Created
April 15, 2010 20:45
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bfast bwa bfast2
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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 | |
| 04-15-2010 15:43:30 >> postprocess: -O3 | |
| 04-15-2010 15:43:30 >> BF postprocess | |
| 04-15-2010 15:43:30 >> Converting from SAM to BAM and sorting | |
| 04-15-2010 15:43:30 >> BF indexes already there, skipping. | |
| 04-15-2010 15:43:30 >> BF match | |
| 04-15-2010 15:44:05 >> BF local | |
| 04-15-2010 15:44:06 >> BF version: 0.6.3d | |
| 04-15-2010 15:44:06 >> postprocess: -O3 | |
| 04-15-2010 15:44:06 >> BF postprocess | |
| 04-15-2010 15:44:06 >> Converting from SAM to BAM and sorting | |
| 04-15-2010 15:44:07 >> Space: 0 () | |
| bwa stats: | |
| ----------------------------------------------------------------- | |
| 60 1644 / 1644 1644 1644 20000 1.000e+00 1.000e+00 8.220e-02 8.220e-02 | |
| 50 508 / 508 2152 2152 20000 1.000e+00 1.000e+00 2.540e-02 1.076e-01 | |
| 37 58 / 58 2210 2210 20000 1.000e+00 1.000e+00 2.900e-03 1.105e-01 | |
| 36 3 / 3 2213 2213 20000 1.000e+00 1.000e+00 1.500e-04 1.106e-01 | |
| 30 1 / 1 2214 2214 20000 1.000e+00 1.000e+00 5.000e-05 1.107e-01 | |
| 29 4932 / 4970 7146 7184 20000 9.924e-01 9.947e-01 2.466e-01 3.573e-01 | |
| 25 70 / 71 7216 7255 20000 9.859e-01 9.946e-01 3.500e-03 3.608e-01 | |
| 23 1 / 1 7217 7256 20000 1.000e+00 9.946e-01 5.000e-05 3.609e-01 | |
| 17 4740 / 4792 11957 12048 20000 9.891e-01 9.924e-01 2.370e-01 5.978e-01 | |
| 15 27 / 28 11984 12076 20000 9.643e-01 9.924e-01 1.350e-03 5.992e-01 | |
| 11 2 / 2 11986 12078 20000 1.000e+00 9.924e-01 1.000e-04 5.993e-01 | |
| 09 2 / 2 11988 12080 20000 1.000e+00 9.924e-01 1.000e-04 5.994e-01 | |
| 04 1 / 1 11989 12081 20000 1.000e+00 9.924e-01 5.000e-05 5.995e-01 | |
| 00 54 / 184 12043 12265 20000 2.935e-01 9.819e-01 2.700e-03 6.021e-01 | |
| --------- | |
| 12265 mapped (61.33%) | |
| 245 singletons (1.22%) | |
| --------- | |
| ./bwa.sorted.bam. | |
| Number of raw paired reads:10000 | |
| Number of raw single end reads:0 | |
| Number of mapped paired reads:6010 | |
| Number of mapped unpaired reads:245 | |
| 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 | |
| bf stats: | |
| ----------------------------------------------------------------- | |
| 255 9196 / 9200 9196 9200 20000 9.996e-01 9.996e-01 4.598e-01 4.598e-01 | |
| 102 1 / 1 9197 9201 20000 1.000e+00 9.996e-01 5.000e-05 4.598e-01 | |
| 93 1 / 1 9198 9202 20000 1.000e+00 9.996e-01 5.000e-05 4.599e-01 | |
| 92 1 / 1 9199 9203 20000 1.000e+00 9.996e-01 5.000e-05 4.600e-01 | |
| 81 1 / 1 9200 9204 20000 1.000e+00 9.996e-01 5.000e-05 4.600e-01 | |
| 80 1 / 1 9201 9205 20000 1.000e+00 9.996e-01 5.000e-05 4.601e-01 | |
| 76 2 / 2 9203 9207 20000 1.000e+00 9.996e-01 1.000e-04 4.602e-01 | |
| 72 1 / 1 9204 9208 20000 1.000e+00 9.996e-01 5.000e-05 4.602e-01 | |
| 71 1 / 1 9205 9209 20000 1.000e+00 9.996e-01 5.000e-05 4.602e-01 | |
| 70 1 / 1 9206 9210 20000 1.000e+00 9.996e-01 5.000e-05 4.603e-01 | |
| 67 1 / 1 9207 9211 20000 1.000e+00 9.996e-01 5.000e-05 4.603e-01 | |
| 66 1 / 1 9208 9212 20000 1.000e+00 9.996e-01 5.000e-05 4.604e-01 | |
| 63 1 / 1 9209 9213 20000 1.000e+00 9.996e-01 5.000e-05 4.605e-01 | |
| 62 2 / 2 9211 9215 20000 1.000e+00 9.996e-01 1.000e-04 4.606e-01 | |
| 60 4 / 4 9215 9219 20000 1.000e+00 9.996e-01 2.000e-04 4.607e-01 | |
| 57 2 / 2 9217 9221 20000 1.000e+00 9.996e-01 1.000e-04 4.608e-01 | |
| 56 1 / 1 9218 9222 20000 1.000e+00 9.996e-01 5.000e-05 4.609e-01 | |
| 52 2 / 2 9220 9224 20000 1.000e+00 9.996e-01 1.000e-04 4.610e-01 | |
| 50 1 / 1 9221 9225 20000 1.000e+00 9.996e-01 5.000e-05 4.611e-01 | |
| 47 2 / 2 9223 9227 20000 1.000e+00 9.996e-01 1.000e-04 4.612e-01 | |
| 46 1 / 1 9224 9228 20000 1.000e+00 9.996e-01 5.000e-05 4.612e-01 | |
| 43 1 / 1 9225 9229 20000 1.000e+00 9.996e-01 5.000e-05 4.612e-01 | |
| 42 1 / 1 9226 9230 20000 1.000e+00 9.996e-01 5.000e-05 4.613e-01 | |
| 40 1 / 1 9227 9231 20000 1.000e+00 9.996e-01 5.000e-05 4.613e-01 | |
| 38 1 / 1 9228 9232 20000 1.000e+00 9.996e-01 5.000e-05 4.614e-01 | |
| 37 1 / 1 9229 9233 20000 1.000e+00 9.996e-01 5.000e-05 4.615e-01 | |
| 36 3 / 3 9232 9236 20000 1.000e+00 9.996e-01 1.500e-04 4.616e-01 | |
| 33 1 / 1 9233 9237 20000 1.000e+00 9.996e-01 5.000e-05 4.617e-01 | |
| 32 2 / 2 9235 9239 20000 1.000e+00 9.996e-01 1.000e-04 4.617e-01 | |
| 31 1 / 1 9236 9240 20000 1.000e+00 9.996e-01 5.000e-05 4.618e-01 | |
| 30 3 / 3 9239 9243 20000 1.000e+00 9.996e-01 1.500e-04 4.620e-01 | |
| 27 1 / 1 9240 9244 20000 1.000e+00 9.996e-01 5.000e-05 4.620e-01 | |
| 26 4 / 4 9244 9248 20000 1.000e+00 9.996e-01 2.000e-04 4.622e-01 | |
| 21 3 / 3 9247 9251 20000 1.000e+00 9.996e-01 1.500e-04 4.623e-01 | |
| 20 10 / 10 9257 9261 20000 1.000e+00 9.996e-01 5.000e-04 4.628e-01 | |
| 18 2 / 2 9259 9263 20000 1.000e+00 9.996e-01 1.000e-04 4.629e-01 | |
| 17 2 / 2 9261 9265 20000 1.000e+00 9.996e-01 1.000e-04 4.631e-01 | |
| 16 2 / 2 9263 9267 20000 1.000e+00 9.996e-01 1.000e-04 4.632e-01 | |
| 15 2 / 2 9265 9269 20000 1.000e+00 9.996e-01 1.000e-04 4.632e-01 | |
| 11 2 / 2 9267 9271 20000 1.000e+00 9.996e-01 1.000e-04 4.633e-01 | |
| 10 26 / 27 9293 9298 20000 9.630e-01 9.995e-01 1.300e-03 4.647e-01 | |
| 08 2 / 3 9295 9301 20000 6.667e-01 9.994e-01 1.000e-04 4.647e-01 | |
| 07 1 / 1 9296 9302 20000 1.000e+00 9.994e-01 5.000e-05 4.648e-01 | |
| 01 1 / 2 9297 9304 20000 5.000e-01 9.992e-01 5.000e-05 4.648e-01 | |
| --------- | |
| 9304 mapped (46.52%) | |
| 7330 singletons (36.65%) | |
| --------- | |
| ./bf.sorted.bam. | |
| Number of raw paired reads:10000 | |
| Number of raw single end reads:0 | |
| Number of mapped paired reads:987 | |
| Number of mapped unpaired reads:7330 | |
| 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 | |
| bf.bwt stats: | |
| ----------------------------------------------------------------- | |
| 255 7150 / 7153 7150 7153 20000 9.996e-01 9.996e-01 3.575e-01 3.575e-01 | |
| 10 14 / 15 7164 7168 20000 9.333e-01 9.994e-01 7.000e-04 3.582e-01 | |
| 06 1 / 1 7165 7169 20000 1.000e+00 9.994e-01 5.000e-05 3.583e-01 | |
| --------- | |
| 7169 mapped (35.84%) | |
| 5011 singletons (25.06%) | |
| --------- | |
| ./bf.bwt.sorted.bam. | |
| Number of raw paired reads:10000 | |
| Number of raw single end reads:0 | |
| Number of mapped paired reads:1079 | |
| Number of mapped unpaired reads:5011 | |
| 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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