Mercurial > repos > bgruening > trim_galore
annotate test-data/paired_example_results2.txt @ 15:084bbd8ba7b8 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 10a9de2adae04249830c880cf0c55edaa196f3f7
author | bgruening |
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date | Tue, 30 Jul 2019 06:26:49 -0400 |
parents | 80cd83b11214 |
children | cd7e644cae1d |
rev | line source |
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4 | 1 |
2 SUMMARISING RUN PARAMETERS | |
3 ========================== | |
10
b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
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4 Input filename: input_1.fastq |
4 | 5 Trimming mode: paired-end |
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084bbd8ba7b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 10a9de2adae04249830c880cf0c55edaa196f3f7
bgruening
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6 Trim Galore version: 0.6.3 |
084bbd8ba7b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 10a9de2adae04249830c880cf0c55edaa196f3f7
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7 Cutadapt version: 2.4 |
084bbd8ba7b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 10a9de2adae04249830c880cf0c55edaa196f3f7
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8 Number of cores used for trimming: 1 |
4 | 9 Quality Phred score cutoff: 20 |
10 Quality encoding type selected: ASCII+33 | |
6
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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11 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected) |
4 | 12 Maximum trimming error rate: 0.1 (default) |
13 Minimum required adapter overlap (stringency): 1 bp | |
14 Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp | |
15 | |
16 | |
15
084bbd8ba7b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 10a9de2adae04249830c880cf0c55edaa196f3f7
bgruening
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changeset
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17 This is cutadapt 2.4 with Python 3.7.3 |
084bbd8ba7b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 10a9de2adae04249830c880cf0c55edaa196f3f7
bgruening
parents:
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18 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq |
084bbd8ba7b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 10a9de2adae04249830c880cf0c55edaa196f3f7
bgruening
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19 Processing reads on 1 core in single-end mode ... |
084bbd8ba7b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 10a9de2adae04249830c880cf0c55edaa196f3f7
bgruening
parents:
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20 Finished in 0.01 s (75 us/read; 0.80 M reads/minute). |
6
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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21 |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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22 === Summary === |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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23 |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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24 Total reads processed: 99 |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
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25 Reads with adapters: 52 (52.5%) |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
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26 Reads written (passing filters): 99 (100.0%) |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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27 |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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28 Total basepairs processed: 24,849 bp |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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29 Quality-trimmed: 205 bp (0.8%) |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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30 Total written (filtered): 23,339 bp (93.9%) |
4 | 31 |
32 === Adapter 1 === | |
33 | |
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11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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34 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 52 times. |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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35 |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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36 No. of allowed errors: |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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37 0-9 bp: 0; 10-12 bp: 1 |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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38 |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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39 Bases preceding removed adapters: |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
parents:
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40 A: 9.6% |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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41 C: 38.5% |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
bgruening
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42 G: 23.1% |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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43 T: 28.8% |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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44 none/other: 0.0% |
4 | 45 |
6
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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46 Overview of removed sequences |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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47 length count expect max.err error counts |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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48 1 11 24.8 0 11 |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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49 2 5 6.2 0 5 |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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50 3 3 1.5 0 3 |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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51 4 3 0.4 0 3 |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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52 12 1 0.0 1 1 |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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53 13 2 0.0 1 2 |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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54 14 1 0.0 1 1 |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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55 16 1 0.0 1 1 |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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56 17 1 0.0 1 0 1 |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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57 20 2 0.0 1 2 |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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58 21 1 0.0 1 1 |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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59 24 1 0.0 1 1 |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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60 26 2 0.0 1 2 |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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61 31 1 0.0 1 1 |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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62 33 1 0.0 1 1 |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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63 41 2 0.0 1 2 |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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64 49 1 0.0 1 1 |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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65 50 1 0.0 1 1 |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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66 54 1 0.0 1 1 |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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67 56 1 0.0 1 1 |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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68 58 2 0.0 1 2 |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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69 60 1 0.0 1 1 |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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70 67 2 0.0 1 2 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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71 68 1 0.0 1 1 |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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72 69 1 0.0 1 1 |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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73 73 1 0.0 1 1 |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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74 80 1 0.0 1 1 |
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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75 86 1 0.0 1 1 |
4 | 76 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
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77 RUN STATISTICS FOR INPUT FILE: input_1.fastq |
4 | 78 ============================================= |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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79 99 sequences processed in total |
4 | 80 |
81 | |
82 SUMMARISING RUN PARAMETERS | |
83 ========================== | |
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b4e39d993fc8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
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84 Input filename: input_2.fastq |
4 | 85 Trimming mode: paired-end |
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084bbd8ba7b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 10a9de2adae04249830c880cf0c55edaa196f3f7
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86 Trim Galore version: 0.6.3 |
084bbd8ba7b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 10a9de2adae04249830c880cf0c55edaa196f3f7
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87 Cutadapt version: 2.4 |
084bbd8ba7b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 10a9de2adae04249830c880cf0c55edaa196f3f7
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88 Number of cores used for trimming: 1 |
4 | 89 Quality Phred score cutoff: 20 |
90 Quality encoding type selected: ASCII+33 | |
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11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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91 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected) |
4 | 92 Maximum trimming error rate: 0.1 (default) |
93 Minimum required adapter overlap (stringency): 1 bp | |
94 Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp | |
95 | |
96 | |
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084bbd8ba7b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 10a9de2adae04249830c880cf0c55edaa196f3f7
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97 This is cutadapt 2.4 with Python 3.7.3 |
084bbd8ba7b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 10a9de2adae04249830c880cf0c55edaa196f3f7
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98 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq |
084bbd8ba7b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 10a9de2adae04249830c880cf0c55edaa196f3f7
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99 Processing reads on 1 core in single-end mode ... |
084bbd8ba7b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 10a9de2adae04249830c880cf0c55edaa196f3f7
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100 Finished in 0.00 s (50 us/read; 1.19 M reads/minute). |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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101 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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102 === Summary === |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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103 |
15
084bbd8ba7b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 10a9de2adae04249830c880cf0c55edaa196f3f7
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104 Total reads processed: 99 |
084bbd8ba7b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 10a9de2adae04249830c880cf0c55edaa196f3f7
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105 Reads with adapters: 58 (58.6%) |
084bbd8ba7b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 10a9de2adae04249830c880cf0c55edaa196f3f7
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106 Reads written (passing filters): 99 (100.0%) |
6
11962ce40855
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
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107 |
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108 Total basepairs processed: 24,849 bp |
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109 Quality-trimmed: 745 bp (3.0%) |
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110 Total written (filtered): 23,035 bp (92.7%) |
4 | 111 |
112 === Adapter 1 === | |
113 | |
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114 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 58 times. |
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115 |
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116 No. of allowed errors: |
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117 0-9 bp: 0; 10-12 bp: 1 |
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118 |
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119 Bases preceding removed adapters: |
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120 A: 12.1% |
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121 C: 37.9% |
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122 G: 8.6% |
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123 T: 41.4% |
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124 none/other: 0.0% |
4 | 125 |
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126 Overview of removed sequences |
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127 length count expect max.err error counts |
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128 1 16 24.8 0 16 |
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129 2 7 6.2 0 7 |
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130 3 1 1.5 0 1 |
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131 4 2 0.4 0 2 |
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132 6 2 0.0 0 2 |
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133 9 1 0.0 0 1 |
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134 10 1 0.0 1 1 |
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135 13 1 0.0 1 1 |
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136 14 2 0.0 1 2 |
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137 15 1 0.0 1 1 |
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138 16 1 0.0 1 1 |
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139 17 1 0.0 1 1 |
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140 19 2 0.0 1 2 |
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141 21 1 0.0 1 1 |
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142 25 1 0.0 1 1 |
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143 30 1 0.0 1 1 |
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144 32 2 0.0 1 2 |
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145 34 1 0.0 1 1 |
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146 36 2 0.0 1 2 |
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147 38 1 0.0 1 1 |
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148 40 1 0.0 1 1 |
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149 41 1 0.0 1 1 |
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150 42 1 0.0 1 1 |
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151 43 1 0.0 1 1 |
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152 49 1 0.0 1 1 |
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153 51 1 0.0 1 1 |
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154 56 1 0.0 1 1 |
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155 57 1 0.0 1 1 |
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156 60 1 0.0 1 1 |
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157 67 1 0.0 1 1 |
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158 80 1 0.0 1 1 |
4 | 159 |
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160 RUN STATISTICS FOR INPUT FILE: input_2.fastq |
4 | 161 ============================================= |
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162 99 sequences processed in total |
4 | 163 |
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164 Total number of sequences analysed for the sequence pair length validation: 99 |
4 | 165 |
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166 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1 (1.01%) |