Mercurial > repos > thanhlv > fargene

annotate test-data/paired/retrievedFragments/trimmedReads/reads__1_retrieved.fastq_trimming_report.txt @ 0:6f78bc71eb12 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
author thanhlv
date Fri, 19 Jul 2019 08:42:37 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
1
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
2 SUMMARISING RUN PARAMETERS
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
3 ==========================
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
4 Input filename: /home/ubuntu/data/fargene/tutorial/tutorialdata/tutorial_output_1/retrievedFragments/reads__1_retrieved.fastq
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
5 Trimming mode: paired-end
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
6 Trim Galore version: 0.6.3
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
7 Cutadapt version: 1.18
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
8 Number of cores used for trimming: 1
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
9 Quality Phred score cutoff: 30
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
10 Quality encoding type selected: ASCII+33
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
11 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection))
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
12 Maximum trimming error rate: 0.1 (default)
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
13 Minimum required adapter overlap (stringency): 1 bp
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
14 Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
15
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
16
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
17 This is cutadapt 1.18 with Python 2.7.15
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
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__1_retrieved.fastq
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
19 Processing reads on 1 core in single-end mode ...
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
20 Finished in 0.01 s (27 us/read; 2.19 M reads/minute).
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
21
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
22 === Summary ===
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
23
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
24 Total reads processed: 393
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
25 Reads with adapters: 102 (26.0%)
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
26 Reads written (passing filters): 393 (100.0%)
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
27
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
28 Total basepairs processed: 39,300 bp
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
29 Quality-trimmed: 156 bp (0.4%)
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
30 Total written (filtered): 39,001 bp (99.2%)
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
31
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
32 === Adapter 1 ===
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
33
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
34 Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 102 times.
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
35
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
36 No. of allowed errors:
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
37 0-9 bp: 0; 10-13 bp: 1
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
38
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
39 Bases preceding removed adapters:
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
40 A: 24.5%
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
41 C: 35.3%
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
42 G: 31.4%
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
43 T: 8.8%
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
44 none/other: 0.0%
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
45
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
46 Overview of removed sequences
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
47 length count expect max.err error counts
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
48 1 72 98.2 0 72
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
49 2 24 24.6 0 24
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
50 3 3 6.1 0 3
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
51 4 2 1.5 0 2
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
52 6 1 0.1 0 1
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
53
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
54
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
55 RUN STATISTICS FOR INPUT FILE: /home/ubuntu/data/fargene/tutorial/tutorialdata/tutorial_output_1/retrievedFragments/reads__1_retrieved.fastq
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
56 =============================================
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
57 393 sequences processed in total
6f78bc71eb12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fargene commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff changeset
58