/test-data/peakcalling_macs/macs_test_1_out.html
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- \<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\ call\ peak\ candidates\
- INFO\ \ \@\ .*\:\ \#3\ shift\ control\ data\
- INFO\ \ \@\ .*\:\ \#3\ merge\ \+\/\-\ strand\ of\ control\ data\
- 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\>