htsworkflow/pipelines/test/testdata/run_FC12150_2007-09-27.xml

   1 <PipelineRun>
   2   <FlowcellID>FC12150</FlowcellID>
   3   <Firecrest>
   4     <version>1.8.28</version>
   5     <FirstCycle>1</FirstCycle>
   6     <LastCycle>36</LastCycle>
   7     <run_time>1190876400.0</run_time>
   8     <matrix># Auto-generated frequency response matrix
   9 &gt; A
  10 &gt; C
  11 &gt; G
  12 &gt; T
  13 2.19 0.39 -0.03 -0.02
  14 3.09 2.85 -0.15 -0.12
  15 -0.02 -0.01 0.39 -0.00
  16 -0.02 -0.02 0.37 0.51
  17 </matrix>
  18   </Firecrest>
  19   <Bustard>
  20     <version>1.8.28</version>
  21     <run_time>1190876400.0</run_time>
  22   </Bustard>
  23   <Gerald>
  24     <RunParameters>
  25       <ChipWideRunParameters>
  26         <ANALYSIS>default</ANALYSIS>
  27         <BAD_LANES />
  28         <BAD_TILES />
  29         <CONTAM_DIR>/data-store01/compbio/genomes</CONTAM_DIR>
  30         <CONTAM_FILE />
  31         <ELAND_GENOME>Need_to_specify_ELAND_genome_directory</ELAND_GENOME>
  32         <ELAND_MULTIPLE_INSTANCES>8</ELAND_MULTIPLE_INSTANCES>
  33         <ELAND_REPEAT />
  34         <EMAIL_DOMAIN>domain.com</EMAIL_DOMAIN>
  35         <EMAIL_LIST>diane</EMAIL_LIST>
  36         <EMAIL_SERVER>localhost:25</EMAIL_SERVER>
  37         <EXPT_DIR>/zpool1/compbio/diane/sequencer/070924_USI-EAS44_0022_FC12150/Data/C1-36_Firecrest1.8.28_27-09-2007_diane/Bustard1.8.28_27-09-2007_diane</EXPT_DIR>
  38         <EXPT_DIR_ROOT>/zpool1/compbio/diane/sequencer</EXPT_DIR_ROOT>
  39         <FORCE>1</FORCE>
  40         <GENOME_DIR>/data-store01/compbio/genomes</GENOME_DIR>
  41         <GENOME_FILE>Need_to_specify_genome_file_name</GENOME_FILE>
  42         <HAMSTER_FLAG>genome</HAMSTER_FLAG>
  43         <OUT_DIR>/zpool1/compbio/diane/sequencer/070924_USI-EAS44_0022_FC12150/Data/C1-36_Firecrest1.8.28_27-09-2007_diane/Bustard1.8.28_27-09-2007_diane/GERALD_27-09-2007_diane</OUT_DIR>
  44         <POST_RUN_COMMAND />
  45         <PRB_FILE_SUFFIX>_prb.txt</PRB_FILE_SUFFIX>
  46         <PURE_BASES>12</PURE_BASES>
  47         <QF_PARAMS>'((CHASTITY&gt;=0.6))'</QF_PARAMS>
  48         <QHG_FILE_SUFFIX>_qhg.txt</QHG_FILE_SUFFIX>
  49         <QUALITY_FORMAT>--symbolic</QUALITY_FORMAT>
  50         <READ_LENGTH>32</READ_LENGTH>
  51         <SEQUENCE_FORMAT>--scarf</SEQUENCE_FORMAT>
  52         <SEQ_FILE_SUFFIX>_seq.txt</SEQ_FILE_SUFFIX>
  53         <SIG_FILE_SUFFIX_DEPHASED>_sig2.txt</SIG_FILE_SUFFIX_DEPHASED>
  54         <SIG_FILE_SUFFIX_NOT_DEPHASED>_sig.txt</SIG_FILE_SUFFIX_NOT_DEPHASED>
  55         <SOFTWARE_VERSION>@(#) Id: GERALD.pl,v 1.68.2.2 2007/06/13 11:08:49 km Exp</SOFTWARE_VERSION>
  56         <TILE_REGEX>s_[1-8]_[0-9][0-9][0-9][0-9]</TILE_REGEX>
  57         <TILE_ROOT>s</TILE_ROOT>
  58         <TIME_STAMP>Thu Sep 27 14:22:54 2007</TIME_STAMP>
  59         <TOOLS_DIR>/home/diane/proj/SolexaPipeline-0.2.2.6/Goat/../Gerald</TOOLS_DIR>
  60         <USE_BASES>all</USE_BASES>
  61         <WEB_DIR_ROOT>http://host.domain.com/yourshare/</WEB_DIR_ROOT>
  62       </ChipWideRunParameters>
  63       <LaneSpecificRunParameters>
  64         <ANALYSIS>
  65           <s_1>eland</s_1>
  66           <s_2>eland</s_2>
  67           <s_3>eland</s_3>
  68           <s_4>eland</s_4>
  69           <s_5>eland</s_5>
  70           <s_6>eland</s_6>
  71           <s_7>eland</s_7>
  72           <s_8>eland</s_8>
  73         </ANALYSIS>
  74         <ELAND_GENOME>
  75           <s_1>/data-store01/compbio/genomes/hg18</s_1>
  76           <s_2>/data-store01/compbio/genomes/hg18</s_2>
  77           <s_3>/data-store01/compbio/genomes/hg18</s_3>
  78           <s_4>/data-store01/compbio/genomes/hg18</s_4>
  79           <s_5>/data-store01/compbio/genomes/hg18</s_5>
  80           <s_6>/data-store01/compbio/genomes/hg18</s_6>
  81           <s_7>/data-store01/compbio/genomes/hg18</s_7>
  82           <s_8>/data-store01/compbio/genomes/hg18</s_8>
  83         </ELAND_GENOME>
  84         <READ_LENGTH>
  85           <s_1>32</s_1>
  86           <s_2>32</s_2>
  87           <s_3>32</s_3>
  88           <s_4>32</s_4>
  89           <s_5>32</s_5>
  90           <s_6>32</s_6>
  91           <s_7>32</s_7>
  92           <s_8>32</s_8>
  93         </READ_LENGTH>
  94         <USE_BASES>
  95           <s_1>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_1>
  96           <s_2>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_2>
  97           <s_3>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_3>
  98           <s_4>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_4>
  99           <s_5>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_5>
 100           <s_6>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_6>
 101           <s_7>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_7>
 102           <s_8>YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY</s_8>
 103         </USE_BASES>
 104       </LaneSpecificRunParameters>
 105     </RunParameters>
 106     <Summary>
 107       <LaneResultSummary lane="1">
 108         <Cluster deviation="6010" mean="31261" />
 109         <AverageFirstCycleIntensity deviation="36" mean="500" />
 110         <PercentIntensityAfter20Cycles deviation="3.78" mean="74.74" />
 111         <PercentPassFilterClusters deviation="7.31" mean="27.38" />
 112         <AverageAlignmentScore deviation="596.07" mean="12116.63" />
 113         <PercentErrorRate deviation="0.38" mean="2.07" />
 114       </LaneResultSummary>
 115       <LaneResultSummary lane="2">
 116         <Cluster deviation="1595" mean="33336" />
 117         <AverageFirstCycleIntensity deviation="18" mean="610" />
 118         <PercentIntensityAfter20Cycles deviation="1.54" mean="72.76" />
 119         <PercentPassFilterClusters deviation="3.49" mean="32.73" />
 120         <AverageAlignmentScore deviation="251.86" mean="12681.91" />
 121         <PercentErrorRate deviation="0.09" mean="1.69" />
 122       </LaneResultSummary>
 123       <LaneResultSummary lane="3">
 124         <Cluster deviation="1596" mean="33860" />
 125         <AverageFirstCycleIntensity deviation="25" mean="642" />
 126         <PercentIntensityAfter20Cycles deviation="1.52" mean="74.67" />
 127         <PercentPassFilterClusters deviation="2.87" mean="35.05" />
 128         <AverageAlignmentScore deviation="245.19" mean="12940.51" />
 129         <PercentErrorRate deviation="0.1" mean="1.65" />
 130       </LaneResultSummary>
 131       <LaneResultSummary lane="4">
 132         <Cluster deviation="1481" mean="32524" />
 133         <AverageFirstCycleIntensity deviation="22" mean="639" />
 134         <PercentIntensityAfter20Cycles deviation="2.35" mean="75.1" />
 135         <PercentPassFilterClusters deviation="2.25" mean="37.61" />
 136         <AverageAlignmentScore deviation="204.7" mean="12841.73" />
 137         <PercentErrorRate deviation="0.09" mean="1.61" />
 138       </LaneResultSummary>
 139       <LaneResultSummary lane="5">
 140         <Cluster deviation="1791" mean="32612" />
 141         <AverageFirstCycleIntensity deviation="27" mean="668" />
 142         <PercentIntensityAfter20Cycles deviation="2.15" mean="78.4" />
 143         <PercentPassFilterClusters deviation="2.52" mean="38.56" />
 144         <AverageAlignmentScore deviation="221.56" mean="12920.71" />
 145         <PercentErrorRate deviation="0.1" mean="1.66" />
 146       </LaneResultSummary>
 147       <LaneResultSummary lane="6">
 148         <Cluster deviation="1901" mean="35452" />
 149         <AverageFirstCycleIntensity deviation="37" mean="707" />
 150         <PercentIntensityAfter20Cycles deviation="2.53" mean="77.42" />
 151         <PercentPassFilterClusters deviation="2.21" mean="35.38" />
 152         <AverageAlignmentScore deviation="223.73" mean="12393.36" />
 153         <PercentErrorRate deviation="0.1" mean="1.63" />
 154       </LaneResultSummary>
 155       <LaneResultSummary lane="7">
 156         <Cluster deviation="1765" mean="33031" />
 157         <AverageFirstCycleIntensity deviation="23" mean="669" />
 158         <PercentIntensityAfter20Cycles deviation="1.71" mean="79.27" />
 159         <PercentPassFilterClusters deviation="2.29" mean="37.84" />
 160         <AverageAlignmentScore deviation="241.37" mean="12489.76" />
 161         <PercentErrorRate deviation="0.1" mean="1.68" />
 162       </LaneResultSummary>
 163       <LaneResultSummary lane="8">
 164         <Cluster deviation="1531" mean="29782" />
 165         <AverageFirstCycleIntensity deviation="86" mean="440" />
 166         <PercentIntensityAfter20Cycles deviation="2.07" mean="79.97" />
 167         <PercentPassFilterClusters deviation="3.97" mean="32.72" />
 168         <AverageAlignmentScore deviation="1059.46" mean="11087.61" />
 169         <PercentErrorRate deviation="0.45" mean="2.35" />
 170       </LaneResultSummary>
 171     </Summary>
 172   </Gerald>
 173 </PipelineRun>