comparison test-data/peakcalling_macs/macs_test_3_out.html @ 0:512c6b2dba00 draft

Imported from capsule None
author devteam
date Thu, 23 Jan 2014 12:32:02 -0500
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-1:000000000000 0:512c6b2dba00
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\
21 INFO\ \ \@\ .*\:\ \#1\ read\ tag\ files\.\.\.\
22 INFO\ \ \@\ .*\:\ \#1\ read\ treatment\ tags\.\.\.\
23 INFO\ \ \@\ .*\:\ \#1\.2\ read\ input\ tags\.\.\.\
24 INFO\ \ \@\ .*\:\ \#1\ \ Background\ Redundant\ rate\:\ 1\.00\
25 INFO\ \ \@\ .*\:\ \#1\ finished\!\
26 INFO\ \ \@\ .*\:\ \#2\ Build\ Peak\ Model\.\.\.\
27 INFO\ \ \@\ .*\:\ \#2\ number\ of\ paired\ peaks\:\ 549\
28 WARNING\ \@\ .*\:\ 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\!\
29 INFO\ \ \@\ .*\:\ \#2\ finished\!\
30 INFO\ \ \@\ .*\:\ \#2\.2\ Generate\ R\ script\ for\ model\ \:\ Galaxy\_Test\_Run\_model\.r\
31 INFO\ \ \@\ .*\:\ \#3\ Call\ peaks\.\.\.\
32 INFO\ \ \@\ .*\:\ \#3\ shift\ treatment\ data\
33 INFO\ \ \@\ .*\:\ \#3\ merge\ \+\/\-\ strand\ of\ treatment\ data\
34 INFO\ \ \@\ .*\:\ \#3\ save\ the\ shifted\ and\ merged\ tag\ counts\ into\ wiggle\ file\.\.\.\
35 INFO\ \ \@\ .*\:\ write\ to\ Galaxy\_Test\_Run\_MACS\_wiggle\/treat\/Galaxy\_Test\_Run\_treat\_afterfiting\_chr1\.wig\ for\ chromosome\ chr1\
36 INFO\ \ \@\ .*\:\ compress\ the\ wiggle\ file\ using\ gzip\.\.\.\
37 INFO\ \ \@\ .*\:\ \#3\ call\ peak\ candidates\
38 INFO\ \ \@\ .*\:\ \#3\ shift\ control\ data\
39 INFO\ \ \@\ .*\:\ \#3\ merge\ \+\/\-\ strand\ of\ control\ data\
40 INFO\ \ \@\ .*\:\ \#3\ save\ the\ shifted\ and\ merged\ tag\ counts\ into\ wiggle\ file\.\.\.\
41 INFO\ \ \@\ .*\:\ write\ to\ Galaxy\_Test\_Run\_MACS\_wiggle\/control\/Galaxy\_Test\_Run\_control\_afterfiting\_chr1\.wig\ for\ chromosome\ chr1\
42 INFO\ \ \@\ .*\:\ compress\ the\ wiggle\ file\ using\ gzip\.\.\.\
43 INFO\ \ \@\ .*\:\ \#3\ call\ negative\ peak\ candidates\
44 INFO\ \ \@\ .*\:\ \#3\ use\ control\ data\ to\ filter\ peak\ candidates\.\.\.\
45 INFO\ \ \@\ .*\:\ \#3\ Finally\,\ 1270\ peaks\ are\ called\!\
46 INFO\ \ \@\ .*\:\ \#3\ find\ negative\ peaks\ by\ reversing\ treat\ and\ control\
47 INFO\ \ \@\ .*\:\ \#3\ Finally\,\ 57\ peaks\ are\ called\!\
48 INFO\ \ \@\ .*\:\ \#4\ Write\ output\ xls\ file\.\.\.\ Galaxy\_Test\_Run\_peaks\.xls\
49 INFO\ \ \@\ .*\:\ \#4\ Write\ output\ bed\ file\.\.\.\ Galaxy\_Test\_Run\_peaks\.bed\
50 INFO\ \ \@\ .*\:\ \#4\ Write\ output\ xls\ file\ for\ negative\ peaks\.\.\.\ Galaxy\_Test\_Run\_negative\_peaks\.xls\
51 INFO\ \ \@\ .*\:\ \#5\ Done\!\ Check\ the\ output\ files\!
52 \
53 \<\/pre\>\<\/p\>
54 \<\/body\>\<\/html\>