0 1 0 6 24 6 1.0 1 0 6 25 3 1.0 1 0 3 26 5 1.0 1 0 5 27 6 1.0 1 0 6 28 1 1.0 1 0 1 29 2 1.0 1 0 2 30 2 1.0 1 0 2 31 1 1.0 1 0 1 32 4 1.0 1 0 4 33 1 1.0 1 0 1 34 2 1.0 1 0 2 35 1 1.0 1 0 1 36 2 1.0 1 0 2 RUN STATISTICS FOR INPUT FILE: zr1394_13_s456.fastq.gz ============================================= 65081682 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 729132 (1.1%) >>> Now running FastQC on the data <<< Can't exec "fastqc": No such file or directory at /home/shared/TrimGalore-0.4.5/trim_galore line 785. Writing report to '/home/sam/analyses/20180503_trimgalore/zr1394_14_s456.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: zr1394_14_s456.fastq.gz Trimming mode: single-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 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 before a sequence 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 1 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 /home/sam/analyses/20180503_trimgalore/20180503_trim_fastqc --threads 16' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr1394_14_s456_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file zr1394_14_s456.fastq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC zr1394_14_s456.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 1678.65 s (19 us/read; 3.17 M reads/minute). === Summary === Total reads processed: 88,771,906 Reads with adapters: 35,258,873 (39.7%) Reads written (passing filters): 88,771,906 (100.0%) Total basepairs processed: 4,466,488,793 bp Quality-trimmed: 4,892,927 bp (0.1%) Total written (filtered): 4,424,568,817 bp (99.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 35258873 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 47.0% C: 10.0% G: 3.1% T: 39.1% none/other: 0.7% Overview of removed sequences length count expect max.err error counts 1 34062365 22192976.5 0 34062365 2 773540 5548244.1 0 773540 3 330019 1387061.0 0 330019 4 74729 346765.3 0 74729 5 9827 86691.3 0 9827 6 972 21672.8 0 972 7 2801 5418.2 0 2801 8 877 1354.6 0 877 9 531 338.6 0 40 491 10 1365 84.7 1 5 1360 11 365 21.2 1 35 330 12 159 5.3 1 0 159 13 67 1.3 1 0 67 14 58 1.3 1 0 58 15 70 1.3 1 0 70 16 216 1.3 1 0 216 17 461 1.3 1 0 461 18 365 1.3 1 0 365 19 26 1.3 1 0 26 20 10 1.3 1 0 10 21 3 1.3 1 0 3 22 1 1.3 1 0 1 23 1 1.3 1 0 1 24 2 1.3 1 0 2 25 5 1.3 1 0 5 26 5 1.3 1 0 5 27 13 1.3 1 0 13 28 3 1.3 1 0 3 29 2 1.3 1 0 2 30 2 1.3 1 0 2 32 2 1.3 1 0 2 33 6 1.3 1 0 6 34 3 1.3 1 0 3 35 1 1.3 1 0 1 36 1 1.3 1 0 1 RUN STATISTICS FOR INPUT FILE: zr1394_14_s456.fastq.gz ============================================= 88771906 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 937269 (1.1%) >>> Now running FastQC on the data <<< Can't exec "fastqc": No such file or directory at /home/shared/TrimGalore-0.4.5/trim_galore line 785. Writing report to '/home/sam/analyses/20180503_trimgalore/zr1394_15_s456.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: zr1394_15_s456.fastq.gz Trimming mode: single-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 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 before a sequence 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 1 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 /home/sam/analyses/20180503_trimgalore/20180503_trim_fastqc --threads 16' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr1394_15_s456_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file zr1394_15_s456.fastq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC zr1394_15_s456.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 1315.43 s (19 us/read; 3.14 M reads/minute). === Summary === Total reads processed: 68,857,992 Reads with adapters: 26,803,401 (38.9%) Reads written (passing filters): 68,857,992 (100.0%) Total basepairs processed: 3,459,545,810 bp Quality-trimmed: 4,066,729 bp (0.1%) Total written (filtered): 3,427,098,592 bp (99.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 26803401 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 46.2% C: 10.8% G: 3.9% T: 38.4% none/other: 0.7% Overview of removed sequences length count expect max.err error counts 1 25748064 17214498.0 0 25748064 2 670246 4303624.5 0 670246 3 304450 1075906.1 0 304450 4 62669 268976.5 0 62669 5 9679 67244.1 0 9679 6 889 16811.0 0 889 7 2500 4202.8 0 2500 8 1116 1050.7 0 1116 9 540 262.7 0 51 489 10 1303 65.7 1 15 1288 11 391 16.4 1 46 345 12 184 4.1 1 1 183 13 70 1.0 1 0 70 14 75 1.0 1 0 75 15 96 1.0 1 0 96 16 221 1.0 1 0 221 17 442 1.0 1 0 442 18 360 1.0 1 0 360 19 38 1.0 1 0 38 20 11 1.0 1 0 11 21 8 1.0 1 0 8 22 8 1.0 1 0 8 23 6 1.0 1 0 6 24 2 1.0 1 0 2 25 5 1.0 1 0 5 26 4 1.0 1 0 4 27 9 1.0 1 0 9 28 1 1.0 1 0 1 29 2 1.0 1 0 2 30 2 1.0 1 0 2 31 2 1.0 1 0 2 32 3 1.0 1 0 3 33 1 1.0 1 0 1 34 1 1.0 1 0 1 35 2 1.0 1 0 2 36 1 1.0 1 0 1 RUN STATISTICS FOR INPUT FILE: zr1394_15_s456.fastq.gz ============================================= 68857992 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 873787 (1.3%) >>> Now running FastQC on the data <<< Can't exec "fastqc": No such file or directory at /home/shared/TrimGalore-0.4.5/trim_galore line 785. Writing report to '/home/sam/analyses/20180503_trimgalore/zr1394_16_s456.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: zr1394_16_s456.fastq.gz Trimming mode: single-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 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 before a sequence 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 1 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 /home/sam/analyses/20180503_trimgalore/20180503_trim_fastqc --threads 16' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr1394_16_s456_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file zr1394_16_s456.fastq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC zr1394_16_s456.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 1422.20 s (19 us/read; 3.18 M reads/minute). === Summary === Total reads processed: 75,450,315 Reads with adapters: 29,474,701 (39.1%) Reads written (passing filters): 75,450,315 (100.0%) Total basepairs processed: 3,791,761,278 bp Quality-trimmed: 4,327,306 bp (0.1%) Total written (filtered): 3,756,311,075 bp (99.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 29474701 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 46.2% C: 10.3% G: 3.7% T: 39.1% none/other: 0.7% Overview of removed sequences length count expect max.err error counts 1 28373958 18862578.8 0 28373958 2 697695 4715644.7 0 697695 3 317779 1178911.2 0 317779 4 66050 294727.8 0 66050 5 10402 73681.9 0 10402 6 960 18420.5 0 960 7 2933 4605.1 0 2933 8 1094 1151.3 0 1094 9 602 287.8 0 66 536 10 1198 72.0 1 9 1189 11 374 18.0 1 39 335 12 182 4.5 1 1 181 13 69 1.1 1 0 69 14 71 1.1 1 0 71 15 90 1.1 1 0 90 16 235 1.1 1 0 235 17 515 1.1 1 0 515 18 381 1.1 1 0 381 19 42 1.1 1 0 42 20 12 1.1 1 0 12 21 4 1.1 1 0 4 22 4 1.1 1 0 4 23 1 1.1 1 0 1 24 5 1.1 1 0 5 25 4 1.1 1 0 4 26 3 1.1 1 0 3 27 13 1.1 1 0 13 28 2 1.1 1 0 2 29 9 1.1 1 0 9 30 2 1.1 1 0 2 31 4 1.1 1 0 4 32 4 1.1 1 0 4 33 1 1.1 1 0 1 34 1 1.1 1 0 1 35 1 1.1 1 0 1 36 1 1.1 1 0 1 RUN STATISTICS FOR INPUT FILE: zr1394_16_s456.fastq.gz ============================================= 75450315 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 919259 (1.2%) >>> Now running FastQC on the data <<< Can't exec "fastqc": No such file or directory at /home/shared/TrimGalore-0.4.5/trim_galore line 785. Writing report to '/home/sam/analyses/20180503_trimgalore/zr1394_17_s456.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: zr1394_17_s456.fastq.gz Trimming mode: single-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 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 before a sequence 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 1 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 /home/sam/analyses/20180503_trimgalore/20180503_trim_fastqc --threads 16' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr1394_17_s456_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file zr1394_17_s456.fastq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC zr1394_17_s456.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 798.85 s (19 us/read; 3.21 M reads/minute). === Summary === Total reads processed: 42,730,485 Reads with adapters: 16,838,546 (39.4%) Reads written (passing filters): 42,730,485 (100.0%) Total basepairs processed: 2,143,526,203 bp Quality-trimmed: 2,502,691 bp (0.1%) Total written (filtered): 2,123,026,980 bp (99.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 16838546 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.5% C: 11.5% G: 4.6% T: 37.8% none/other: 0.7% Overview of removed sequences length count expect max.err error counts 1 16087858 10682621.2 0 16087858 2 461836 2670655.3 0 461836 3 232097 667663.8 0 232097 4 41330 166916.0 0 41330 5 7514 41729.0 0 7514 6 690 10432.2 0 690 7 1822 2608.1 0 1822 8 1037 652.0 0 1037 9 422 163.0 0 61 361 10 920 40.8 1 8 912 11 430 10.2 1 86 344 12 213 2.5 1 0 213 13 151 0.6 1 0 151 14 137 0.6 1 0 137 15 184 0.6 1 0 184 16 404 0.6 1 0 404 17 816 0.6 1 0 816 18 502 0.6 1 0 502 19 62 0.6 1 0 62 20 18 0.6 1 0 18 21 3 0.6 1 0 3 22 13 0.6 1 0 13 23 11 0.6 1 0 11 24 6 0.6 1 0 6 25 7 0.6 1 0 7 26 12 0.6 1 0 12 27 15 0.6 1 0 15 28 4 0.6 1 0 4 29 4 0.6 1 0 4 30 4 0.6 1 0 4 31 3 0.6 1 0 3 32 3 0.6 1 0 3 33 4 0.6 1 0 4 34 6 0.6 1 0 6 35 5 0.6 1 0 5 36 1 0.6 1 0 1 37 2 0.6 1 0 2 RUN STATISTICS FOR INPUT FILE: zr1394_17_s456.fastq.gz ============================================= 42730485 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 659939 (1.5%) >>> Now running FastQC on the data <<< Can't exec "fastqc": No such file or directory at /home/shared/TrimGalore-0.4.5/trim_galore line 785. Writing report to '/home/sam/analyses/20180503_trimgalore/zr1394_18_s456.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: zr1394_18_s456.fastq.gz Trimming mode: single-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 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 before a sequence 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 1 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 /home/sam/analyses/20180503_trimgalore/20180503_trim_fastqc --threads 16' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr1394_18_s456_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file zr1394_18_s456.fastq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC zr1394_18_s456.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 1049.98 s (19 us/read; 3.17 M reads/minute). === Summary === Total reads processed: 55,559,681 Reads with adapters: 22,333,371 (40.2%) Reads written (passing filters): 55,559,681 (100.0%) Total basepairs processed: 2,797,597,463 bp Quality-trimmed: 2,697,516 bp (0.1%) Total written (filtered): 2,771,263,695 bp (99.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 22333371 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 47.0% C: 10.9% G: 3.5% T: 38.0% none/other: 0.7% Overview of removed sequences length count expect max.err error counts 1 21444400 13889920.2 0 21444400 2 578360 3472480.1 0 578360 3 244932 868120.0 0 244932 4 53822 217030.0 0 53822 5 6117 54257.5 0 6117 6 628 13564.4 0 628 7 1872 3391.1 0 1872 8 655 847.8 0 655 9 371 211.9 0 27 344 10 865 53.0 1 10 855 11 285 13.2 1 31 254 12 142 3.3 1 1 141 13 71 0.8 1 0 71 14 64 0.8 1 0 64 15 76 0.8 1 0 76 16 170 0.8 1 0 170 17 266 0.8 1 0 266 18 201 0.8 1 0 201 19 26 0.8 1 0 26 20 6 0.8 1 0 6 21 4 0.8 1 0 4 22 3 0.8 1 0 3 23 4 0.8 1 0 4 24 6 0.8 1 0 6 25 3 0.8 1 0 3 26 9 0.8 1 0 9 27 2 0.8 1 0 2 28 1 0.8 1 0 1 29 4 0.8 1 0 4 31 2 0.8 1 0 2 32 1 0.8 1 0 1 33 1 0.8 1 0 1 35 2 0.8 1 0 2 RUN STATISTICS FOR INPUT FILE: zr1394_18_s456.fastq.gz ============================================= 55559681 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 511575 (0.9%) >>> Now running FastQC on the data <<< Can't exec "fastqc": No such file or directory at /home/shared/TrimGalore-0.4.5/trim_galore line 785. Writing report to '/home/sam/analyses/20180503_trimgalore/zr1394_1_s456.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: zr1394_1_s456.fastq.gz Trimming mode: single-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 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 before a sequence 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 1 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 /home/sam/analyses/20180503_trimgalore/20180503_trim_fastqc --threads 16' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr1394_1_s456_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file zr1394_1_s456.fastq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC zr1394_1_s456.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 894.57 s (19 us/read; 3.18 M reads/minute). === Summary === Total reads processed: 47,399,413 Reads with adapters: 19,203,284 (40.5%) Reads written (passing filters): 47,399,413 (100.0%) Total basepairs processed: 2,382,626,805 bp Quality-trimmed: 2,279,442 bp (0.1%) Total written (filtered): 2,359,943,952 bp (99.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 19203284 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 46.5% C: 10.8% G: 3.8% T: 38.3% none/other: 0.7% Overview of removed sequences length count expect max.err error counts 1 18444214 11849853.2 0 18444214 2 469739 2962463.3 0 469739 3 227505 740615.8 0 227505 4 45947 185154.0 0 45947 5 6341 46288.5 0 6341 6 636 11572.1 0 636 7 1722 2893.0 0 1722 8 731 723.3 0 731 9 358 180.8 0 43 315 10 835 45.2 1 19 816 11 429 11.3 1 46 383 12 264 2.8 1 4 260 13 130 0.7 1 0 130 14 131 0.7 1 0 131 15 205 0.7 1 0 205 16 539 0.7 1 0 539 17 1620 0.7 1 0 1620 18 1478 0.7 1 0 1478 19 166 0.7 1 0 166 20 33 0.7 1 0 33 21 15 0.7 1 0 15 22 7 0.7 1 0 7 23 14 0.7 1 0 14 24 13 0.7 1 0 13 25 14 0.7 1 0 14 26 38 0.7 1 0 38 27 34 0.7 1 0 34 28 17 0.7 1 0 17 29 12 0.7 1 0 12 30 11 0.7 1 0 11 31 21 0.7 1 0 21 32 15 0.7 1 0 15 33 15 0.7 1 0 15 34 19 0.7 1 0 19 35 11 0.7 1 0 11 36 3 0.7 1 0 3 37 1 0.7 1 0 1 38 1 0.7 1 0 1 RUN STATISTICS FOR INPUT FILE: zr1394_1_s456.fastq.gz ============================================= 47399413 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 607127 (1.3%) >>> Now running FastQC on the data <<< Can't exec "fastqc": No such file or directory at /home/shared/TrimGalore-0.4.5/trim_galore line 785. Writing report to '/home/sam/analyses/20180503_trimgalore/zr1394_2_s456.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: zr1394_2_s456.fastq.gz Trimming mode: single-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 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 before a sequence 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 1 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 /home/sam/analyses/20180503_trimgalore/20180503_trim_fastqc --threads 16' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr1394_2_s456_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file zr1394_2_s456.fastq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC zr1394_2_s456.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 881.68 s (19 us/read; 3.18 M reads/minute). === Summary === Total reads processed: 46,666,438 Reads with adapters: 18,885,170 (40.5%) Reads written (passing filters): 46,666,438 (100.0%) Total basepairs processed: 2,346,424,714 bp Quality-trimmed: 2,397,497 bp (0.1%) Total written (filtered): 2,323,928,233 bp (99.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 18885170 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 46.3% C: 10.8% G: 3.9% T: 38.3% none/other: 0.7% Overview of removed sequences length count expect max.err error counts 1 18095290 11666609.5 0 18095290 2 496013 2916652.4 0 496013 3 231867 729163.1 0 231867 4 47968 182290.8 0 47968 5 5845 45572.7 0 5845 6 652 11393.2 0 652 7 1874 2848.3 0 1874 8 729 712.1 0 729 9 427 178.0 0 33 394 10 865 44.5 1 9 856 11 376 11.1 1 57 319 12 209 2.8 1 0 209 13 100 0.7 1 0 100 14 99 0.7 1 0 99 15 182 0.7 1 0 182 16 439 0.7 1 0 439 17 1067 0.7 1 0 1067 18 932 0.7 1 0 932 19 83 0.7 1 0 83 20 22 0.7 1 0 22 21 7 0.7 1 0 7 22 14 0.7 1 0 14 23 6 0.7 1 0 6 24 6 0.7 1 0 6 25 13 0.7 1 0 13 26 16 0.7 1 0 16 27 8 0.7 1 0 8 28 8 0.7 1 0 8 29 13 0.7 1 0 13 30 3 0.7 1 0 3 31 8 0.7 1 0 8 32 12 0.7 1 0 12 33 7 0.7 1 0 7 34 6 0.7 1 0 6 35 1 0.7 1 0 1 36 1 0.7 1 0 1 37 1 0.7 1 0 1 39 1 0.7 1 0 1 RUN STATISTICS FOR INPUT FILE: zr1394_2_s456.fastq.gz ============================================= 46666438 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 561298 (1.2%) >>> Now running FastQC on the data <<< Can't exec "fastqc": No such file or directory at /home/shared/TrimGalore-0.4.5/trim_galore line 785. Writing report to '/home/sam/analyses/20180503_trimgalore/zr1394_3_s456.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: zr1394_3_s456.fastq.gz Trimming mode: single-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 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 before a sequence 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 1 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 /home/sam/analyses/20180503_trimgalore/20180503_trim_fastqc --threads 16' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr1394_3_s456_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file zr1394_3_s456.fastq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC zr1394_3_s456.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 928.08 s (19 us/read; 3.16 M reads/minute). === Summary === Total reads processed: 48,926,620 Reads with adapters: 19,871,742 (40.6%) Reads written (passing filters): 48,926,620 (100.0%) Total basepairs processed: 2,461,374,827 bp Quality-trimmed: 2,449,172 bp (0.1%) Total written (filtered): 2,437,911,467 bp (99.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 19871742 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 46.6% C: 10.4% G: 3.5% T: 38.8% none/other: 0.7% Overview of removed sequences length count expect max.err error counts 1 19123736 12231655.0 0 19123736 2 469996 3057913.8 0 469996 3 219964 764478.4 0 219964 4 45745 191119.6 0 45745 5 5398 47779.9 0 5398 6 518 11945.0 0 518 7 1564 2986.2 0 1564 8 655 746.6 0 655 9 292 186.6 0 30 262 10 785 46.7 1 17 768 11 299 11.7 1 20 279 12 194 2.9 1 2 192 13 108 0.7 1 0 108 14 60 0.7 1 0 60 15 155 0.7 1 0 155 16 357 0.7 1 0 357 17 945 0.7 1 0 945 18 761 0.7 1 0 761 19 71 0.7 1 0 71 20 18 0.7 1 0 18 21 7 0.7 1 0 7 22 3 0.7 1 0 3 23 6 0.7 1 0 6 24 5 0.7 1 0 5 25 9 0.7 1 0 9 26 12 0.7 1 0 12 27 10 0.7 1 0 10 28 13 0.7 1 0 13 29 6 0.7 1 0 6 30 8 0.7 1 0 8 31 10 0.7 1 0 10 32 8 0.7 1 0 8 33 5 0.7 1 0 5 34 10 0.7 1 0 10 35 3 0.7 1 0 3 36 2 0.7 1 0 2 37 2 0.7 1 0 2 38 2 0.7 1 0 2 RUN STATISTICS FOR INPUT FILE: zr1394_3_s456.fastq.gz ============================================= 48926620 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 549891 (1.1%) >>> Now running FastQC on the data <<< Can't exec "fastqc": No such file or directory at /home/shared/TrimGalore-0.4.5/trim_galore line 785. Writing report to '/home/sam/analyses/20180503_trimgalore/zr1394_4_s456.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: zr1394_4_s456.fastq.gz Trimming mode: single-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 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 before a sequence 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 1 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 /home/sam/analyses/20180503_trimgalore/20180503_trim_fastqc --threads 16' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr1394_4_s456_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file zr1394_4_s456.fastq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC zr1394_4_s456.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 860.55 s (19 us/read; 3.17 M reads/minute). === Summary === Total reads processed: 45,411,925 Reads with adapters: 18,217,042 (40.1%) Reads written (passing filters): 45,411,925 (100.0%) Total basepairs processed: 2,284,287,588 bp Quality-trimmed: 2,381,487 bp (0.1%) Total written (filtered): 2,262,602,788 bp (99.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 18217042 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 46.8% C: 10.7% G: 3.6% T: 38.2% none/other: 0.7% Overview of removed sequences length count expect max.err error counts 1 17501301 11352981.2 0 17501301 2 455423 2838245.3 0 455423 3 205565 709561.3 0 205565 4 42473 177390.3 0 42473 5 5508 44347.6 0 5508 6 614 11086.9 0 614 7 1579 2771.7 0 1579 8 658 692.9 0 658 9 360 173.2 0 34 326 10 696 43.3 1 11 685 11 290 10.8 1 42 248 12 178 2.7 1 3 175 13 87 0.7 1 0 87 14 73 0.7 1 0 73 15 140 0.7 1 0 140 16 323 0.7 1 0 323 17 895 0.7 1 0 895 18 680 0.7 1 0 680 19 79 0.7 1 0 79 20 14 0.7 1 0 14 21 12 0.7 1 0 12 22 9 0.7 1 0 9 23 4 0.7 1 0 4 24 7 0.7 1 0 7 25 9 0.7 1 0 9 26 18 0.7 1 0 18 27 7 0.7 1 0 7 28 6 0.7 1 0 6 29 5 0.7 1 0 5 30 5 0.7 1 0 5 31 4 0.7 1 0 4 32 1 0.7 1 0 1 33 8 0.7 1 0 8 34 8 0.7 1 0 8 35 1 0.7 1 0 1 36 1 0.7 1 0 1 37 1 0.7 1 0 1 RUN STATISTICS FOR INPUT FILE: zr1394_4_s456.fastq.gz ============================================= 45411925 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 506847 (1.1%) >>> Now running FastQC on the data <<< Can't exec "fastqc": No such file or directory at /home/shared/TrimGalore-0.4.5/trim_galore line 785. Writing report to '/home/sam/analyses/20180503_trimgalore/zr1394_5_s456.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: zr1394_5_s456.fastq.gz Trimming mode: single-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 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 before a sequence 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 1 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 /home/sam/analyses/20180503_trimgalore/20180503_trim_fastqc --threads 16' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr1394_5_s456_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file zr1394_5_s456.fastq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC zr1394_5_s456.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 907.10 s (19 us/read; 3.18 M reads/minute). === Summary === Total reads processed: 48,050,056 Reads with adapters: 19,818,564 (41.2%) Reads written (passing filters): 48,050,056 (100.0%) Total basepairs processed: 2,414,803,052 bp Quality-trimmed: 2,459,373 bp (0.1%) Total written (filtered): 2,391,223,773 bp (99.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 19818564 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 46.2% C: 11.2% G: 4.0% T: 37.9% none/other: 0.7% Overview of removed sequences length count expect max.err error counts 1 18984030 12012514.0 0 18984030 2 513786 3003128.5 0 513786 3 253524 750782.1 0 253524 4 51698 187695.5 0 51698 5 6400 46923.9 0 6400 6 650 11731.0 0 650 7 1757 2932.7 0 1757 8 1013 733.2 0 1013 9 476 183.3 0 60 416 10 803 45.8 1 16 787 11 402 11.5 1 50 352 12 289 2.9 1 1 288 13 129 0.7 1 0 129 14 140 0.7 1 0 140 15 231 0.7 1 0 231 16 572 0.7 1 0 572 17 1330 0.7 1 0 1330 18 1058 0.7 1 0 1058 19 104 0.7 1 0 104 20 22 0.7 1 0 22 21 10 0.7 1 0 10 22 10 0.7 1 0 10 23 11 0.7 1 0 11 24 10 0.7 1 0 10 25 9 0.7 1 0 9 26 17 0.7 1 0 17 27 18 0.7 1 0 18 28 11 0.7 1 0 11 29 8 0.7 1 0 8 30 11 0.7 1 0 11 31 7 0.7 1 0 7 32 4 0.7 1 0 4 33 7 0.7 1 0 7 34 10 0.7 1 0 10 35 5 0.7 1 0 5 36 2 0.7 1 0 2 RUN STATISTICS FOR INPUT FILE: zr1394_5_s456.fastq.gz ============================================= 48050056 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 648320 (1.3%) >>> Now running FastQC on the data <<< Can't exec "fastqc": No such file or directory at /home/shared/TrimGalore-0.4.5/trim_galore line 785. Writing report to '/home/sam/analyses/20180503_trimgalore/zr1394_6_s456.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: zr1394_6_s456.fastq.gz Trimming mode: single-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 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 before a sequence 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 1 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 /home/sam/analyses/20180503_trimgalore/20180503_trim_fastqc --threads 16' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr1394_6_s456_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file zr1394_6_s456.fastq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC zr1394_6_s456.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 934.29 s (20 us/read; 3.01 M reads/minute). === Summary === Total reads processed: 46,944,411 Reads with adapters: 19,526,974 (41.6%) Reads written (passing filters): 46,944,411 (100.0%) Total basepairs processed: 2,363,416,290 bp Quality-trimmed: 2,138,751 bp (0.1%) Total written (filtered): 2,340,634,139 bp (99.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 19526974 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 47.4% C: 10.6% G: 3.2% T: 38.2% none/other: 0.7% Overview of removed sequences length count expect max.err error counts 1 18794438 11736102.8 0 18794438 2 469350 2934025.7 0 469350 3 205047 733506.4 0 205047 4 46939 183376.6 0 46939 5 4257 45844.2 0 4257 6 546 11461.0 0 546 7 1292 2865.3 0 1292 8 569 716.3 0 569 9 311 179.1 0 31 280 10 633 44.8 1 10 623 11 287 11.2 1 35 252 12 205 2.8 1 1 204 13 93 0.7 1 0 93 14 89 0.7 1 0 89 15 163 0.7 1 0 163 16 366 0.7 1 0 366 17 1103 0.7 1 0 1103 18 992 0.7 1 0 992 19 108 0.7 1 0 108 20 16 0.7 1 0 16 21 11 0.7 1 0 11 22 7 0.7 1 0 7 23 9 0.7 1 0 9 24 12 0.7 1 0 12 25 16 0.7 1 0 16 26 23 0.7 1 0 23 27 13 0.7 1 0 13 28 8 0.7 1 0 8 29 6 0.7 1 0 6 30 14 0.7 1 0 14 31 8 0.7 1 0 8 32 13 0.7 1 0 13 33 13 0.7 1 0 13 34 12 0.7 1 0 12 35 4 0.7 1 0 4 39 1 0.7 1 0 1 RUN STATISTICS FOR INPUT FILE: zr1394_6_s456.fastq.gz ============================================= 46944411 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 489263 (1.0%) >>> Now running FastQC on the data <<< Can't exec "fastqc": No such file or directory at /home/shared/TrimGalore-0.4.5/trim_galore line 785. Writing report to '/home/sam/analyses/20180503_trimgalore/zr1394_7_s456.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: zr1394_7_s456.fastq.gz Trimming mode: single-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 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 before a sequence 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 1 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 /home/sam/analyses/20180503_trimgalore/20180503_trim_fastqc --threads 16' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr1394_7_s456_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file zr1394_7_s456.fastq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC zr1394_7_s456.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 962.12 s (19 us/read; 3.14 M reads/minute). === Summary === Total reads processed: 50,399,353 Reads with adapters: 20,325,988 (40.3%) Reads written (passing filters): 50,399,353 (100.0%) Total basepairs processed: 2,532,578,583 bp Quality-trimmed: 2,675,889 bp (0.1%) Total written (filtered): 2,508,324,225 bp (99.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 20325988 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 46.2% C: 10.8% G: 3.8% T: 38.5% none/other: 0.7% Overview of removed sequences length count expect max.err error counts 1 19528112 12599838.2 0 19528112 2 499729 3149959.6 0 499729 3 233073 787489.9 0 233073 4 47951 196872.5 0 47951 5 6971 49218.1 0 6971 6 678 12304.5 0 678 7 1959 3076.1 0 1959 8 1002 769.0 0 1002 9 471 192.3 0 58 413 10 855 48.1 1 19 836 11 465 12.0 1 57 408 12 302 3.0 1 4 298 13 133 0.8 1 0 133 14 127 0.8 1 0 127 15 216 0.8 1 0 216 16 561 0.8 1 0 561 17 1592 0.8 1 0 1592 18 1378 0.8 1 0 1378 19 143 0.8 1 0 143 20 22 0.8 1 0 22 21 16 0.8 1 0 16 22 6 0.8 1 0 6 23 12 0.8 1 0 12 24 16 0.8 1 0 16 25 15 0.8 1 0 15 26 33 0.8 1 0 33 27 32 0.8 1 0 32 28 21 0.8 1 0 21 29 5 0.8 1 0 5 30 10 0.8 1 0 10 31 18 0.8 1 0 18 32 23 0.8 1 0 23 33 15 0.8 1 0 15 34 15 0.8 1 0 15 35 7 0.8 1 0 7 36 2 0.8 1 0 2 37 2 0.8 1 0 2 RUN STATISTICS FOR INPUT FILE: zr1394_7_s456.fastq.gz ============================================= 50399353 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 669240 (1.3%) >>> Now running FastQC on the data <<< Can't exec "fastqc": No such file or directory at /home/shared/TrimGalore-0.4.5/trim_galore line 785. Writing report to '/home/sam/analyses/20180503_trimgalore/zr1394_8_s456.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: zr1394_8_s456.fastq.gz Trimming mode: single-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 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 before a sequence 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 1 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 /home/sam/analyses/20180503_trimgalore/20180503_trim_fastqc --threads 16' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr1394_8_s456_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file zr1394_8_s456.fastq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC zr1394_8_s456.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 737.40 s (19 us/read; 3.18 M reads/minute). === Summary === Total reads processed: 39,136,514 Reads with adapters: 15,691,880 (40.1%) Reads written (passing filters): 39,136,514 (100.0%) Total basepairs processed: 1,968,545,164 bp Quality-trimmed: 2,012,847 bp (0.1%) Total written (filtered): 1,949,900,521 bp (99.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 15691880 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 46.8% C: 10.5% G: 3.7% T: 38.3% none/other: 0.7% Overview of removed sequences length count expect max.err error counts 1 15065221 9784128.5 0 15065221 2 395817 2446032.1 0 395817 3 184704 611508.0 0 184704 4 36406 152877.0 0 36406 5 4814 38219.3 0 4814 6 470 9554.8 0 470 7 1447 2388.7 0 1447 8 486 597.2 0 486 9 271 149.3 0 21 250 10 614 37.3 1 13 601 11 250 9.3 1 26 224 12 135 2.3 1 0 135 13 62 0.6 1 0 62 14 50 0.6 1 0 50 15 78 0.6 1 0 78 16 178 0.6 1 0 178 17 460 0.6 1 0 460 18 320 0.6 1 0 320 19 42 0.6 1 0 42 20 4 0.6 1 0 4 21 5 0.6 1 0 5 22 4 0.6 1 0 4 23 3 0.6 1 0 3 24 3 0.6 1 0 3 25 7 0.6 1 0 7 26 3 0.6 1 0 3 27 6 0.6 1 0 6 28 7 0.6 1 0 7 29 2 0.6 1 0 2 30 1 0.6 1 0 1 31 1 0.6 1 0 1 32 2 0.6 1 0 2 33 3 0.6 1 0 3 34 2 0.6 1 0 2 35 1 0.6 1 0 1 37 1 0.6 1 0 1 RUN STATISTICS FOR INPUT FILE: zr1394_8_s456.fastq.gz ============================================= 39136514 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 439325 (1.1%) >>> Now running FastQC on the data <<< Can't exec "fastqc": No such file or directory at /home/shared/TrimGalore-0.4.5/trim_galore line 785. Writing report to '/home/sam/analyses/20180503_trimgalore/zr1394_9_s456.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: zr1394_9_s456.fastq.gz Trimming mode: single-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 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 before a sequence 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 1 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 /home/sam/analyses/20180503_trimgalore/20180503_trim_fastqc --threads 16' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr1394_9_s456_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file zr1394_9_s456.fastq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC zr1394_9_s456.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 1517.94 s (19 us/read; 3.09 M reads/minute). === Summary === Total reads processed: 78,146,508 Reads with adapters: 32,115,155 (41.1%) Reads written (passing filters): 78,146,508 (100.0%) Total basepairs processed: 3,934,245,065 bp Quality-trimmed: 3,699,261 bp (0.1%) Total written (filtered): 3,896,717,530 bp (99.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 32115155 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 47.1% C: 10.3% G: 3.1% T: 38.8% none/other: 0.7% Overview of removed sequences length count expect max.err error counts 1 30946269 19536627.0 0 30946269 2 755555 4884156.8 0 755555 3 325643 1221039.2 0 325643 4 73128 305259.8 0 73128 5 8030 76314.9 0 8030 6 742 19078.7 0 742 7 2218 4769.7 0 2218 8 800 1192.4 0 800 9 473 298.1 0 40 433 10 852 74.5 1 8 844 11 285 18.6 1 24 261 12 140 4.7 1 0 140 13 50 1.2 1 0 50 14 51 1.2 1 0 51 15 69 1.2 1 0 69 16 154 1.2 1 0 154 17 392 1.2 1 0 392 18 245 1.2 1 0 245 19 20 1.2 1 0 20 20 4 1.2 1 0 4 21 2 1.2 1 0 2 22 2 1.2 1 0 2 23 1 1.2 1 0 1 24 5 1.2 1 0 5 25 3 1.2 1 0 3 26 3 1.2 1 0 3 27 6 1.2 1 0 6 28 5 1.2 1 0 5 29 2 1.2 1 0 2 31 1 1.2 1 0 1 32 2 1.2 1 0 2 33 2 1.2 1 0 2 34 1 1.2 1 0 1 RUN STATISTICS FOR INPUT FILE: zr1394_9_s456.fastq.gz ============================================= 78146508 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 795586 (1.0%) >>> Now running FastQC on the data <<< Can't exec "fastqc": No such file or directory at /home/shared/TrimGalore-0.4.5/trim_galore line 785. gzip: stdout: Broken pipe