view test-data/paired_example_results2.txt @ 18:150999d4b92a draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f8ccc97b827b98db1bcf42073d3c5eb4e3f134c4

SUMMARISING RUN PARAMETERS
==========================
Input filename: input_1.fastq
Trimming mode: paired-end
Trim Galore version: 0.6.10
Cutadapt version: 5.0
Python version: 3.12.10
Number of cores used for trimming: 4
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Using Nextera adapter for trimming (count: 29). Second best hit was smallRNA (count: 0)
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


This is cutadapt 5.0 with Python 3.12.10
Command line parameters: -j 4 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq
Processing single-end reads on 4 cores ...

=== 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

Minimum overlap: 1
No. of allowed errors:
1-9 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: 0.6.10
Cutadapt version: 5.0
Python version: 3.12.10
Number of cores used for trimming: 4
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Using Nextera adapter for trimming (count: 29). Second best hit was smallRNA (count: 0)
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


This is cutadapt 5.0 with Python 3.12.10
Command line parameters: -j 4 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq
Processing single-end reads on 4 cores ...

=== 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

Minimum overlap: 1
No. of allowed errors:
1-9 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%)