Mercurial > repos > iuc > fargene

annotate test-data/paired/retrievedFragments/trimmedReads/reads__2_retrieved.fastq_trimming_report.txt @ 2:b982a9ea939c draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit d5aed24826ee23758798b458334b2f5e7c84eb0f
author iuc
date Fri, 09 Feb 2024 21:30:09 +0000
parents 6f743c615c41
children
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6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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2 SUMMARISING RUN PARAMETERS
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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3 ==========================
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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4 Input filename: /home/ubuntu/data/fargene/tutorial/tutorialdata/tutorial_output_1/retrievedFragments/reads__2_retrieved.fastq
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5 Trimming mode: paired-end
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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6 Trim Galore version: 0.6.3
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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7 Cutadapt version: 1.18
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8 Number of cores used for trimming: 1
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9 Quality Phred score cutoff: 30
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10 Quality encoding type selected: ASCII+33
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11 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection))
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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12 Maximum trimming error rate: 0.1 (default)
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13 Minimum required adapter overlap (stringency): 1 bp
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14 Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
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17 This is cutadapt 1.18 with Python 2.7.15
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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
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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19 Processing reads on 1 core in single-end mode ...
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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20 Finished in 0.01 s (28 us/read; 2.17 M reads/minute).
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22 === Summary ===
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24 Total reads processed: 393
6f743c615c41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
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25 Reads with adapters: 91 (23.2%)
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26 Reads written (passing filters): 393 (100.0%)
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28 Total basepairs processed: 39,300 bp
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29 Quality-trimmed: 435 bp (1.1%)
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30 Total written (filtered): 38,735 bp (98.6%)
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32 === Adapter 1 ===
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34 Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 91 times.
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36 No. of allowed errors:
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37 0-9 bp: 0; 10-13 bp: 1
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39 Bases preceding removed adapters:
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40 A: 20.9%
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41 C: 44.0%
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42 G: 27.5%
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43 T: 7.7%
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44 none/other: 0.0%
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46 Overview of removed sequences
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47 length count expect max.err error counts
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48 1 65 98.2 0 65
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49 2 20 24.6 0 20
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50 3 2 6.1 0 2
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51 4 2 1.5 0 2
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52 5 1 0.4 0 1
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53 6 1 0.1 0 1
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56 RUN STATISTICS FOR INPUT FILE: /home/ubuntu/data/fargene/tutorial/tutorialdata/tutorial_output_1/retrievedFragments/reads__2_retrieved.fastq
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57 =============================================
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58 393 sequences processed in total
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60 Total number of sequences analysed for the sequence pair length validation: 393
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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%)