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

\<html\>\<head\>\<title\>Additional\ output\ created\ by\ MACS\ \(Galaxy\_Test\_Run\)\<\/title\>\<\/head\>\<body\>\<h3\>Additional\ Files\:\<\/h3\>\<p\>\<ul\>
\<li\>\<a\ href\=\"Galaxy\_Test\_Run\_model\.pdf\"\>Galaxy\_Test\_Run\_model\.pdf\<\/a\>\<\/li\>
\<li\>\<a\ href\=\"Galaxy\_Test\_Run\_model\.r\"\>Galaxy\_Test\_Run\_model\.r\<\/a\>\<\/li\>
\<li\>\<a\ href\=\"Galaxy\_Test\_Run\_model\.r\.log\"\>Galaxy\_Test\_Run\_model\.r\.log\<\/a\>\<\/li\>
\<li\>\<a\ href\=\"Galaxy\_Test\_Run\_negative\_peaks\.xls\"\>Galaxy\_Test\_Run\_negative\_peaks\.xls\<\/a\>\<\/li\>
\<li\>\<a\ href\=\"Galaxy\_Test\_Run\_peaks\.xls\"\>Galaxy\_Test\_Run\_peaks\.xls\<\/a\>\<\/li\>
\<\/ul\>\<\/p\>
\<h3\>Messages\ from\ MACS\:\<\/h3\>
\<p\>\<pre\>INFO\ \ \@\ .*\:\ 
\#\ ARGUMENTS\ LIST\:
\#\ name\ \=\ Galaxy\_Test\_Run
\#\ format\ \=\ BED
\#\ ChIP\-seq\ file\ \=\ .*\.dat
\#\ control\ file\ \=\ .*\.dat
\#\ effective\ genome\ size\ \=\ 2\.70e\+09
\#\ tag\ size\ \=\ 36
\#\ band\ width\ \=\ 300
\#\ model\ fold\ \=\ 13
\#\ pvalue\ cutoff\ \=\ 1\.00e\-05
\#\ Ranges\ for\ calculating\ regional\ lambda\ are\ \:\ peak\_region\,1000\,5000\,10000\ 
INFO\ \ \@\ .*\:\ \#1\ read\ tag\ files\.\.\.\ 
INFO\ \ \@\ .*\:\ \#1\ read\ treatment\ tags\.\.\.\ 
INFO\ \ \@\ .*\:\ \#1\.2\ read\ input\ tags\.\.\.\ 
INFO\ \ \@\ .*\:\ \#1\ \ Background\ Redundant\ rate\:\ 1\.00\ 
INFO\ \ \@\ .*\:\ \#1\ finished\!\ 
INFO\ \ \@\ .*\:\ \#2\ Build\ Peak\ Model\.\.\.\ 
INFO\ \ \@\ .*\:\ \#2\ number\ of\ paired\ peaks\:\ 549\ 
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\!\ 
INFO\ \ \@\ .*\:\ \#2\ finished\!\ 
INFO\ \ \@\ .*\:\ \#2\.2\ Generate\ R\ script\ for\ model\ \:\ Galaxy\_Test\_Run\_model\.r\ 
INFO\ \ \@\ .*\:\ \#3\ Call\ peaks\.\.\.\ 
INFO\ \ \@\ .*\:\ \#3\ shift\ treatment\ data\ 
INFO\ \ \@\ .*\:\ \#3\ merge\ \+\/\-\ strand\ of\ treatment\ data\ 
INFO\ \ \@\ .*\:\ \#3\ save\ the\ shifted\ and\ merged\ tag\ counts\ into\ wiggle\ file\.\.\.\ 
INFO\ \ \@\ .*\:\ write\ to\ Galaxy\_Test\_Run\_MACS\_wiggle\/treat\/Galaxy\_Test\_Run\_treat\_afterfiting\_chr1\.wig\ for\ chromosome\ chr1\ 
INFO\ \ \@\ .*\:\ compress\ the\ wiggle\ file\ using\ gzip\.\.\.\ 
INFO\ \ \@\ .*\:\ \#3\ call\ peak\ candidates\ 
INFO\ \ \@\ .*\:\ \#3\ shift\ control\ data\ 
INFO\ \ \@\ .*\:\ \#3\ merge\ \+\/\-\ strand\ of\ control\ data\ 
INFO\ \ \@\ .*\:\ \#3\ save\ the\ shifted\ and\ merged\ tag\ counts\ into\ wiggle\ file\.\.\.\ 
INFO\ \ \@\ .*\:\ write\ to\ Galaxy\_Test\_Run\_MACS\_wiggle\/control\/Galaxy\_Test\_Run\_control\_afterfiting\_chr1\.wig\ for\ chromosome\ chr1\ 
INFO\ \ \@\ .*\:\ compress\ the\ wiggle\ file\ using\ gzip\.\.\.\ 
INFO\ \ \@\ .*\:\ \#3\ call\ negative\ peak\ candidates\ 
INFO\ \ \@\ .*\:\ \#3\ use\ control\ data\ to\ filter\ peak\ candidates\.\.\.\ 
INFO\ \ \@\ .*\:\ \#3\ Finally\,\ 1270\ peaks\ are\ called\!\ 
INFO\ \ \@\ .*\:\ \#3\ find\ negative\ peaks\ by\ reversing\ treat\ and\ control\ 
INFO\ \ \@\ .*\:\ \#3\ Finally\,\ 57\ peaks\ are\ called\!\ 
INFO\ \ \@\ .*\:\ \#4\ Write\ output\ xls\ file\.\.\.\ Galaxy\_Test\_Run\_peaks\.xls\ 
INFO\ \ \@\ .*\:\ \#4\ Write\ output\ bed\ file\.\.\.\ Galaxy\_Test\_Run\_peaks\.bed\ 
INFO\ \ \@\ .*\:\ \#4\ Write\ output\ xls\ file\ for\ negative\ peaks\.\.\.\ Galaxy\_Test\_Run\_negative\_peaks\.xls\ 
INFO\ \ \@\ .*\:\ \#5\ Done\!\ Check\ the\ output\ files\!
\ 
\<\/pre\>\<\/p\>
\<\/body\>\<\/html\>