annotate test-data/paired_collection_example_results3gz.txt @ 14:949f01671246 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 6aa3014c2c6f9ef9ee71b20cfffec461b3a102a5

SUMMARISING RUN PARAMETERS
==========================
Input filename: input_1.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.3
Cutadapt version: 1.13
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)
Output file will be GZIP compressed


This is cutadapt 1.13 with Python 3.5.3
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 0.01 s (101 us/read; 0.59 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.gz
=============================================
99 sequences processed in total


SUMMARISING RUN PARAMETERS
==========================
Input filename: input_2.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.3
Cutadapt version: 1.13
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)
Output file will be GZIP compressed


This is cutadapt 1.13 with Python 3.5.3
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 0.01 s (100 us/read; 0.60 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 ===

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%

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_2.fastq.gz
=============================================
100 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%)