drio
/ gist:363229
Created
April 12, 2010 02:57
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| test drio |
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| Sun Apr 11 21:58:24 CDT 2010 |
drio
/ gist:363232
Created
April 12, 2010 03:00
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| Sun Apr 11 22:00:14 CDT 2010 |
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| #!/usr/bin/env ruby19 | |
| # | |
| ses = %w{ | |
| /stornext/snfs1/next-gen/solid/results/solid0301/0301_20091103_1_SP/AWG_TCGA_GBM_02_T_000sA_01003244545_1/results.F1B1 | |
| /stornext/snfs1/next-gen/solid/results/solid0301/0301_20091103_1_SP/AWG_TCGA_GBM_02_T_000sA_01003244545_2/results.F1B1 | |
| /stornext/snfs1/next-gen/solid/results/solid0301/0301_20091103_1_SP/ANG_HSAP_NG_003sA_01003244545_3/results.F1B1 | |
| /stornext/snfs1/next-gen/solid/results/solid0301/0301_20091103_1_SP/ANG_HSAP_NG_003sA_01003244545_4/results.F1B1 | |
| /stornext/snfs4/next-gen/solid/results/solid0446/0446_20091125_1_SL/AWG_TCGA_OVA_01_T_000sA_01003244597_1/results.F1B1 | |
| } |
drio
/ gist:364970
Created
April 13, 2010 19:12
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| Tue Apr 13 14:12:19 CDT 2010 |
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| cat cluster_JOBS.sh | grep -E "\-e" | ruby -ne 'o = $_[/\.([01]+)\./, 1]; puts o if o' | head -10 |
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| sh ./clean.sh && ./run_experiment.sh 0 2>&1 | grep "versions" | grep -E "^\+ \/Users" > /tmp/out.txt | |
| + /Users/drio/projects/bfast_related/versions/bfast/bfast/bfast fasta2brg -A0 -f ecoli.drio.test.fa | |
| + /Users/drio/projects/bfast_related/versions/bfast/bfast/bfast fasta2brg -A1 -f ecoli.drio.test.fa | |
| + /Users/drio/projects/bfast_related/versions/bfast/bfast/bfast bwaaln -t8 ./bfast.bwt.indexes/ecoli.drio.test.fa ./bf.reads.fastq | |
| + /Users/drio/projects/bfast_related/versions/bfast/bfast/bfast localalign -u -n1 -A0 -f ./bfast.bwt.indexes/ecoli.drio.test.fa -m bf.matches.bmf | |
| + /Users/drio/projects/bfast_related/versions/bfast/bfast/bfast postprocess -f ./bfast.bwt.indexes/ecoli.drio.test.fa -i bf.aligned.baf -n3 -a3 -O3 |
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| 04-15-2010 15:43:17 >> Generating 10000 reads | |
| 04-15-2010 15:43:17 >> Creating BWA indexes | |
| 04-15-2010 15:43:22 >> Aligning with BWA (read1 / read2) | |
| 04-15-2010 15:43:23 >> Converting BWA aligments to sam | |
| 04-15-2010 15:43:24 >> Converting from SAM to BAM and sorting | |
| 04-15-2010 15:43:25 >> Converting REF to BF bin (CS|SS) | |
| 04-15-2010 15:43:27 >> BF (BWT) indexes already there, skipping. | |
| 04-15-2010 15:43:27 >> BF match (BWT - bwaaln) | |
| 04-15-2010 15:43:28 >> BF local (BWT) -U | |
| 04-15-2010 15:43:30 >> BF version: 0.6.3d |
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| 04-15-2010 15:49:05 >> Generating 10000 reads (50+25) | |
| 04-15-2010 15:49:05 >> Creating BWA indexes | |
| 04-15-2010 15:49:11 >> Aligning with BWA (read1 / read2) | |
| 04-15-2010 15:49:12 >> Converting BWA aligments to sam | |
| 04-15-2010 15:49:13 >> Converting from SAM to BAM and sorting | |
| 04-15-2010 15:49:13 >> Converting REF to BF bin (CS|SS) | |
| 04-15-2010 15:49:15 >> BF (BWT) indexes already there, skipping. | |
| 04-15-2010 15:49:15 >> BF match (BWT - bwaaln) | |
| 04-15-2010 15:49:17 >> BF local (BWT) -U | |
| 04-15-2010 15:49:18 >> BF version: 0.6.3d |
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| 04-16-2010 11:36:56 >> Space: 0 () | |
| 04-16-2010 11:36:56 >> Generating 10000 reads (50+25) | |
| 04-16-2010 11:36:56 >> Creating BWA indexes | |
| [bwa_index] Pack FASTA... 0.06 sec | |
| [bwa_index] Reverse the packed sequence... 0.02 sec | |
| [bwa_index] Construct BWT for the packed sequence... | |
| [bwa_index] 0.98 seconds elapse. | |
| [bwa_index] Construct BWT for the reverse packed sequence... | |
| [bwa_index] 0.97 seconds elapse. | |
| [bwa_index] Update BWT... 0.02 sec |