Mercurial > repos > iuc > fargene
comparison test-data/paired/retrievedFragments/trimmedReads/reads__2_retrieved.fastq_trimming_report.txt @ 0:6f743c615c41 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 867e4a6fad4c2622ad69517e2d4d9ba185109b72"
| author | iuc |
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| date | Thu, 28 Nov 2019 14:39:41 -0500 |
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| -1:000000000000 | 0:6f743c615c41 |
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| 1 | |
| 2 SUMMARISING RUN PARAMETERS | |
| 3 ========================== | |
| 4 Input filename: /home/ubuntu/data/fargene/tutorial/tutorialdata/tutorial_output_1/retrievedFragments/reads__2_retrieved.fastq | |
| 5 Trimming mode: paired-end | |
| 6 Trim Galore version: 0.6.3 | |
| 7 Cutadapt version: 1.18 | |
| 8 Number of cores used for trimming: 1 | |
| 9 Quality Phred score cutoff: 30 | |
| 10 Quality encoding type selected: ASCII+33 | |
| 11 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection)) | |
| 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 | |
| 17 This is cutadapt 1.18 with Python 2.7.15 | |
| 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 | |
| 19 Processing reads on 1 core in single-end mode ... | |
| 20 Finished in 0.01 s (28 us/read; 2.17 M reads/minute). | |
| 21 | |
| 22 === Summary === | |
| 23 | |
| 24 Total reads processed: 393 | |
| 25 Reads with adapters: 91 (23.2%) | |
| 26 Reads written (passing filters): 393 (100.0%) | |
| 27 | |
| 28 Total basepairs processed: 39,300 bp | |
| 29 Quality-trimmed: 435 bp (1.1%) | |
| 30 Total written (filtered): 38,735 bp (98.6%) | |
| 31 | |
| 32 === Adapter 1 === | |
| 33 | |
| 34 Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 91 times. | |
| 35 | |
| 36 No. of allowed errors: | |
| 37 0-9 bp: 0; 10-13 bp: 1 | |
| 38 | |
| 39 Bases preceding removed adapters: | |
| 40 A: 20.9% | |
| 41 C: 44.0% | |
| 42 G: 27.5% | |
| 43 T: 7.7% | |
| 44 none/other: 0.0% | |
| 45 | |
| 46 Overview of removed sequences | |
| 47 length count expect max.err error counts | |
| 48 1 65 98.2 0 65 | |
| 49 2 20 24.6 0 20 | |
| 50 3 2 6.1 0 2 | |
| 51 4 2 1.5 0 2 | |
| 52 5 1 0.4 0 1 | |
| 53 6 1 0.1 0 1 | |
| 54 | |
| 55 | |
| 56 RUN STATISTICS FOR INPUT FILE: /home/ubuntu/data/fargene/tutorial/tutorialdata/tutorial_output_1/retrievedFragments/reads__2_retrieved.fastq | |
| 57 ============================================= | |
| 58 393 sequences processed in total | |
| 59 | |
| 60 Total number of sequences analysed for the sequence pair length validation: 393 | |
| 61 | |
| 62 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 0 (0.00%) |