Mercurial > repos > bgruening > trim_galore
diff test-data/paired_collection_example_results3.txt @ 6:11962ce40855 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
| author | bgruening |
|---|---|
| date | Wed, 07 Oct 2015 08:39:59 -0400 |
| parents | 2c1f0fe810f7 |
| children | b4e39d993fc8 |
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--- a/test-data/paired_collection_example_results3.txt Wed Apr 15 17:31:52 2015 -0400 +++ b/test-data/paired_collection_example_results3.txt Wed Oct 07 08:39:59 2015 -0400 @@ -3,84 +3,168 @@ ========================== Input filename: ./input_mate1 Trimming mode: paired-end -Trim Galore version: 0.3.7 +Trim Galore version: 0.4.0 +Cutadapt version: 1.8 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 -Adapter sequence: 'AGATCGGAAGAGC' +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) -cutadapt version 1.1 -Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC ./input_mate1 -Maximum error rate: 10.00% - Processed reads: 100 - Trimmed reads: 20 ( 20.0%) - Total basepairs: 24894 (0.0 Mbp) - Trimmed basepairs: 26 (0.0 Mbp) (0.10% of total) - Too short reads: 0 ( 0.0% of processed reads) - Too long reads: 0 ( 0.0% of processed reads) - Total time: 0.00 s - Time per read: 0.03 ms +This is cutadapt 1.8 with Python 2.7.9 +Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA ./input_mate1 +Trimming 1 adapter(s) with at most 10.0% errors in single-end mode ... +Finished in 0.10 s (1010 us/read; 0.06 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 === -Adapter 'AGATCGGAAGAGC', length 13, was trimmed 20 times. +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% -Lengths of removed sequences -length count expected -1 16 25.0 -2 2 6.2 -3 2 1.6 +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_mate1 ============================================= -100 sequences processed in total +99 sequences processed in total SUMMARISING RUN PARAMETERS ========================== Input filename: ./input_mate2 Trimming mode: paired-end -Trim Galore version: 0.3.7 +Trim Galore version: 0.4.0 +Cutadapt version: 1.8 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 -Adapter sequence: 'AGATCGGAAGAGC' +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) -cutadapt version 1.1 -Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC ./input_mate2 -Maximum error rate: 10.00% - Processed reads: 100 - Trimmed reads: 24 ( 24.0%) - Total basepairs: 24354 (0.0 Mbp) - Trimmed basepairs: 36 (0.0 Mbp) (0.15% of total) - Too short reads: 0 ( 0.0% of processed reads) - Too long reads: 0 ( 0.0% of processed reads) - Total time: 0.01 s - Time per read: 0.10 ms +This is cutadapt 1.8 with Python 2.7.9 +Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA ./input_mate2 +Trimming 1 adapter(s) with at most 10.0% errors in single-end mode ... +Finished in 0.10 s (1000 us/read; 0.06 M reads/minute). + +=== Summary === + +Total reads processed: 100 +Reads with adapters: 59 (59.0%) +Reads written (passing filters): 100 (100.0%) + +Total basepairs processed: 25,100 bp +Quality-trimmed: 746 bp (3.0%) +Total written (filtered): 23,276 bp (92.7%) === Adapter 1 === -Adapter 'AGATCGGAAGAGC', length 13, was trimmed 24 times. +Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 59 times. + +No. of allowed errors: +0-9 bp: 0; 10-12 bp: 1 + +Bases preceding removed adapters: + A: 11.9% + C: 39.0% + G: 8.5% + T: 40.7% + none/other: 0.0% -Lengths of removed sequences -length count expected -1 15 25.0 -2 7 6.2 -3 1 1.6 -4 1 0.4 +Overview of removed sequences +length count expect max.err error counts +1 16 25.0 0 16 +2 7 6.2 0 7 +3 1 1.6 0 1 +4 2 0.4 0 2 +6 2 0.0 0 2 +9 2 0.0 0 2 +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_mate2 ============================================= 100 sequences processed in total -Total number of sequences analysed for the sequence pair length validation: 100 +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 (1.00%) +Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1 (1.01%)