Class org.broadinstitute.hellbender.tools.walkers.bqsr.BothStepsOfBQSRIntegrationTest
Tests
| Test |
Duration |
Result |
| testIndelRemoval |
43.752s |
passed |
Standard output
-----------CompareMatrix summary------------
all 22733989 quality scores are the same
---------CompareMatrix full matrix (non-zero entries) ----------
QRead1 QRead2 diff count
1 1 0 530
2 2 0 1919913
3 3 0 1968
4 4 0 7162
5 5 0 6946
10 10 0 11
11 11 0 338
12 12 0 362
13 13 0 2339
14 14 0 4286
15 15 0 7477
16 16 0 5222
17 17 0 7365
18 18 0 6140
19 19 0 3369
20 20 0 3797
21 21 0 4331
22 22 0 5406
23 23 0 10420
24 24 0 14815
25 25 0 38943
26 26 0 120096
27 27 0 310555
28 28 0 536450
29 29 0 1140288
30 30 0 1627584
31 31 0 1935120
32 32 0 1371365
33 33 0 2812141
34 34 0 4307237
35 35 0 2978373
36 36 0 2946446
37 37 0 597194
-----------CompareMatrix-binned summary------------
all 22733989 quality scores are the same
---------CompareMatrix-binned full matrix (non-zero entries) ----------
QRead1 QRead2 diff count
1 1 0 530
2 2 0 1919913
3 3 0 1968
4 4 0 7162
5 5 0 6946
10 10 0 11
11 11 0 338
12 12 0 362
13 13 0 2339
14 14 0 4286
15 15 0 7477
16 16 0 5222
17 17 0 7365
18 18 0 6140
19 19 0 3369
20 20 0 3797
21 21 0 4331
22 22 0 5406
23 23 0 10420
24 24 0 14815
25 25 0 38943
26 26 0 120096
27 27 0 310555
28 28 0 536450
29 29 0 1140288
30 30 0 1627584
31 31 0 1935120
32 32 0 1371365
33 33 0 2812141
34 34 0 4307237
35 35 0 2978373
36 36 0 2946446
37 37 0 597194
Standard error
[March 28, 2025 at 10:49:00 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.30 minutes.
Runtime.totalMemory()=1153433600
[March 28, 2025 at 10:49:04 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.ApplyBQSR done. Elapsed time: 0.08 minutes.
Runtime.totalMemory()=1153433600
[March 28, 2025 at 10:49:20 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.26 minutes.
Runtime.totalMemory()=1153433600
[March 28, 2025 at 10:49:25 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.ApplyBQSR done. Elapsed time: 0.08 minutes.
Runtime.totalMemory()=1153433600
[March 28, 2025 at 10:49:25 PM UTC] org.broadinstitute.hellbender.tools.validation.CompareBaseQualities done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1153433600