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==SOAP3 (latest version)== * Downloaded and install the latest binary release of SOAP3 from http://www.cs.hku.hk/2bwt-tools/soap3/ genemapster: /media/2TB_store2/Dinh_Scratch/softwares/soap3-r146 * Add to path: export PATH=/media/2TB_store2/Dinh_Scratch/softwares/soap3-r146:$PATH * Index reference hg18 In directory /media/2TB_store2/Dinh_Scratch/HsRef/Hg18/ soap3-builder genome.fa * Convert to GPU Index BGS-Build genome.fa.index * Edit soap3_aligner.ini file: SaValueFileExt=.sa NumOfCpuThreads=4 HostAlignmentModel=16G MaxOutputPerRead=1 StrandArrangement=+/- MaxOutputPerPair=1 GPUMemory=4 * Ran soap3_aligner (2 mismatch, unique best alignments only): soap3_aligner single /media/2TB_store2/Dinh_Scratch/HsRef/Hg18/HsGenome18.fa.index test1000000reads.fastq -m 2 -h 3 * Outputs: [Main] Finished parsing ini file soap3_aligner.ini. [Main] Finished loading index into host. [Main] Loading time : 3.0066 seconds [Main] Reference sequence length : 2858029421 [Main] Finished copying index into device (GPU). [Main] Loading time : 0.8665 seconds [Main] Loaded 1000000 short reads from the query file. [Main] Elapsed time on host : 1.3785 seconds Finished alignment with <= 2 mismatches Elapsed time : 0.1998 seconds Number of reads aligned: 1000000 (number of alignments: 1000000) [Main] Overall number of reads aligned: 1000000 (number of alignments: 1000000) [Main] Overall number of unaligned reads: 0 [Main] Overall read load time : 1.3785 seconds [Main] Overall alignment time (excl. read loading) : 0.1998 seconds [Main] Free device memory.. [Main] Free index from host memory.. [Main] Free host memory.. [Main] soap3_aligner terminated. Please type the following command to merge the alignment results into one file: ./make_view_simple.sh test1000000reads.fastq * Run make_view_simple.sh make_view_simple.sh test1000000reads.fastq * Outputs: ------------------------------------------------------------- Alignment file - test1000000reads.fastq.out has been created Format: Read #, Chromosome Id#, Offset, Strand, # of Mismatch ------------------------------------------------------------- * head -5 test1000000reads.fastq.out 1 1 50000 + 0 2 1 50000 + 0 3 1 50000 + 0 4 1 50000 + 0 5 1 50000 + 0 * Alignments are all wrong ===SOAP3 try compiling from source=== * Downloaded http://www.cs.hku.hk/2bwt-tools/downloads/soap3-r146-source.tar.gz * Still didn't work * '''SOAP3 requires a GPU with compute capability of 2.0 (Tesla C1060 is of 1.3)''' * SOAP3 website only mentioned that they require CUDA Driver version 3.2...they should probably also state the compute capability requirement.
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