Mercurial > repos > devteam > macs
diff test-data/peakcalling_macs/macs_test_3_out.html @ 0:512c6b2dba00 draft
Imported from capsule None
author | devteam |
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date | Thu, 23 Jan 2014 12:32:02 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peakcalling_macs/macs_test_3_out.html Thu Jan 23 12:32:02 2014 -0500 @@ -0,0 +1,54 @@ +\<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\>