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annotate test-data/peakcalling_macs/macs_test_3_out.html @ 2:5d67bc6f385f draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/macs commit 206cd8245e7619b0e924c5066d0172129222993d"
author devteam
date Wed, 05 Feb 2020 15:28:57 +0000
parents 512c6b2dba00
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 \<html\>\<head\>\<title\>Additional\ output\ created\ by\ MACS\ \(Galaxy\_Test\_Run\)\<\/title\>\<\/head\>\<body\>\<h3\>Additional\ Files\:\<\/h3\>\<p\>\<ul\>
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2 \<li\>\<a\ href\=\"Galaxy\_Test\_Run\_model\.pdf\"\>Galaxy\_Test\_Run\_model\.pdf\<\/a\>\<\/li\>
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3 \<li\>\<a\ href\=\"Galaxy\_Test\_Run\_model\.r\"\>Galaxy\_Test\_Run\_model\.r\<\/a\>\<\/li\>
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4 \<li\>\<a\ href\=\"Galaxy\_Test\_Run\_model\.r\.log\"\>Galaxy\_Test\_Run\_model\.r\.log\<\/a\>\<\/li\>
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5 \<li\>\<a\ href\=\"Galaxy\_Test\_Run\_negative\_peaks\.xls\"\>Galaxy\_Test\_Run\_negative\_peaks\.xls\<\/a\>\<\/li\>
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6 \<li\>\<a\ href\=\"Galaxy\_Test\_Run\_peaks\.xls\"\>Galaxy\_Test\_Run\_peaks\.xls\<\/a\>\<\/li\>
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7 \<\/ul\>\<\/p\>
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8 \<h3\>Messages\ from\ MACS\:\<\/h3\>
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9 \<p\>\<pre\>INFO\ \ \@\ .*\:\
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10 \#\ ARGUMENTS\ LIST\:
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11 \#\ name\ \=\ Galaxy\_Test\_Run
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12 \#\ format\ \=\ BED
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13 \#\ ChIP\-seq\ file\ \=\ .*\.dat
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14 \#\ control\ file\ \=\ .*\.dat
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15 \#\ effective\ genome\ size\ \=\ 2\.70e\+09
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16 \#\ tag\ size\ \=\ 36
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17 \#\ band\ width\ \=\ 300
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18 \#\ model\ fold\ \=\ 13
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19 \#\ pvalue\ cutoff\ \=\ 1\.00e\-05
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20 \#\ Ranges\ for\ calculating\ regional\ lambda\ are\ \:\ peak\_region\,1000\,5000\,10000\
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21 INFO\ \ \@\ .*\:\ \#1\ read\ tag\ files\.\.\.\
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22 INFO\ \ \@\ .*\:\ \#1\ read\ treatment\ tags\.\.\.\
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23 INFO\ \ \@\ .*\:\ \#1\.2\ read\ input\ tags\.\.\.\
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24 INFO\ \ \@\ .*\:\ \#1\ \ Background\ Redundant\ rate\:\ 1\.00\
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25 INFO\ \ \@\ .*\:\ \#1\ finished\!\
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26 INFO\ \ \@\ .*\:\ \#2\ Build\ Peak\ Model\.\.\.\
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27 INFO\ \ \@\ .*\:\ \#2\ number\ of\ paired\ peaks\:\ 549\
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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\!\
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29 INFO\ \ \@\ .*\:\ \#2\ finished\!\
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30 INFO\ \ \@\ .*\:\ \#2\.2\ Generate\ R\ script\ for\ model\ \:\ Galaxy\_Test\_Run\_model\.r\
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31 INFO\ \ \@\ .*\:\ \#3\ Call\ peaks\.\.\.\
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32 INFO\ \ \@\ .*\:\ \#3\ shift\ treatment\ data\
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33 INFO\ \ \@\ .*\:\ \#3\ merge\ \+\/\-\ strand\ of\ treatment\ data\
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34 INFO\ \ \@\ .*\:\ \#3\ save\ the\ shifted\ and\ merged\ tag\ counts\ into\ wiggle\ file\.\.\.\
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35 INFO\ \ \@\ .*\:\ write\ to\ Galaxy\_Test\_Run\_MACS\_wiggle\/treat\/Galaxy\_Test\_Run\_treat\_afterfiting\_chr1\.wig\ for\ chromosome\ chr1\
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36 INFO\ \ \@\ .*\:\ compress\ the\ wiggle\ file\ using\ gzip\.\.\.\
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37 INFO\ \ \@\ .*\:\ \#3\ call\ peak\ candidates\
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38 INFO\ \ \@\ .*\:\ \#3\ shift\ control\ data\
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39 INFO\ \ \@\ .*\:\ \#3\ merge\ \+\/\-\ strand\ of\ control\ data\
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40 INFO\ \ \@\ .*\:\ \#3\ save\ the\ shifted\ and\ merged\ tag\ counts\ into\ wiggle\ file\.\.\.\
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41 INFO\ \ \@\ .*\:\ write\ to\ Galaxy\_Test\_Run\_MACS\_wiggle\/control\/Galaxy\_Test\_Run\_control\_afterfiting\_chr1\.wig\ for\ chromosome\ chr1\
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42 INFO\ \ \@\ .*\:\ compress\ the\ wiggle\ file\ using\ gzip\.\.\.\
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43 INFO\ \ \@\ .*\:\ \#3\ call\ negative\ peak\ candidates\
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44 INFO\ \ \@\ .*\:\ \#3\ use\ control\ data\ to\ filter\ peak\ candidates\.\.\.\
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45 INFO\ \ \@\ .*\:\ \#3\ Finally\,\ 1270\ peaks\ are\ called\!\
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46 INFO\ \ \@\ .*\:\ \#3\ find\ negative\ peaks\ by\ reversing\ treat\ and\ control\
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47 INFO\ \ \@\ .*\:\ \#3\ Finally\,\ 57\ peaks\ are\ called\!\
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48 INFO\ \ \@\ .*\:\ \#4\ Write\ output\ xls\ file\.\.\.\ Galaxy\_Test\_Run\_peaks\.xls\
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49 INFO\ \ \@\ .*\:\ \#4\ Write\ output\ bed\ file\.\.\.\ Galaxy\_Test\_Run\_peaks\.bed\
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50 INFO\ \ \@\ .*\:\ \#4\ Write\ output\ xls\ file\ for\ negative\ peaks\.\.\.\ Galaxy\_Test\_Run\_negative\_peaks\.xls\
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51 INFO\ \ \@\ .*\:\ \#5\ Done\!\ Check\ the\ output\ files\!
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52 \
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53 \<\/pre\>\<\/p\>
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54 \<\/body\>\<\/html\>