Mercurial > repos > bgruening > trim_galore
view test-data/paired_collection_example_results3.txt @ 15:313e04fe07cd draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 10a9de2adae04249830c880cf0c55edaa196f3f7
| author | bgruening |
|---|---|
| date | Tue, 30 Jul 2019 06:26:22 -0400 |
| parents | 09219a47e3a7 |
| children | cc01cbc4e7f7 |
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SUMMARISING RUN PARAMETERS ========================== Input filename: input_1.fastq Trimming mode: paired-end Trim Galore version: 0.6.3 Cutadapt version: 2.4 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp Length cut-off for read 1: 35 bp (default) Length cut-off for read 2: 35 bp (default) This is cutadapt 2.4 with Python 3.7.3 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq Processing reads on 1 core in single-end mode ... Finished in 0.01 s (72 us/read; 0.83 M reads/minute). === Summary === Total reads processed: 99 Reads with adapters: 52 (52.5%) Reads written (passing filters): 99 (100.0%) Total basepairs processed: 24,849 bp Quality-trimmed: 205 bp (0.8%) Total written (filtered): 23,339 bp (93.9%) === Adapter 1 === Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 52 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 9.6% C: 38.5% G: 23.1% T: 28.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 11 24.8 0 11 2 5 6.2 0 5 3 3 1.5 0 3 4 3 0.4 0 3 12 1 0.0 1 1 13 2 0.0 1 2 14 1 0.0 1 1 16 1 0.0 1 1 17 1 0.0 1 0 1 20 2 0.0 1 2 21 1 0.0 1 1 24 1 0.0 1 1 26 2 0.0 1 2 31 1 0.0 1 1 33 1 0.0 1 1 41 2 0.0 1 2 49 1 0.0 1 1 50 1 0.0 1 1 54 1 0.0 1 1 56 1 0.0 1 1 58 2 0.0 1 2 60 1 0.0 1 1 67 2 0.0 1 2 68 1 0.0 1 1 69 1 0.0 1 1 73 1 0.0 1 1 80 1 0.0 1 1 86 1 0.0 1 1 RUN STATISTICS FOR INPUT FILE: input_1.fastq ============================================= 99 sequences processed in total SUMMARISING RUN PARAMETERS ========================== Input filename: input_2.fastq Trimming mode: paired-end Trim Galore version: 0.6.3 Cutadapt version: 2.4 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp Length cut-off for read 1: 35 bp (default) Length cut-off for read 2: 35 bp (default) This is cutadapt 2.4 with Python 3.7.3 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq Processing reads on 1 core in single-end mode ... Finished in 0.01 s (55 us/read; 1.08 M reads/minute). === Summary === Total reads processed: 99 Reads with adapters: 58 (58.6%) Reads written (passing filters): 99 (100.0%) Total basepairs processed: 24,849 bp Quality-trimmed: 745 bp (3.0%) Total written (filtered): 23,035 bp (92.7%) === Adapter 1 === Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 58 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 12.1% C: 37.9% G: 8.6% T: 41.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 16 24.8 0 16 2 7 6.2 0 7 3 1 1.5 0 1 4 2 0.4 0 2 6 2 0.0 0 2 9 1 0.0 0 1 10 1 0.0 1 1 13 1 0.0 1 1 14 2 0.0 1 2 15 1 0.0 1 1 16 1 0.0 1 1 17 1 0.0 1 1 19 2 0.0 1 2 21 1 0.0 1 1 25 1 0.0 1 1 30 1 0.0 1 1 32 2 0.0 1 2 34 1 0.0 1 1 36 2 0.0 1 2 38 1 0.0 1 1 40 1 0.0 1 1 41 1 0.0 1 1 42 1 0.0 1 1 43 1 0.0 1 1 49 1 0.0 1 1 51 1 0.0 1 1 56 1 0.0 1 1 57 1 0.0 1 1 60 1 0.0 1 1 67 1 0.0 1 1 80 1 0.0 1 1 RUN STATISTICS FOR INPUT FILE: input_2.fastq ============================================= 99 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 99 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1 (1.01%)