Mercurial > repos > thanhlv > fargene
annotate test-data/paired/retrievedFragments/trimmedReads/reads__2_retrieved.fastq_trimming_report.txt @ 0:6f78bc71eb12 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
author | thanhlv |
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date | Fri, 19 Jul 2019 08:42:37 -0400 |
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6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
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1 |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
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2 SUMMARISING RUN PARAMETERS |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
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3 ========================== |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
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4 Input filename: /home/ubuntu/data/fargene/tutorial/tutorialdata/tutorial_output_1/retrievedFragments/reads__2_retrieved.fastq |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
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5 Trimming mode: paired-end |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
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6 Trim Galore version: 0.6.3 |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
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7 Cutadapt version: 1.18 |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
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8 Number of cores used for trimming: 1 |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
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9 Quality Phred score cutoff: 30 |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
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10 Quality encoding type selected: ASCII+33 |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
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11 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection)) |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
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12 Maximum trimming error rate: 0.1 (default) |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
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13 Minimum required adapter overlap (stringency): 1 bp |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
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14 Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
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15 |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
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16 |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
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17 This is cutadapt 1.18 with Python 2.7.15 |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
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18 Command line parameters: -j 1 -e 0.1 -q 30 -O 1 -a AGATCGGAAGAGC /home/ubuntu/data/fargene/tutorial/tutorialdata/tutorial_output_1/retrievedFragments/reads__2_retrieved.fastq |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
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19 Processing reads on 1 core in single-end mode ... |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
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20 Finished in 0.01 s (28 us/read; 2.17 M reads/minute). |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
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21 |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
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22 === Summary === |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
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23 |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
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24 Total reads processed: 393 |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
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25 Reads with adapters: 91 (23.2%) |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
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26 Reads written (passing filters): 393 (100.0%) |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
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27 |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
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28 Total basepairs processed: 39,300 bp |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
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29 Quality-trimmed: 435 bp (1.1%) |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
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30 Total written (filtered): 38,735 bp (98.6%) |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
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31 |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
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32 === Adapter 1 === |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
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33 |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
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34 Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 91 times. |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
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35 |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
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36 No. of allowed errors: |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
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37 0-9 bp: 0; 10-13 bp: 1 |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
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38 |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
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39 Bases preceding removed adapters: |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
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40 A: 20.9% |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
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41 C: 44.0% |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
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42 G: 27.5% |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
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43 T: 7.7% |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
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44 none/other: 0.0% |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
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45 |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
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46 Overview of removed sequences |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
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47 length count expect max.err error counts |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
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48 1 65 98.2 0 65 |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
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49 2 20 24.6 0 20 |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
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50 3 2 6.1 0 2 |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
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51 4 2 1.5 0 2 |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
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52 5 1 0.4 0 1 |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
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53 6 1 0.1 0 1 |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
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54 |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
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55 |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
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56 RUN STATISTICS FOR INPUT FILE: /home/ubuntu/data/fargene/tutorial/tutorialdata/tutorial_output_1/retrievedFragments/reads__2_retrieved.fastq |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
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57 ============================================= |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
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58 393 sequences processed in total |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
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59 |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
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60 Total number of sequences analysed for the sequence pair length validation: 393 |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
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61 |
6f78bc71eb12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
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parents:
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62 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 0 (0.00%) |