Open iskandr opened 5 years ago
Here are steps from a recent run whose benchmarks showed they took more than 1000 seconds:
==> dna_indel_realigner_10.txt <== 2232.3606 0:37:12 7345.22 25516.19 7317.20 7320.92 24.18 2038.69 0.00 ==> dna_indel_realigner_11.txt <== 6291.8371 1:44:51 7311.09 25513.62 7281.90 7285.59 793.64 3602.06 0.00 ==> dna_indel_realigner_12.txt <== 4230.6952 1:10:30 5818.19 25513.62 5787.84 5791.54 24.73 2894.29 0.00 ==> dna_indel_realigner_13.txt <== 1468.8043 0:24:28 7221.28 25513.62 7191.81 7195.53 0.00 1069.15 0.00 ==> dna_indel_realigner_14.txt <== 3579.2174 0:59:39 6232.40 25513.62 6201.90 6205.65 4.43 2015.45 0.00 ==> dna_indel_realigner_15.txt <== 2926.9650 0:48:46 7081.42 25513.62 7052.04 7055.79 0.00 1964.56 0.00 ==> dna_indel_realigner_16.txt <== 3972.0825 1:06:12 7202.23 25513.62 7172.73 7176.40 313.71 2434.78 0.00 ==> dna_indel_realigner_17.txt <== 4168.9924 1:09:28 7156.39 25513.62 7127.02 7130.69 0.00 2946.00 0.00 ==> dna_indel_realigner_19.txt <== 5485.6922 1:31:25 5961.20 25515.46 5930.61 5934.34 233.41 3154.30 0.00 ==> dna_indel_realigner_1.txt <== 6361.7157 1:46:01 7317.08 25513.62 7288.31 7292.02 1305.05 7902.32 0.00 ==> dna_indel_realigner_20.txt <== 2541.8745 0:42:21 5274.98 25513.62 5245.59 5249.32 0.08 2276.02 0.00 ==> dna_indel_realigner_21.txt <== ==> dna_indel_realigner_22.txt <== 1661.3689 0:27:41 5509.75 25515.47 5481.68 5485.37 0.02 1120.68 0.00 ==> dna_indel_realigner_2.txt <== 5512.6300 1:31:52 6227.10 25513.62 6199.05 6202.76 110.49 4104.15 0.00 ==> dna_indel_realigner_3.txt <== 3747.2937 1:02:27 7312.88 25513.74 7283.37 7287.06 588.59 4374.61 0.00 ==> dna_indel_realigner_4.txt <== 3302.1961 0:55:02 6254.44 25513.62 6226.50 6230.90 0.00 2266.16 0.00 ==> dna_indel_realigner_5.txt <== 3000.0765 0:50:00 6466.55 25513.62 6436.05 6439.74 0.00 2389.16 0.00 ==> dna_indel_realigner_6.txt <== 3980.8258 1:06:20 5680.93 25513.68 5650.43 5654.19 253.09 2785.27 0.00 ==> dna_indel_realigner_7.txt <== 4667.4566 1:17:47 6016.04 25513.62 5986.89 5990.59 0.00 3018.75 0.00 ==> dna_indel_realigner_8.txt <== 3179.9276 0:52:59 6304.45 25513.62 6275.17 6278.84 177.08 2060.52 0.00 ==> dna_indel_realigner_9.txt <== 2470.5035 0:41:10 7317.67 25513.62 7288.70 7292.44 0.01 2001.30 0.00 ==> mutect_10.txt <== 4747.0189 1:19:07 1505.48 4580.24 1482.28 1483.99 3050.38 244.46 0.00 ==> mutect_11.txt <== 7434.6895 2:03:54 1752.22 4580.24 1727.98 1730.40 5022.91 265.66 0.00 ==> mutect_12.txt <== 5590.2279 1:33:10 1583.18 4580.24 1560.18 1563.48 5369.45 244.69 0.00 ==> mutect_13.txt <== 2798.7419 0:46:38 1343.87 4580.24 1318.77 1321.61 1616.30 168.26 0.00 ==> mutect_14.txt <== 3846.6900 1:04:06 1417.46 4580.24 1393.11 1397.59 3858.72 171.23 0.00 ==> mutect_15.txt <== 3695.7094 1:01:35 1443.46 4580.24 1420.16 1426.62 3539.88 160.98 0.00 ==> mutect_16.txt <== 4601.7273 1:16:41 1567.40 4580.24 1543.46 1545.04 2173.40 171.55 0.00 ==> mutect_17.txt <== 5116.0675 1:25:16 1538.50 4580.24 1515.50 1518.83 4814.71 164.08 0.00 ==> mutect_18.txt <== 2185.7486 0:36:25 1269.51 4580.24 1245.20 1249.70 1631.26 131.03 0.00 ==> mutect_19.txt <== 5452.0785 1:30:52 1525.74 4580.24 1501.88 1503.75 1802.42 134.32 0.00 ==> mutect_1.txt <== 9886.8023 2:44:46 1996.97 4580.24 1972.92 1976.19 9535.76 425.77 0.00 ==> mutect_20.txt <== 3147.6437 0:52:27 1391.55 4580.24 1367.55 1369.04 868.11 126.37 0.00 ==> mutect2_10.txt <== 99847.8984 1 day, 3:44:07 1525.08 5387.58 1493.20 1495.17 3506.81 64.66 0.00 ==> mutect2_11.txt <== 184300.3277 2 days, 3:11:40 1555.01 5404.02 1523.30 1525.29 6177.75 115.43 0.00 ==> mutect2_12.txt <== 154445.7718 1 day, 18:54:05 1501.15 5382.78 1469.77 1471.87 5458.34 97.23 0.00 ==> mutect2_13.txt <== 57713.5828 16:01:53 1281.04 5383.56 1249.61 1250.71 1710.05 39.32 0.00 ==> mutect2_14.txt <== 109842.1128 1 day, 6:30:42 1460.52 5406.49 1429.01 1430.46 2961.88 69.78 0.00 ==> mutect2_15.txt <== 103270.8924 1 day, 4:41:10 1432.85 5401.40 1401.12 1402.50 2156.99 65.73 0.00 ==> mutect2_16.txt <== 126177.3335 1 day, 11:02:57 1509.33 5401.82 1477.66 1479.35 3975.56 79.19 0.00 ==> mutect2_17.txt <== 160714.2310 1 day, 20:38:34 1508.52 5406.33 1480.32 1482.18 4687.88 100.00 0.00 ==> mutect2_18.txt <== 46132.8540 12:48:52 1258.10 5380.63 1227.00 1228.04 423.54 31.15 0.00 ==> mutect2_19.txt <== 165973.6274 1 day, 22:06:13 1625.34 5393.67 1598.53 1599.31 5304.61 102.87 0.00 ==> mutect_21.txt <== 1419.4974 0:23:39 1125.20 4580.24 1101.30 1102.55 362.21 67.10 0.00 ==> mutect2_1.txt <== 215570.6517 2 days, 11:52:50 1607.38 5404.89 1579.32 1581.15 9928.94 136.78 0.00 ==> mutect2_20.txt <== 87936.4660 1 day, 0:25:36 1333.81 5393.47 1303.21 1304.49 2378.94 55.84 0.00 ==> mutect2_21.txt <== 31767.5137 8:49:27 1241.53 5501.50 1210.05 1211.05 1029.50 21.78 0.00 ==> mutect2_22.txt <== 65424.0151 18:10:24 1315.78 5393.84 1284.41 1285.63 1913.00 42.99 0.00 ==> mutect_22.txt <== 2232.6226 0:37:12 1246.06 4580.24 1222.29 1223.62 712.41 78.19 0.00 ==> mutect2_2.txt <== 189937.6815 2 days, 4:45:37 1535.52 5396.07 1503.79 1505.15 8586.79 119.77 0.00 ==> mutect2_3.txt <== 141593.6697 1 day, 15:19:53 1548.27 5391.41 1519.81 1520.57 6159.18 91.39 0.00 ==> mutect2_4.txt <== 113204.2565 1 day, 7:26:44 1432.26 5408.98 1400.68 1402.46 2423.45 72.86 0.00 ==> mutect2_5.txt <== 117168.8867 1 day, 8:32:48 1482.88 5394.94 1451.24 1453.36 4578.30 75.65 0.00 ==> mutect2_6.txt <== 142789.9733 1 day, 15:39:49 1547.14 5397.13 1518.93 1519.64 5609.93 91.24 0.00 ==> mutect2_7.txt <== 148948.1393 1 day, 17:22:28 1545.62 5515.08 1517.29 1519.29 4926.46 93.47 0.00 ==> mutect2_8.txt <== 103571.2659 1 day, 4:46:11 1555.79 5426.49 1524.32 1525.67 2596.15 66.94 0.00 ==> mutect2_9.txt <== 102204.6028 1 day, 4:23:24 1556.36 5408.69 1526.38 1527.73 3265.65 65.40 0.00 ==> mutect_2.txt <== 9308.3525 2:35:08 2035.54 4580.24 2011.67 2014.94 8306.65 442.30 0.00 ==> mutect2_X.txt <== 53637.3633 14:53:57 1477.18 5378.54 1445.34 1446.48 2492.98 36.46 0.00 ==> mutect_3.txt <== 6777.5392 1:52:57 1731.80 4580.24 1706.88 1709.02 5779.87 338.80 0.00 ==> mutect_4.txt <== 5300.7566 1:28:20 1649.19 4580.24 1638.20 1638.52 4672.53 318.21 0.00 ==> mutect_5.txt <== 5567.3555 1:32:47 1649.34 4580.24 1624.54 1626.43 4321.95 310.42 0.00 ==> mutect_6.txt <== 6180.6757 1:43:00 1723.32 4580.24 1699.39 1701.28 4786.73 305.54 0.00 ==> mutect_7.txt <== 6604.0332 1:50:04 1682.11 4580.24 1657.68 1659.80 4765.41 297.65 0.00 ==> mutect_8.txt <== 4554.1054 1:15:54 1582.31 4580.24 1557.82 1564.30 4068.04 262.54 0.00 ==> mutect_9.txt <== 4280.9887 1:11:20 1516.35 4580.24 1491.96 1496.41 4026.20 211.96 0.00 ==> mutect_X.txt <== 3356.4529 0:55:56 1306.22 4580.24 1282.06 1283.43 814.54 199.17 0.00 ==> normal_base_recalibrator_print_reads.txt <== 7333.5113 2:02:13 19376.15 25963.44 19355.18 19364.42 1.76 31430.47 0.00 ==> normal_base_recalibrator.txt <== 3939.9578 1:05:39 16444.89 25965.17 16422.63 16431.80 27037.62 2.97 0.00 ==> normal_L001_bwa_mem.txt <== 2234.3952 0:37:14 6870.79 7291.71 6866.65 6867.23 10296.33 39711.67 0.00 ==> normal_L001_convert_alignment_to_sorted_bam.txt <== 3674.1591 1:01:14 7876.03 26597.21 7857.97 7862.03 54319.19 24833.54 0.00 ==> normal_L002_bwa_mem.txt <== 2357.2039 0:39:17 6877.92 7291.71 6873.72 6874.49 10557.05 40379.54 0.00 ==> normal_L002_convert_alignment_to_sorted_bam.txt <== 5430.6143 1:30:30 7767.41 26596.21 7747.61 7753.03 56225.77 25460.14 0.00 ==> normal_mark_dups.txt <== 4972.0290 1:22:52 21101.26 26596.22 21081.06 21089.34 8985.15 23725.14 0.00 ==> rna_mark_dups.txt <== 2748.3613 0:45:48 15598.45 26596.21 15578.65 15584.00 1.18 9703.38 0.00 ==> strelka.txt <== 2223.0812 0:37:03 1799.47 2865.69 1569.11 1576.18 91426.98 20.17 0.00 ==> tumor_base_recalibrator_print_reads.txt <== 14999.3291 4:09:59 21091.40 25963.44 21084.58 21086.95 8134.49 64833.70 0.00 ==> tumor_base_recalibrator.txt <== 6228.1026 1:43:48 19438.90 25963.12 19416.99 19426.12 36039.72 4.61 0.00 ==> tumor_indel_realigner.txt <== 1735.2163 0:28:55 2050.04 5219.57 2048.14 2049.17 35440.06 35960.85 0.00 ==> tumor_L001_bwa_mem.txt <== 5687.1797 1:34:47 7638.33 8057.71 7633.55 7635.22 24849.09 88688.13 0.00 ==> tumor_L001_convert_alignment_to_sorted_bam.txt <== 7133.6827 1:58:53 7803.98 26596.21 7785.31 7790.73 124347.63 55247.35 0.00 ==> tumor_L002_bwa_mem.txt <== 5866.9096 1:37:46 7662.25 8057.71 7657.48 7659.15 26003.46 90356.66 0.00 ==> tumor_L002_convert_alignment_to_sorted_bam.txt <== 7022.1991 1:57:02 7792.38 26596.21 7773.64 7779.07 126950.95 56813.34 0.00 ==> tumor_mark_dups.txt <== 10748.2751 2:59:08 19735.49 26596.22 19718.01 19724.98 50041.64 51629.68 0.00
Here are steps from a recent run whose benchmarks showed they took more than 1000 seconds: