root/galaxy-central/test-data/peakcalling_macs/macs_test_3_out.html

リビジョン 2, 3.4 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1\<html\>\<head\>\<title\>Additional\ output\ created\ by\ MACS\ \(Galaxy\_Test\_Run\)\<\/title\>\<\/head\>\<body\>\<h3\>Additional\ Files\:\<\/h3\>\<p\>\<ul\>
2\<li\>\<a\ href\=\"Galaxy\_Test\_Run\_model\.pdf\"\>Galaxy\_Test\_Run\_model\.pdf\<\/a\>\<\/li\>
3\<li\>\<a\ href\=\"Galaxy\_Test\_Run\_model\.r\"\>Galaxy\_Test\_Run\_model\.r\<\/a\>\<\/li\>
4\<li\>\<a\ href\=\"Galaxy\_Test\_Run\_model\.r\.log\"\>Galaxy\_Test\_Run\_model\.r\.log\<\/a\>\<\/li\>
5\<li\>\<a\ href\=\"Galaxy\_Test\_Run\_negative\_peaks\.xls\"\>Galaxy\_Test\_Run\_negative\_peaks\.xls\<\/a\>\<\/li\>
6\<li\>\<a\ href\=\"Galaxy\_Test\_Run\_peaks\.xls\"\>Galaxy\_Test\_Run\_peaks\.xls\<\/a\>\<\/li\>
7\<\/ul\>\<\/p\>
8\<h3\>Messages\ from\ MACS\:\<\/h3\>
9\<p\>\<pre\>INFO\ \ \@\ .*\:\
10\#\ ARGUMENTS\ LIST\:
11\#\ name\ \=\ Galaxy\_Test\_Run
12\#\ format\ \=\ BED
13\#\ ChIP\-seq\ file\ \=\ .*\.dat
14\#\ control\ file\ \=\ .*\.dat
15\#\ effective\ genome\ size\ \=\ 2\.70e\+09
16\#\ tag\ size\ \=\ 36
17\#\ band\ width\ \=\ 300
18\#\ model\ fold\ \=\ 13
19\#\ pvalue\ cutoff\ \=\ 1\.00e\-05
20\#\ Ranges\ for\ calculating\ regional\ lambda\ are\ \:\ peak\_region\,1000\,5000\,10000\
21INFO\ \ \@\ .*\:\ \#1\ read\ tag\ files\.\.\.\
22INFO\ \ \@\ .*\:\ \#1\ read\ treatment\ tags\.\.\.\
23INFO\ \ \@\ .*\:\ \#1\.2\ read\ input\ tags\.\.\.\
24INFO\ \ \@\ .*\:\ \#1\ \ Background\ Redundant\ rate\:\ 1\.00\
25INFO\ \ \@\ .*\:\ \#1\ finished\!\
26INFO\ \ \@\ .*\:\ \#2\ Build\ Peak\ Model\.\.\.\
27INFO\ \ \@\ .*\:\ \#2\ number\ of\ paired\ peaks\:\ 549\
28WARNING\ \@\ .*\:\ Fewer\ paired\ peaks\ \(549\)\ than\ 1000\!\ Model\ may\ not\ be\ build\ well\!\ Lower\ your\ MFOLD\ parameter\ may\ erase\ this\ warning\.\ Now\ I\ will\ use\ 549\ pairs\ to\ build\ model\!\
29INFO\ \ \@\ .*\:\ \#2\ finished\!\
30INFO\ \ \@\ .*\:\ \#2\.2\ Generate\ R\ script\ for\ model\ \:\ Galaxy\_Test\_Run\_model\.r\
31INFO\ \ \@\ .*\:\ \#3\ Call\ peaks\.\.\.\
32INFO\ \ \@\ .*\:\ \#3\ shift\ treatment\ data\
33INFO\ \ \@\ .*\:\ \#3\ merge\ \+\/\-\ strand\ of\ treatment\ data\
34INFO\ \ \@\ .*\:\ \#3\ save\ the\ shifted\ and\ merged\ tag\ counts\ into\ wiggle\ file\.\.\.\
35INFO\ \ \@\ .*\:\ write\ to\ Galaxy\_Test\_Run\_MACS\_wiggle\/treat\/Galaxy\_Test\_Run\_treat\_afterfiting\_chr1\.wig\ for\ chromosome\ chr1\
36INFO\ \ \@\ .*\:\ compress\ the\ wiggle\ file\ using\ gzip\.\.\.\
37INFO\ \ \@\ .*\:\ \#3\ call\ peak\ candidates\
38INFO\ \ \@\ .*\:\ \#3\ shift\ control\ data\
39INFO\ \ \@\ .*\:\ \#3\ merge\ \+\/\-\ strand\ of\ control\ data\
40INFO\ \ \@\ .*\:\ \#3\ save\ the\ shifted\ and\ merged\ tag\ counts\ into\ wiggle\ file\.\.\.\
41INFO\ \ \@\ .*\:\ write\ to\ Galaxy\_Test\_Run\_MACS\_wiggle\/control\/Galaxy\_Test\_Run\_control\_afterfiting\_chr1\.wig\ for\ chromosome\ chr1\
42INFO\ \ \@\ .*\:\ compress\ the\ wiggle\ file\ using\ gzip\.\.\.\
43INFO\ \ \@\ .*\:\ \#3\ call\ negative\ peak\ candidates\
44INFO\ \ \@\ .*\:\ \#3\ use\ control\ data\ to\ filter\ peak\ candidates\.\.\.\
45INFO\ \ \@\ .*\:\ \#3\ Finally\,\ 1270\ peaks\ are\ called\!\
46INFO\ \ \@\ .*\:\ \#3\ find\ negative\ peaks\ by\ reversing\ treat\ and\ control\
47INFO\ \ \@\ .*\:\ \#3\ Finally\,\ 57\ peaks\ are\ called\!\
48INFO\ \ \@\ .*\:\ \#4\ Write\ output\ xls\ file\.\.\.\ Galaxy\_Test\_Run\_peaks\.xls\
49INFO\ \ \@\ .*\:\ \#4\ Write\ output\ bed\ file\.\.\.\ Galaxy\_Test\_Run\_peaks\.bed\
50INFO\ \ \@\ .*\:\ \#4\ Write\ output\ xls\ file\ for\ negative\ peaks\.\.\.\ Galaxy\_Test\_Run\_negative\_peaks\.xls\
51INFO\ \ \@\ .*\:\ \#5\ Done\!\ Check\ the\ output\ files\!
52\
53\<\/pre\>\<\/p\>
54\<\/body\>\<\/html\>
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