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NOTES.DOPTE.unfiltered.txt
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NOTES.DOPTE.unfiltered.txt
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cd /fast/bakeoff_merged_analysis_sequences_unfiltered
tar xzf archive/processed_lists_raw_fixed_withSampleDatesAndReadyForResults.tar.gz
mv processed_lists results
tar xzf archive/bounds.tar.gz
ln -s /fast/bakeoff_merged_analysis_sequences_unfiltered/bounds results/raw_fixed/bounds
## For main results:
cd ~/src/from-git/hiv-founder-id
# nflg
./runAllListsLocally2.sh /fast/bakeoff_merged_analysis_sequences_unfiltered/results/raw_fixed/nflg/1m/ /fast/bakeoff_merged_analysis_sequences_unfiltered/results/raw_fixed/nflg/1m/ &
./runAllListsLocally2.sh /fast/bakeoff_merged_analysis_sequences_unfiltered/results/raw_fixed/nflg/6m/ /fast/bakeoff_merged_analysis_sequences_unfiltered/results/raw_fixed/nflg/6m/ &
./runAllListsLocally2.sh /fast/bakeoff_merged_analysis_sequences_unfiltered/results/raw_fixed/nflg/1m6m/ /fast/bakeoff_merged_analysis_sequences_unfiltered/results/raw_fixed/nflg/1m6m/ &
# v3
./runAllListsLocally2.sh /fast/bakeoff_merged_analysis_sequences_unfiltered/results/raw_fixed/v3/1m/ /fast/bakeoff_merged_analysis_sequences_unfiltered/results/raw_fixed/v3/1m/ &
./runAllListsLocally2.sh /fast/bakeoff_merged_analysis_sequences_unfiltered/results/raw_fixed/v3/6m/ /fast/bakeoff_merged_analysis_sequences_unfiltered/results/raw_fixed/v3/6m/ &
./runAllListsLocally2.sh /fast/bakeoff_merged_analysis_sequences_unfiltered/results/raw_fixed/v3/1m6m/ /fast/bakeoff_merged_analysis_sequences_unfiltered/results/raw_fixed/v3/1m6m/ &
## To fix because I forgot to install phyml the first time oops:
cd ~/src/from-git/hiv-founder-id
# nflg
./runAllListsLocallyPhyML.sh /fast/bakeoff_merged_analysis_sequences_unfiltered/results/raw_fixed/nflg/1m/ &
./runAllListsLocallyPhyML.sh /fast/bakeoff_merged_analysis_sequences_unfiltered/results/raw_fixed/nflg/6m/ &
./runAllListsLocallyPhyML.sh /fast/bakeoff_merged_analysis_sequences_unfiltered/results/raw_fixed/nflg/1m6m/ &
# v3
./runAllListsLocallyPhyML.sh /fast/bakeoff_merged_analysis_sequences_unfiltered/results/raw_fixed/v3/1m/ &
./runAllListsLocallyPhyML.sh /fast/bakeoff_merged_analysis_sequences_unfiltered/results/raw_fixed/v3/6m/ &
./runAllListsLocallyPhyML.sh /fast/bakeoff_merged_analysis_sequences_unfiltered/results/raw_fixed/v3/1m6m/ &
## For the PREAST/PrankenBeast/Infer results:
cd ~/src/from-git/PREAST
## unbounded results:
#./runAllListsLocally.sh /fast/bakeoff_merged_analysis_sequences_results_2019/results/raw_fixed/v3/1m/ &
# ... skipping these for now.
## bounded results:
# nflg
./runAllListsBoundsLocally.sh /fast/bakeoff_merged_analysis_sequences_unfiltered/results/raw_fixed/bounds/nflg/1m/artificialBounds_sampledwidth_uniform_mtn003.tab /fast/bakeoff_merged_analysis_sequences_unfiltered/results/raw_fixed/nflg/1m/ &
./runAllListsBoundsLocally.sh /fast/bakeoff_merged_analysis_sequences_unfiltered/results/raw_fixed/bounds/nflg/6m/artificialBounds_sampledwidth_uniform_hvtn502.tab /fast/bakeoff_merged_analysis_sequences_unfiltered/results/raw_fixed/nflg/6m/ &
./runAllListsBoundsLocally.sh /fast/bakeoff_merged_analysis_sequences_unfiltered/results/raw_fixed/bounds/nflg/1m6m/artificialBounds_sampledwidth_uniform_mtn003.tab /fast/bakeoff_merged_analysis_sequences_unfiltered/results/raw_fixed/nflg/1m6m/ &
# v3
./runAllListsBoundsLocally.sh /fast/bakeoff_merged_analysis_sequences_unfiltered/results/raw_fixed/bounds/v3/1m/artificialBounds_sampledwidth_uniform_mtn003.tab /fast/bakeoff_merged_analysis_sequences_unfiltered/results/raw_fixed/v3/1m/ &
./runAllListsBoundsLocally.sh /fast/bakeoff_merged_analysis_sequences_unfiltered/results/raw_fixed/bounds/v3/6m/artificialBounds_sampledwidth_uniform_hvtn502.tab /fast/bakeoff_merged_analysis_sequences_unfiltered/results/raw_fixed/v3/6m/ &
./runAllListsBoundsLocally.sh /fast/bakeoff_merged_analysis_sequences_unfiltered/results/raw_fixed/bounds/v3/1m6m/artificialBounds_sampledwidth_uniform_mtn003.tab /fast/bakeoff_merged_analysis_sequences_unfiltered/results/raw_fixed/v3/1m6m/ &
############################################################
## FOR ANALYSIS OF evaluateIsMultiple and evaluateTimings ##
############################################################
mkdir /fast/bakeoff_merged_analysis_sequences_unfiltered/results/raw_fixed/report/
cp ~/src/from-git/projects/pedlefse/BakeOff/BakeOff.Rnw /fast/bakeoff_merged_analysis_sequences_unfiltered/results/raw_fixed/report/BakeOff-Unfiltered.Rnw
cd /fast/bakeoff_merged_analysis_sequences_unfiltered/results/raw_fixed/report/
export BakeOff_RESULTS.DIR = "/fast/bakeoff_merged_analysis_sequences_unfiltered/results/"; R -e ' Sweave("BakeOff-Unfiltered.Rnw")';