Mercurial > repos > bgruening > bismark

annotate test-data/mapping_report_mate.txt @ 16:a4504327c890 draft

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/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
author bgruening
date Wed, 21 Aug 2019 12:59:48 -0400
parents b6aa3b6ba129
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
14
b6aa3b6ba129 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
diff changeset
1 Bismark report for: input1_fq_1.fq and input1_fq_2.fq (version: v0.22.1)
b6aa3b6ba129 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
diff changeset
2 Bismark was run with Bowtie 2 against the bisulfite genome of /tmp/tmpAHSx4i/ with the specified options: -q -L 20 -D 15 -R 2 --score-min L,0,-0.2 --ignore-quals --no-mixed --no-discordant --dovetail --minins 0 --maxins 500 --quiet
b6aa3b6ba129 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
diff changeset
3 Option '--directional' specified (default mode): alignments to complementary strands (CTOT, CTOB) were ignored (i.e. not performed)
b6aa3b6ba129 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
diff changeset
4
b6aa3b6ba129 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
diff changeset
5 Final Alignment report
b6aa3b6ba129 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
diff changeset
6 ======================
b6aa3b6ba129 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
diff changeset
7 Sequence pairs analysed in total: 1000
b6aa3b6ba129 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
diff changeset
8 Number of paired-end alignments with a unique best hit: 0
b6aa3b6ba129 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
diff changeset
9 Mapping efficiency: 0.0%
b6aa3b6ba129 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
diff changeset
10 Sequence pairs with no alignments under any condition: 1000
b6aa3b6ba129 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
diff changeset
11 Sequence pairs did not map uniquely: 0
b6aa3b6ba129 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
diff changeset
12 Sequence pairs which were discarded because genomic sequence could not be extracted: 0
b6aa3b6ba129 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
diff changeset
13
b6aa3b6ba129 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
diff changeset
14 Number of sequence pairs with unique best (first) alignment came from the bowtie output:
b6aa3b6ba129 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
diff changeset
15 CT/GA/CT: 0 ((converted) top strand)
b6aa3b6ba129 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
diff changeset
16 GA/CT/CT: 0 (complementary to (converted) top strand)
b6aa3b6ba129 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
diff changeset
17 GA/CT/GA: 0 (complementary to (converted) bottom strand)
b6aa3b6ba129 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
diff changeset
18 CT/GA/GA: 0 ((converted) bottom strand)
b6aa3b6ba129 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
diff changeset
19
b6aa3b6ba129 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
diff changeset
20 Number of alignments to (merely theoretical) complementary strands being rejected in total: 0
b6aa3b6ba129 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
diff changeset
21
b6aa3b6ba129 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
diff changeset
22 Final Cytosine Methylation Report
b6aa3b6ba129 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
diff changeset
23 =================================
b6aa3b6ba129 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
diff changeset
24 Total number of C's analysed: 0
b6aa3b6ba129 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
diff changeset
25
b6aa3b6ba129 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
diff changeset
26 Total methylated C's in CpG context: 0
b6aa3b6ba129 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
diff changeset
27 Total methylated C's in CHG context: 0
b6aa3b6ba129 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
diff changeset
28 Total methylated C's in CHH context: 0
b6aa3b6ba129 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
diff changeset
29 Total methylated C's in Unknown context: 0
b6aa3b6ba129 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
diff changeset
30
b6aa3b6ba129 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
diff changeset
31 Total unmethylated C's in CpG context: 0
b6aa3b6ba129 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
diff changeset
32 Total unmethylated C's in CHG context: 0
b6aa3b6ba129 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
diff changeset
33 Total unmethylated C's in CHH context: 0
b6aa3b6ba129 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
diff changeset
34 Total unmethylated C's in Unknown context: 0
b6aa3b6ba129 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
diff changeset
35
b6aa3b6ba129 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
diff changeset
36 Can't determine percentage of methylated Cs in CpG context if value was 0
b6aa3b6ba129 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
diff changeset
37 Can't determine percentage of methylated Cs in CHG context if value was 0
b6aa3b6ba129 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
diff changeset
38 Can't determine percentage of methylated Cs in CHH context if value was 0
b6aa3b6ba129 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
diff changeset
39 Can't determine percentage of methylated Cs in unknown context (CN or CHN) if value was 0
b6aa3b6ba129 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
diff changeset
40
b6aa3b6ba129 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
diff changeset
41
b6aa3b6ba129 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit f57cd875407ce987c4897fc352c5db0eeb8e9efe
bgruening
parents:
diff changeset
42 Bismark completed in 0d 0h 0m 5s