Created
April 15, 2010 20:54
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bfast bfast2 bwa
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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 | |
| 04-15-2010 15:49:18 >> postprocess: -O3 | |
| 04-15-2010 15:49:18 >> BF postprocess | |
| 04-15-2010 15:49:18 >> Converting from SAM to BAM and sorting | |
| 04-15-2010 15:49:19 >> BF indexes already there, skipping. | |
| 04-15-2010 15:49:19 >> BF match | |
| 04-15-2010 15:49:53 >> BF local | |
| 04-15-2010 15:49:54 >> BF version: 0.6.3d | |
| 04-15-2010 15:49:54 >> postprocess: -O3 | |
| 04-15-2010 15:49:54 >> BF postprocess | |
| 04-15-2010 15:49:55 >> Converting from SAM to BAM and sorting | |
| 04-15-2010 15:49:55 >> Space: 0 () | |
| bwa stats: | |
| ----------------------------------------------------------------- | |
| 60 1618 / 1618 1618 1618 20000 1.000e+00 1.000e+00 8.090e-02 8.090e-02 | |
| 50 518 / 518 2136 2136 20000 1.000e+00 1.000e+00 2.590e-02 1.068e-01 | |
| 48 12 / 12 2148 2148 20000 1.000e+00 1.000e+00 6.000e-04 1.074e-01 | |
| 37 70 / 70 2218 2218 20000 1.000e+00 1.000e+00 3.500e-03 1.109e-01 | |
| 36 3 / 3 2221 2221 20000 1.000e+00 1.000e+00 1.500e-04 1.110e-01 | |
| 29 4900 / 4945 7121 7166 20000 9.909e-01 9.937e-01 2.450e-01 3.560e-01 | |
| 25 57 / 58 7178 7224 20000 9.828e-01 9.936e-01 2.850e-03 3.589e-01 | |
| 17 4939 / 4972 12117 12197 20000 9.934e-01 9.934e-01 2.470e-01 6.058e-01 | |
| 15 26 / 26 12143 12223 20000 1.000e+00 9.935e-01 1.300e-03 6.071e-01 | |
| 00 34 / 156 12177 12379 20000 2.179e-01 9.837e-01 1.700e-03 6.089e-01 | |
| --------- | |
| 12379 mapped (61.90%) | |
| 219 singletons (1.10%) | |
| --------- | |
| ./bwa.sorted.bam. | |
| Number of raw paired reads:10000 | |
| Number of raw single end reads:0 | |
| Number of mapped paired reads:6080 | |
| Number of mapped unpaired reads:219 | |
| 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 9201 / 9210 9201 9210 20000 9.990e-01 9.990e-01 4.601e-01 4.601e-01 | |
| 147 1 / 1 9202 9211 20000 1.000e+00 9.990e-01 5.000e-05 4.601e-01 | |
| 90 1 / 1 9203 9212 20000 1.000e+00 9.990e-01 5.000e-05 4.602e-01 | |
| 81 2 / 2 9205 9214 20000 1.000e+00 9.990e-01 1.000e-04 4.602e-01 | |
| 80 1 / 1 9206 9215 20000 1.000e+00 9.990e-01 5.000e-05 4.603e-01 | |
| 78 1 / 1 9207 9216 20000 1.000e+00 9.990e-01 5.000e-05 4.603e-01 | |
| 76 1 / 1 9208 9217 20000 1.000e+00 9.990e-01 5.000e-05 4.604e-01 | |
| 71 1 / 1 9209 9218 20000 1.000e+00 9.990e-01 5.000e-05 4.605e-01 | |
| 70 1 / 1 9210 9219 20000 1.000e+00 9.990e-01 5.000e-05 4.605e-01 | |
| 68 2 / 2 9212 9221 20000 1.000e+00 9.990e-01 1.000e-04 4.606e-01 | |
| 62 1 / 1 9213 9222 20000 1.000e+00 9.990e-01 5.000e-05 4.607e-01 | |
| 61 1 / 1 9214 9223 20000 1.000e+00 9.990e-01 5.000e-05 4.607e-01 | |
| 60 2 / 2 9216 9225 20000 1.000e+00 9.990e-01 1.000e-04 4.608e-01 | |
| 58 1 / 1 9217 9226 20000 1.000e+00 9.990e-01 5.000e-05 4.608e-01 | |
| 56 1 / 1 9218 9227 20000 1.000e+00 9.990e-01 5.000e-05 4.609e-01 | |
| 55 3 / 3 9221 9230 20000 1.000e+00 9.990e-01 1.500e-04 4.611e-01 | |
| 53 2 / 2 9223 9232 20000 1.000e+00 9.990e-01 1.000e-04 4.612e-01 | |
| 51 1 / 1 9224 9233 20000 1.000e+00 9.990e-01 5.000e-05 4.612e-01 | |
| 50 3 / 3 9227 9236 20000 1.000e+00 9.990e-01 1.500e-04 4.613e-01 | |
| 48 1 / 1 9228 9237 20000 1.000e+00 9.990e-01 5.000e-05 4.614e-01 | |
| 47 1 / 1 9229 9238 20000 1.000e+00 9.990e-01 5.000e-05 4.615e-01 | |
| 46 1 / 1 9230 9239 20000 1.000e+00 9.990e-01 5.000e-05 4.615e-01 | |
| 40 3 / 3 9233 9242 20000 1.000e+00 9.990e-01 1.500e-04 4.617e-01 | |
| 38 2 / 2 9235 9244 20000 1.000e+00 9.990e-01 1.000e-04 4.617e-01 | |
| 37 5 / 5 9240 9249 20000 1.000e+00 9.990e-01 2.500e-04 4.620e-01 | |
| 36 1 / 1 9241 9250 20000 1.000e+00 9.990e-01 5.000e-05 4.621e-01 | |
| 35 1 / 1 9242 9251 20000 1.000e+00 9.990e-01 5.000e-05 4.621e-01 | |
| 31 1 / 1 9243 9252 20000 1.000e+00 9.990e-01 5.000e-05 4.622e-01 | |
| 30 6 / 6 9249 9258 20000 1.000e+00 9.990e-01 3.000e-04 4.625e-01 | |
| 28 2 / 2 9251 9260 20000 1.000e+00 9.990e-01 1.000e-04 4.626e-01 | |
| 27 2 / 2 9253 9262 20000 1.000e+00 9.990e-01 1.000e-04 4.627e-01 | |
| 25 1 / 1 9254 9263 20000 1.000e+00 9.990e-01 5.000e-05 4.627e-01 | |
| 21 1 / 1 9255 9264 20000 1.000e+00 9.990e-01 5.000e-05 4.627e-01 | |
| 20 17 / 17 9272 9281 20000 1.000e+00 9.990e-01 8.500e-04 4.636e-01 | |
| 18 2 / 2 9274 9283 20000 1.000e+00 9.990e-01 1.000e-04 4.637e-01 | |
| 17 1 / 1 9275 9284 20000 1.000e+00 9.990e-01 5.000e-05 4.637e-01 | |
| 16 3 / 3 9278 9287 20000 1.000e+00 9.990e-01 1.500e-04 4.639e-01 | |
| 15 1 / 1 9279 9288 20000 1.000e+00 9.990e-01 5.000e-05 4.639e-01 | |
| 12 1 / 1 9280 9289 20000 1.000e+00 9.990e-01 5.000e-05 4.640e-01 | |
| 11 2 / 2 9282 9291 20000 1.000e+00 9.990e-01 1.000e-04 4.641e-01 | |
| 10 24 / 25 9306 9316 20000 9.600e-01 9.989e-01 1.200e-03 4.653e-01 | |
| 08 1 / 1 9307 9317 20000 1.000e+00 9.989e-01 5.000e-05 4.653e-01 | |
| 07 1 / 1 9308 9318 20000 1.000e+00 9.989e-01 5.000e-05 4.654e-01 | |
| 06 2 / 3 9310 9321 20000 6.667e-01 9.988e-01 1.000e-04 4.655e-01 | |
| 02 1 / 1 9311 9322 20000 1.000e+00 9.988e-01 5.000e-05 4.656e-01 | |
| 01 2 / 2 9313 9324 20000 1.000e+00 9.988e-01 1.000e-04 4.657e-01 | |
| --------- | |
| 9324 mapped (46.62%) | |
| 7342 singletons (36.71%) | |
| --------- | |
| ./bf.sorted.bam. | |
| Number of raw paired reads:10000 | |
| Number of raw single end reads:0 | |
| Number of mapped paired reads:991 | |
| Number of mapped unpaired reads:7342 | |
| 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 7213 / 7216 7213 7216 20000 9.996e-01 9.996e-01 3.607e-01 3.607e-01 | |
| 10 19 / 19 7232 7235 20000 1.000e+00 9.996e-01 9.500e-04 3.616e-01 | |
| 01 1 / 1 7233 7236 20000 1.000e+00 9.996e-01 5.000e-05 3.617e-01 | |
| --------- | |
| 7236 mapped (36.18%) | |
| 5088 singletons (25.44%) | |
| --------- | |
| ./bf.bwt.sorted.bam. | |
| Number of raw paired reads:10000 | |
| Number of raw single end reads:0 | |
| Number of mapped paired reads:1074 | |
| Number of mapped unpaired reads:5088 | |
| 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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