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Created April 16, 2010 16:40
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bfast bfast2 bwa
Raw
gistfile1
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
[bwa_index] Update reverse BWT... 0.02 sec
[bwa_index] Construct SA from BWT and Occ... 0.22 sec
[bwa_index] Construct SA from reverse BWT and Occ... 0.22 sec
[BWTIncConstructFromPacked] 10 iterations done. 1131243 characters processed.
[BWTIncConstructFromPacked] 20 iterations done. 1975531 characters processed.
[BWTIncConstructFromPacked] 30 iterations done. 2637691 characters processed.
[BWTIncConstructFromPacked] 40 iterations done. 3156171 characters processed.
[BWTIncConstructFromPacked] 50 iterations done. 3561355 characters processed.
[BWTIncConstructFromPacked] 60 iterations done. 3877131 characters processed.
[BWTIncConstructFromPacked] 70 iterations done. 4122427 characters processed.
[BWTIncConstructFromPacked] 80 iterations done. 4312059 characters processed.
[BWTIncConstructFromPacked] 90 iterations done. 4457835 characters processed.
[BWTIncConstructFromPacked] 100 iterations done. 4568939 characters processed.
[bwt_gen] Finished constructing BWT in 109 iterations.
[BWTIncConstructFromPacked] 10 iterations done. 1131243 characters processed.
[BWTIncConstructFromPacked] 20 iterations done. 1975531 characters processed.
[BWTIncConstructFromPacked] 30 iterations done. 2637691 characters processed.
[BWTIncConstructFromPacked] 40 iterations done. 3156171 characters processed.
[BWTIncConstructFromPacked] 50 iterations done. 3561355 characters processed.
[BWTIncConstructFromPacked] 60 iterations done. 3877131 characters processed.
[BWTIncConstructFromPacked] 70 iterations done. 4122427 characters processed.
[BWTIncConstructFromPacked] 80 iterations done. 4312059 characters processed.
[BWTIncConstructFromPacked] 90 iterations done. 4457835 characters processed.
[BWTIncConstructFromPacked] 100 iterations done. 4568939 characters processed.
[bwt_gen] Finished constructing BWT in 109 iterations.
[bwa_index] Pack nucleotide FASTA... 0.06 sec
[bwa_index] Convert nucleotide PAC to color PAC... 0.04 sec
[bwa_index] Reverse the packed sequence... 0.02 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 0.94 seconds elapse.
[bwa_index] Construct BWT for the reverse packed sequence...
[bwa_index] 0.94 seconds elapse.
[bwa_index] Update BWT... 0.02 sec
[bwa_index] Update reverse BWT... 0.02 sec
[bwa_index] Construct SA from BWT and Occ... 0.23 sec
[bwa_index] Construct SA from reverse BWT and Occ... 0.22 sec
[BWTIncConstructFromPacked] 10 iterations done. 1131243 characters processed.
[BWTIncConstructFromPacked] 20 iterations done. 1975531 characters processed.
[BWTIncConstructFromPacked] 30 iterations done. 2637691 characters processed.
[BWTIncConstructFromPacked] 40 iterations done. 3156171 characters processed.
[BWTIncConstructFromPacked] 50 iterations done. 3561355 characters processed.
[BWTIncConstructFromPacked] 60 iterations done. 3877131 characters processed.
[BWTIncConstructFromPacked] 70 iterations done. 4122427 characters processed.
[BWTIncConstructFromPacked] 80 iterations done. 4312059 characters processed.
[BWTIncConstructFromPacked] 90 iterations done. 4457835 characters processed.
[BWTIncConstructFromPacked] 100 iterations done. 4568939 characters processed.
[bwt_gen] Finished constructing BWT in 109 iterations.
[BWTIncConstructFromPacked] 10 iterations done. 1131243 characters processed.
[BWTIncConstructFromPacked] 20 iterations done. 1975531 characters processed.
[BWTIncConstructFromPacked] 30 iterations done. 2637691 characters processed.
[BWTIncConstructFromPacked] 40 iterations done. 3156171 characters processed.
[BWTIncConstructFromPacked] 50 iterations done. 3561355 characters processed.
[BWTIncConstructFromPacked] 60 iterations done. 3877131 characters processed.
[BWTIncConstructFromPacked] 70 iterations done. 4122427 characters processed.
[BWTIncConstructFromPacked] 80 iterations done. 4312059 characters processed.
[BWTIncConstructFromPacked] 90 iterations done. 4457835 characters processed.
[BWTIncConstructFromPacked] 100 iterations done. 4568939 characters processed.
[bwt_gen] Finished constructing BWT in 109 iterations.
04-16-2010 11:37:01 >> Aligning with BWA (read1 / read2)
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 0.27 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 10000 sequences have been processed.
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 0.67 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 10000 sequences have been processed.
04-16-2010 11:37:02 >> Converting BWA aligments to sam
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (541, 576, 607)
[infer_isize] low and high boundaries: 409 and 739 for estimating avg and std
[infer_isize] inferred external isize from 1162 pairs: 574.391 +/- 49.407
[infer_isize] skewness: -0.005; kurtosis: -0.112
[infer_isize] inferred maximum insert size: 866 (5.90 sigma)
[bwa_sai2sam_pe_core] time elapses: 0.03 sec
[bwa_sai2sam_pe_core] changing coordinates of 14 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 4895 out of 5005 Q17 singletons are mated.
[bwa_paired_sw] 3 out of 3 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.83 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.01 sec
[bwa_sai2sam_pe_core] print alignments... 0.06 sec
[bwa_sai2sam_pe_core] 10000 sequences have been processed.
04-16-2010 11:37:03 >> Converting from SAM to BAM and sorting
[samopen] SAM header is present: 1 sequences.
bwa stats:
-----------------------------------------------------------------
00 44 / 167 12226 12433 20000 2.635e-01 9.834e-01 2.200e-03 6.113e-01
---------
12433 mapped (62.16%)
241 singletons (1.21%)
---------
./bwa.sorted.bam.
Number of raw paired reads:10000
Number of raw single end reads:0
Number of mapped paired reads:6096
Number of mapped unpaired reads:241
Number of mapped single end reads: 0
Number of mapped paired reads pcr duplicates: 0
Number of mapped unpaired reads pcr duplicates: 0
Number of mapped single end reads pcr duplicates: 0
04-16-2010 11:37:04 >> Converting REF to BF bin (CS|SS)
************************************************************
Checking input parameters supplied by the user ...
Validating fastaFileName ecoli.drio.test.fa.
Input arguments look good!
************************************************************
************************************************************
Printing Program Parameters:
programMode: [ExecuteProgram]
fastaFileName: ecoli.drio.test.fa
space: [NT Space]
timing: [Not Using]
************************************************************
************************************************************
Reading from ecoli.drio.test.fa.
Reading in [contig,pos]:
0 [-------1,----------1] [-------1,----------0] [-------1,----1000000] [-------1,----2000000] [-------1,----3000000] [-------1,----4000000] [-------1,----4639675] [-------1,----4639675]
In total read 1 contigs for a total of 4639675 bases
************************************************************
************************************************************
Outputting to ecoli.drio.test.fa.nt.brg
Outputting Chr1
Output complete.
************************************************************
Terminating successfully!
************************************************************
************************************************************
Checking input parameters supplied by the user ...
Validating fastaFileName ecoli.drio.test.fa.
Input arguments look good!
************************************************************
************************************************************
Printing Program Parameters:
programMode: [ExecuteProgram]
fastaFileName: ecoli.drio.test.fa
space: [Color Space]
timing: [Not Using]
************************************************************
************************************************************
Reading from ecoli.drio.test.fa.
Reading in [contig,pos]:
0 [-------1,----------1] [-------1,----------0] [-------1,----1000000] [-------1,----2000000] [-------1,----3000000] [-------1,----4000000] [-------1,----4639675] [-------1,----4639675]
In total read 1 contigs for a total of 4639675 bases
************************************************************
************************************************************
Outputting to ecoli.drio.test.fa.cs.brg
Outputting Chr1
Output complete.
************************************************************
Terminating successfully!
************************************************************
04-16-2010 11:37:06 >> BF (BWT) indexes already there, skipping.
04-16-2010 11:37:06 >> BF match (BWT - bwaaln)
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 0.94 sec
[bwa_aln_core] write to the disk... 0.36 sec
[bwa_aln_core] 20000 sequences have been processed.
04-16-2010 11:37:08 >> BF local (BWT) -U
************************************************************
Checking input parameters supplied by the user ...
Validating fastaFileName ./bfast.bwt.indexes/ecoli.drio.test.fa.
Validating matchFileNamebf.bwt.matches.bmf.
**** Input arguments look good! *****
************************************************************
************************************************************
Printing Program Parameters:
programMode: [ExecuteProgram]
fastaFileName: ./bfast.bwt.indexes/ecoli.drio.test.fa
matchFileName: bf.bwt.matches.bmf
scoringMatrixFileName: [Not Using]
ungapped: [Not Using]
unconstrained: [Using]
space: [NT Space]
startReadNum: 1
endReadNum: 2147483647
offsetLength: 20
maxNumMatches: 384
avgMismatchQuality: 10
numThreads: 1
queueLength: 10000
pairedEndLength: [Not Using]
mirroringType: [Not Using]
forceMirroring: [Not Using]
timing: [Not Using]
************************************************************
************************************************************
Reading in reference genome from ./bfast.bwt.indexes/ecoli.drio.test.fa.nt.brg.
In total read 1 contigs for a total of 4639675 bases
************************************************************
************************************************************
Reading match file from bf.bwt.matches.bmf.
************************************************************
Performing alignment...
Currently on:
0 thread:0 [0] thread:0 [1000] thread:0 [2000] thread:0 [3000] thread:0 [4000] thread:0 [5000] thread:0 [6000] thread:0 [7000] thread:0 [8000] thread:0 [9000] thread:0 [10000] thread:0 [10000]
Alignment complete.
Performed 8567 local alignments.
Outputted alignments for 6337 reads.
Outputted 3663 reads for which there were no alignments.
Outputting complete.
************************************************************
Terminating successfully!
************************************************************
04-16-2010 11:37:09 >> BF version: 0.6.3d
04-16-2010 11:37:09 >> postprocess: -O3
04-16-2010 11:37:09 >> BF postprocess
************************************************************
Checking input parameters supplied by the user ...
Validating fastaFileName ./bfast.bwt.indexes/ecoli.drio.test.fa.
Validating alignFileName bf.bwt.aligned.baf.
Input arguments look good!
************************************************************
************************************************************
Printing Program Parameters:
programMode: [ExecuteProgram]
fastaFileName: ./bfast.bwt.indexes/ecoli.drio.test.fa
alignFileName: bf.bwt.aligned.baf
algorithm: [Best Score]
pairedEndInfer: [Not Using]
numThreads: 3
queueLength: 10000
outputFormat: [SAM]
unmappedFileName: [Not Using]
outputID: [Not Using]
RGFileName: [Not Using]
timing: [Not Using]
************************************************************
************************************************************
Reading in reference genome from ./bfast.bwt.indexes/ecoli.drio.test.fa.nt.brg.
In total read 1 contigs for a total of 4639675 bases
************************************************************
Processing reads, currently on:
threadID:1 [0] threadID:2 [0] threadID:3 [0] threadID:1 [10000] threadID:1 [10000]
************************************************************
Found 3812 reads with no ends mapped.
Found 5024 reads with 1 end mapped.
Found 1164 reads with 2 ends mapped.
Found 6188 reads with at least one end mapping.
************************************************************
Terminating successfully!
************************************************************
04-16-2010 11:37:09 >> Converting from SAM to BAM and sorting
[samopen] SAM header is present: 1 sequences.
bf.bwt stats:
-----------------------------------------------------------------
10 14 / 16 7346 7352 20000 8.750e-01 9.992e-01 7.000e-04 3.673e-01
---------
7352 mapped (36.76%)
5024 singletons (25.12%)
---------
./bf.bwt.sorted.bam.
Number of raw paired reads:10000
Number of raw single end reads:0
Number of mapped paired reads:1164
Number of mapped unpaired reads:5024
Number of mapped single end reads: 0
Number of mapped paired reads pcr duplicates: 0
Number of mapped unpaired reads pcr duplicates: 0
Number of mapped single end reads pcr duplicates: 0
04-16-2010 11:37:10 >> BF indexes already there, skipping.
04-16-2010 11:37:10 >> BF match
************************************************************
Checking input parameters supplied by the user ...
Validating fastaFileName ./bfast.indexes/ecoli.drio.test.fa.
Validating readsFileName ./bf.reads.fastq.
Validating tmpDir path /tmp/.
**** Input arguments look good!
************************************************************
************************************************************
Printing Program Parameters:
programMode: [ExecuteProgram]
fastaFileName: ./bfast.indexes/ecoli.drio.test.fa
mainIndexes [Auto-recognizing]
secondaryIndexes [Not Using]
readsFileName: ./bf.reads.fastq
offsets: [Using All]
loadAllIndexes: [Using]
compression: [Not Using]
space: [NT Space]
startReadNum: 1
endReadNum: 2147483647
keySize: [Not Using]
maxKeyMatches: 8
maxNumMatches: 384
whichStrand: [Both Strands]
numThreads: 1
queueLength: 250000
tmpDir: /tmp/
timing: [Not Using]
************************************************************
Searching for main indexes...
Found 10 index (10 total files).
Not using secondary indexes.
************************************************************
Reading in reference genome from ./bfast.indexes/ecoli.drio.test.fa.nt.brg.
In total read 1 contigs for a total of 4639675 bases
************************************************************
Reading ./bf.reads.fastq into temp files.
Will process 10000 reads.
Searching index files 1-10...
Reading index from ./bfast.indexes/ecoli.drio.test.fa.nt.1.1.bif.
Read index from ./bfast.indexes/ecoli.drio.test.fa.nt.1.1.bif.
Reading index from ./bfast.indexes/ecoli.drio.test.fa.nt.2.1.bif.
Read index from ./bfast.indexes/ecoli.drio.test.fa.nt.2.1.bif.
Reading index from ./bfast.indexes/ecoli.drio.test.fa.nt.3.1.bif.
Read index from ./bfast.indexes/ecoli.drio.test.fa.nt.3.1.bif.
Reading index from ./bfast.indexes/ecoli.drio.test.fa.nt.4.1.bif.
Read index from ./bfast.indexes/ecoli.drio.test.fa.nt.4.1.bif.
Reading index from ./bfast.indexes/ecoli.drio.test.fa.nt.5.1.bif.
Read index from ./bfast.indexes/ecoli.drio.test.fa.nt.5.1.bif.
Reading index from ./bfast.indexes/ecoli.drio.test.fa.nt.6.1.bif.
Read index from ./bfast.indexes/ecoli.drio.test.fa.nt.6.1.bif.
Reading index from ./bfast.indexes/ecoli.drio.test.fa.nt.7.1.bif.
Read index from ./bfast.indexes/ecoli.drio.test.fa.nt.7.1.bif.
Reading index from ./bfast.indexes/ecoli.drio.test.fa.nt.8.1.bif.
Read index from ./bfast.indexes/ecoli.drio.test.fa.nt.8.1.bif.
Reading index from ./bfast.indexes/ecoli.drio.test.fa.nt.9.1.bif.
Read index from ./bfast.indexes/ecoli.drio.test.fa.nt.9.1.bif.
Reading index from ./bfast.indexes/ecoli.drio.test.fa.nt.10.1.bif.
Read index from ./bfast.indexes/ecoli.drio.test.fa.nt.10.1.bif.
Reads processed: 0 Reads processed: 8506 Reads processed: 8506
Cleaning up indexes.
Searching index files 1-10... complete
Found matches for 8506 reads.
Searching main indexes complete.
************************************************************
************************************************************
In total, found matches for 8506 out of 10000 reads.
************************************************************
Terminating successfully!
************************************************************
04-16-2010 11:37:44 >> BF local
************************************************************
Checking input parameters supplied by the user ...
Validating fastaFileName ./bfast.indexes/ecoli.drio.test.fa.
Validating matchFileNamebf.matches.bmf.
**** Input arguments look good! *****
************************************************************
************************************************************
Printing Program Parameters:
programMode: [ExecuteProgram]
fastaFileName: ./bfast.indexes/ecoli.drio.test.fa
matchFileName: bf.matches.bmf
scoringMatrixFileName: [Not Using]
ungapped: [Not Using]
unconstrained: [Not Using]
space: [NT Space]
startReadNum: 1
endReadNum: 2147483647
offsetLength: 20
maxNumMatches: 384
avgMismatchQuality: 10
numThreads: 1
queueLength: 10000
pairedEndLength: [Not Using]
mirroringType: [Not Using]
forceMirroring: [Not Using]
timing: [Not Using]
************************************************************
************************************************************
Reading in reference genome from ./bfast.indexes/ecoli.drio.test.fa.nt.brg.
In total read 1 contigs for a total of 4639675 bases
************************************************************
************************************************************
Reading match file from bf.matches.bmf.
************************************************************
Performing alignment...
Currently on:
0 thread:0 [0] thread:0 [1000] thread:0 [2000] thread:0 [3000] thread:0 [4000] thread:0 [5000] thread:0 [6000] thread:0 [7000] thread:0 [8000] thread:0 [9000] thread:0 [10000] thread:0 [10000]
Alignment complete.
Performed 10760 local alignments.
Outputted alignments for 8506 reads.
Outputted 1494 reads for which there were no alignments.
Outputting complete.
************************************************************
Terminating successfully!
************************************************************
04-16-2010 11:37:45 >> BF version: 0.6.3d
04-16-2010 11:37:45 >> postprocess: -O3
04-16-2010 11:37:45 >> BF postprocess
************************************************************
Checking input parameters supplied by the user ...
Validating fastaFileName ./bfast.indexes/ecoli.drio.test.fa.
Validating alignFileName bf.aligned.baf.
Input arguments look good!
************************************************************
************************************************************
Printing Program Parameters:
programMode: [ExecuteProgram]
fastaFileName: ./bfast.indexes/ecoli.drio.test.fa
alignFileName: bf.aligned.baf
algorithm: [Best Score]
pairedEndInfer: [Not Using]
numThreads: 3
queueLength: 10000
outputFormat: [SAM]
unmappedFileName: [Not Using]
outputID: [Not Using]
RGFileName: [Not Using]
timing: [Not Using]
************************************************************
************************************************************
Reading in reference genome from ./bfast.indexes/ecoli.drio.test.fa.nt.brg.
In total read 1 contigs for a total of 4639675 bases
************************************************************
Processing reads, currently on:
threadID:1 [0] threadID:3 [0] threadID:2 [0] threadID:1 [10000] threadID:1 [10000]
************************************************************
Found 1660 reads with no ends mapped.
Found 7293 reads with 1 end mapped.
Found 1047 reads with 2 ends mapped.
Found 8340 reads with at least one end mapping.
************************************************************
Terminating successfully!
************************************************************
04-16-2010 11:37:46 >> Converting from SAM to BAM and sorting
[samopen] SAM header is present: 1 sequences.
bf stats:
-----------------------------------------------------------------
01 1 / 1 9375 9387 20000 1.000e+00 9.987e-01 5.000e-05 4.688e-01
---------
9387 mapped (46.94%)
7293 singletons (36.47%)
---------
./bf.sorted.bam.
Number of raw paired reads:10000
Number of raw single end reads:0
Number of mapped paired reads:1047
Number of mapped unpaired reads:7293
Number of mapped single end reads: 0
Number of mapped paired reads pcr duplicates: 0
Number of mapped unpaired reads pcr duplicates: 0
Number of mapped single end reads pcr duplicates: 0
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