Thu Apr 29 10:18:31 2010 - cvsid=$Id: apt-probeset-summarize.cpp,v 1.148 2008/06/19 15:13:29 awilli Exp $
Thu Apr 29 10:18:31 2010 - version=apt-1.10.0
Thu Apr 29 10:18:31 2010 - host=benwyvis
Thu Apr 29 10:18:31 2010 - cwd=/export/data0/xingjun/workspace/ftp/CEL2TXT/ST_1
Thu Apr 29 10:18:31 2010 - command-line=apt-probeset-summarize -a rma-sketch -p MoGene-1_0-st-v1.r4.pgf -c MoGene-1_0-st-v1.r4.clf -b MoGene-1_0-st-v1.r4.bgp -m MoGene-1_0-st-v1.r4.mps --qc-probesets MoGene-1_0-st-v1.r4.qcc -o /net/mahost/export/gudmap0/gudmap_archive/ftp/potter/january_2010/potter_070110_c/data/TXT /net/mahost/export/gudmap0/gudmap_archive/ftp/potter/january_2010/potter_070110_c/data/CEL/DUCT_E10_5_1.CEL /net/mahost/export/gudmap0/gudmap_archive/ftp/potter/january_2010/potter_070110_c/data/CEL/DUCT_E10_5_2.CEL /net/mahost/export/gudmap0/gudmap_archive/ftp/potter/january_2010/potter_070110_c/data/CEL/DUCT_E10_5_3.CEL
Thu Apr 29 10:18:31 2010 - Opening bgp file: MoGene-1_0-st-v1.r4.bgp
Thu Apr 29 10:18:31 2010 - Opening file: MoGene-1_0-st-v1.r4.mps to read.
Thu Apr 29 10:18:31 2010 - Read 35557 probesets.
Thu Apr 29 10:18:31 2010 - Opening clf file: MoGene-1_0-st-v1.r4.clf
Thu Apr 29 10:18:31 2010 - Opening pgf file: MoGene-1_0-st-v1.r4.pgf
Thu Apr 29 10:18:31 2010 - Just before layout.
Thu Apr 29 10:18:31 2010 - Expected=0MB Empirical=19MB
Thu Apr 29 10:18:47 2010 - Before make maps.
Thu Apr 29 10:18:47 2010 - Expected=0MB Empirical=52MB
Thu Apr 29 10:18:47 2010 - After make maps.
Thu Apr 29 10:18:47 2010 - Expected=0MB Empirical=60MB
Thu Apr 29 10:18:47 2010 - Loaded 241577 probe sets.
Thu Apr 29 10:18:47 2010 - Just after layout.
Thu Apr 29 10:18:47 2010 - Expected=0MB Empirical=60MB
Thu Apr 29 10:18:47 2010 - Pgf load took approximately: 16 seconds.
Thu Apr 29 10:18:47 2010 - After metaSets.
Thu Apr 29 10:18:47 2010 - Expected=0MB Empirical=61MB
Thu Apr 29 10:18:47 2010 - After psGroups.
Thu Apr 29 10:18:47 2010 - Expected=0MB Empirical=61MB
Thu Apr 29 10:18:49 2010 - After layout.
Thu Apr 29 10:18:49 2010 - Expected=67MB Empirical=67MB
Thu Apr 29 10:18:49 2010 - Number of pm probes is: 835984
Thu Apr 29 10:18:49 2010 - Number of bgrd probes is: 16943
Thu Apr 29 10:18:49 2010 - Number of mm probes is: 0
Thu Apr 29 10:18:49 2010 - Made ChipStream of type: rma-bg
Thu Apr 29 10:18:49 2010 - Using: 835984 PM probes for analysis.
Thu Apr 29 10:18:49 2010 - Made ChipStream of type: quant-norm
Thu Apr 29 10:18:49 2010 - Setting sketch size to: 50000
Thu Apr 29 10:18:49 2010 - Analysis Info:
apt-info-chiptype=MoGene-1_0-st-v1
apt-info-program-id=
apt-info-program-name=apt-probeset-summarize
apt-info-program-version=apt-1.10.0
apt-info-alg-name=rma-sketch
apt-info-alg-version=1.0
apt-info-num-rows=1050
apt-info-num-cols=1050
apt-info-num-probesets=35557
apt-info-apt-engine=ProbesetSummarizeEngine
apt-info-apt-program-name=apt-probeset-summarize
apt-info-apt-command-line=apt-probeset-summarize -a rma-sketch -p MoGene-1_0-st-v1.r4.pgf -c MoGene-1_0-st-v1.r4.clf -b MoGene-1_0-st-v1.r4.bgp -m MoGene-1_0-st-v1.r4.mps --qc-probesets MoGene-1_0-st-v1.r4.qcc -o /net/mahost/export/gudmap0/gudmap_archive/ftp/potter/january_2010/potter_070110_c/data/TXT /net/mahost/export/gudmap0/gudmap_archive/ftp/potter/january_2010/potter_070110_c/data/CEL/DUCT_E10_5_1.CEL /net/mahost/export/gudmap0/gudmap_archive/ftp/potter/january_2010/potter_070110_c/data/CEL/DUCT_E10_5_2.CEL /net/mahost/export/gudmap0/gudmap_archive/ftp/potter/january_2010/potter_070110_c/data/CEL/DUCT_E10_5_3.CEL
apt-info-apt-exec-guid=0000009007-1272532711-0794569152-1412925037-1936745308
apt-info-apt-analysis-guid=0000009007-1272532729-2029955680-1503490891-0973135049
apt-info-apt-time-str=Thu Apr 29 10:18:31 2010
apt-info-apt-version=apt-1.10.0
apt-info-apt-cvs-id=$Id: apt-probeset-summarize.cpp,v 1.148 2008/06/19 15:13:29 awilli Exp $
apt-info-apt-free-mem=3203026944
apt-info-apt-opt-chip-type=MoGene-1_0-st-v1
apt-info-apt-opt-probe-count=1102500
apt-info-apt-opt-force=false
apt-info-apt-opt-block-size=0
apt-info-apt-opt-mem-usage=0
apt-info-apt-opt-precision=5
apt-info-apt-opt-out-dir=/net/mahost/export/gudmap0/gudmap_archive/ftp/potter/january_2010/potter_070110_c/data/TXT
apt-info-apt-opt-cc-expr-chp-out-dir=
apt-info-apt-opt-cc-md-chp-out-dir=
apt-info-apt-opt-xda-chp-out-dir=
apt-info-apt-opt-cdf-file=
apt-info-apt-opt-spf-file=
apt-info-apt-opt-pgf-file=MoGene-1_0-st-v1.r4.pgf
apt-info-apt-opt-clf-file=MoGene-1_0-st-v1.r4.clf
apt-info-apt-opt-bgp-file=MoGene-1_0-st-v1.r4.bgp
apt-info-apt-opt-ps-list-file=
apt-info-apt-opt-meta-ps-file=MoGene-1_0-st-v1.r4.mps
apt-info-apt-opt-qc-groups-file=MoGene-1_0-st-v1.r4.qcc
apt-info-apt-opt-kill-list=
apt-info-apt-opt-do-ps-names=false
apt-info-apt-opt-use-disk=true
apt-info-apt-opt-disk-dir=
apt-info-apt-opt-diskCache=50
apt-info-apt-opt-cel-count=3
apt-info-apt-opt-cel-1=DUCT_E10_5_1.CEL
apt-info-apt-opt-cel-2=DUCT_E10_5_2.CEL
apt-info-apt-opt-cel-3=DUCT_E10_5_3.CEL
apt-info-apt-opt-analysis-name=rma-sketch
apt-info-apt-opt-set-analysis-name=
apt-info-apt-opt-analysis-spec=rma-bg,quant-norm.sketch=-1.bioc=true.lowprecision=false.usepm=true.target=0.doavg=false.subsetmd5=c9f3c4de4c97903a1de4f29b2507db79,pm-only,med-polish.FixFeatureEffect=false.expon=false.attenuate=true.l=0.005.h=-1,expr.genotype=false.strand=false.allele-a=false
apt-info-apt-opt-feat-effect-file=
apt-info-apt-opt-target-sketch-file=
apt-info-apt-opt-do-residuals=false
apt-info-apt-opt-do-feature-effects=false
apt-info-apt-opt-write-sketch=false
apt-info-quantification-name=med-polish
apt-info-quantification-version=1.0
apt-info-quantification-scale=log2
apt-info-quantification-type=signal

Thu Apr 29 10:18:49 2010 - Mem used so far: 69MB
Thu Apr 29 10:18:49 2010 - So far we've used: 73371648 bytes.
Thu Apr 29 10:18:49 2010 - Estimated available ram: 2048MB
Thu Apr 29 10:18:49 2010 - Adjusting available ram to: 1978MB
Thu Apr 29 10:18:49 2010 - Chipstream memory: 61 MB RAM.
Thu Apr 29 10:18:49 2010 - Avg probes: 25.4845 mem per probe: 4 numChips: 3 num probes: 1102500 mem per annotation: 913.277 num groups: 35557
Thu Apr 29 10:18:49 2010 - Total additional ram: 244MB total available: 1978MB
Thu Apr 29 10:18:49 2010 - Block size is: 35557 maximum probe sets are: 35557
Thu Apr 29 10:18:49 2010 - After delete layout.
Thu Apr 29 10:18:49 2010 - Expected=67MB Empirical=43MB
Thu Apr 29 10:18:49 2010 - Expecting 1 iteration.
Thu Apr 29 10:18:49 2010 - Doing iteration: 1
Thu Apr 29 10:18:49 2010 - Loading 35557 probesets.
Thu Apr 29 10:18:49 2010 - Before layout.
Thu Apr 29 10:18:49 2010 - Expected=67MB Empirical=43MB
Thu Apr 29 10:18:49 2010 - Opening clf file: MoGene-1_0-st-v1.r4.clf
Thu Apr 29 10:18:49 2010 - Opening pgf file: MoGene-1_0-st-v1.r4.pgf
Thu Apr 29 10:18:49 2010 - Just before layout.
Thu Apr 29 10:18:49 2010 - Expected=67MB Empirical=42MB
Thu Apr 29 10:19:05 2010 - Before make maps.
Thu Apr 29 10:19:05 2010 - Expected=67MB Empirical=69MB
Thu Apr 29 10:19:05 2010 - After make maps.
Thu Apr 29 10:19:05 2010 - Expected=67MB Empirical=69MB
Thu Apr 29 10:19:05 2010 - Loaded 241577 probe sets.
Thu Apr 29 10:19:05 2010 - Just after layout.
Thu Apr 29 10:19:05 2010 - Expected=67MB Empirical=69MB
Thu Apr 29 10:19:05 2010 - Pgf load took approximately: 16 seconds.
Thu Apr 29 10:19:05 2010 - After metaSets.
Thu Apr 29 10:19:05 2010 - Expected=67MB Empirical=69MB
Thu Apr 29 10:19:05 2010 - After psGroups.
Thu Apr 29 10:19:05 2010 - Expected=67MB Empirical=69MB
Thu Apr 29 10:19:05 2010 - After layout.
Thu Apr 29 10:19:05 2010 - Expected=277MB Empirical=69MB
Thu Apr 29 10:19:05 2010 - Loading: 1102500 probes
Thu Apr 29 10:19:05 2010 - Loading 35557 probesets and 835984 probes.
Thu Apr 29 10:19:05 2010 - Before reading cel files.
Thu Apr 29 10:19:05 2010 - Expected=277MB Empirical=68MB
Thu Apr 29 10:19:05 2010 - Reading 3 cel files.Thu Apr 29 10:19:06 2010 - Chip 0 using RMA param - alpha: 0.0404264 mu: 46.0069 sigma: 11.6389
.Thu Apr 29 10:19:06 2010 - Chip 1 using RMA param - alpha: 0.070311 mu: 39.4987 sigma: 8.46839
.Thu Apr 29 10:19:07 2010 - Chip 2 using RMA param - alpha: 0.061086 mu: 43.5022 sigma: 11.2461
Done.
Thu Apr 29 10:19:07 2010 - After reading cel files.
Thu Apr 29 10:19:07 2010 - Expected=277MB Empirical=70MB
Thu Apr 29 10:19:07 2010 - Processing Probesets......................Done.
Thu Apr 29 10:19:12 2010 - Flushing output reporters. Finalizing output.
Thu Apr 29 10:19:12 2010 - Done.
Thu Apr 29 10:19:12 2010 - Cleaning up.
Thu Apr 29 10:19:12 2010 - Done.
Thu Apr 29 10:19:12 2010 - Run took approximately: 0.68 minute.