Rescaling

Rescaling base quality scores using aDNA damage profile

The idea of rescaling read base quality scores using damage profile was first introduced by mapDamage2. Rescaling base quality score is one of the way to deal with aDNA damage, which otherwise can introduces biases, in variant calling for example.

However, the runtime necessary to rescale these reads with mapDamage2 made it more than often prohibitive to use this functionality.
Starting from version 0.80, PyDamage now also offers a base quality score rescaling.

This notebook is used to demontrate the performance of PyDamage v0.80 vs the current version of mapDamage2 (v2.2.2 as of 2024/09/18), and compare their rescaling results.

For both PyDamage and mapDamage, the output of the rescaling will be a BAM file with rescaled read base quality score.

[1]:
import pandas as pd
import pysam
from plotnine import *
import numpy as np
[2]:
! pydamage --version
pydamage, version 0.80
[3]:
%%timeit -r 3 -o
! pydamage analyze --rescale --group --force ../../tests/data/bigger_test_data.bam
Estimating and testing Damage
Computing alignment stats for entire reference

Compute damage for entire reference: 0it [00:00, ?it/s]
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Rescaling quality scores:   0%|                         | 0/230 [00:00<?, ?it/s]
Rescaling quality scores:   0%|                 | 1/230 [00:00<02:29,  1.53it/s]
Rescaling quality scores:   1%|▏                | 3/230 [00:00<00:59,  3.81it/s]
Rescaling quality scores:   3%|▍                | 6/230 [00:01<00:27,  8.19it/s]
Rescaling quality scores:   6%|▉               | 13/230 [00:01<00:11, 19.32it/s]
Rescaling quality scores:   8%|█▎              | 19/230 [00:02<00:20, 10.16it/s]
Rescaling quality scores:  14%|██▏             | 32/230 [00:02<00:13, 14.61it/s]
Rescaling quality scores:  15%|██▍             | 35/230 [00:03<00:18, 10.65it/s]
Rescaling quality scores:  17%|██▋             | 38/230 [00:04<00:22,  8.49it/s]
Rescaling quality scores:  17%|██▊             | 40/230 [00:05<00:37,  5.13it/s]
Rescaling quality scores:  18%|██▊             | 41/230 [00:06<00:57,  3.31it/s]
Rescaling quality scores:  19%|███             | 44/230 [00:06<00:41,  4.45it/s]
Rescaling quality scores:  20%|███▏            | 46/230 [00:06<00:36,  5.05it/s]
Rescaling quality scores:  21%|███▍            | 49/230 [00:07<00:29,  6.14it/s]
Rescaling quality scores:  23%|███▌            | 52/230 [00:07<00:28,  6.18it/s]
Rescaling quality scores:  23%|███▊            | 54/230 [00:07<00:26,  6.62it/s]
Rescaling quality scores:  25%|████            | 58/230 [00:07<00:17,  9.60it/s]
Rescaling quality scores:  29%|████▌           | 66/230 [00:08<00:09, 16.60it/s]
Rescaling quality scores:  30%|████▊           | 70/230 [00:08<00:08, 19.35it/s]
Rescaling quality scores:  32%|█████           | 73/230 [00:08<00:10, 15.27it/s]
Rescaling quality scores:  33%|█████▎          | 76/230 [00:09<00:12, 11.91it/s]
Rescaling quality scores:  35%|█████▌          | 80/230 [00:09<00:10, 14.52it/s]
Rescaling quality scores:  40%|██████▍         | 93/230 [00:09<00:04, 30.74it/s]
Rescaling quality scores:  43%|██████▉         | 99/230 [00:09<00:06, 20.53it/s]
Rescaling quality scores:  45%|██████▋        | 103/230 [00:10<00:06, 19.92it/s]
Rescaling quality scores:  47%|██████▉        | 107/230 [00:10<00:10, 11.18it/s]
Rescaling quality scores:  49%|███████▎       | 113/230 [00:11<00:08, 13.60it/s]
Rescaling quality scores:  50%|███████▌       | 116/230 [00:11<00:09, 11.60it/s]
Rescaling quality scores:  52%|███████▊       | 120/230 [00:11<00:07, 14.24it/s]
Rescaling quality scores:  54%|████████▏      | 125/230 [00:12<00:08, 12.08it/s]
Rescaling quality scores:  56%|████████▎      | 128/230 [00:12<00:08, 11.61it/s]
Rescaling quality scores:  57%|████████▍      | 130/230 [00:13<00:11,  9.02it/s]
Rescaling quality scores:  57%|████████▌      | 132/230 [00:13<00:09,  9.89it/s]
Rescaling quality scores:  58%|████████▋      | 134/230 [00:13<00:11,  8.47it/s]
Rescaling quality scores:  59%|████████▊      | 136/230 [00:13<00:11,  8.53it/s]
Rescaling quality scores:  61%|█████████▏     | 141/230 [00:14<00:08, 10.17it/s]
Rescaling quality scores:  65%|█████████▋     | 149/230 [00:14<00:04, 17.52it/s]
Rescaling quality scores:  67%|█████████▉     | 153/230 [00:15<00:09,  7.72it/s]
Rescaling quality scores:  70%|██████████▌    | 162/230 [00:15<00:05, 12.68it/s]
Rescaling quality scores:  73%|██████████▉    | 167/230 [00:16<00:05, 11.53it/s]
Rescaling quality scores:  76%|███████████▍   | 175/230 [00:16<00:04, 12.31it/s]
Rescaling quality scores:  81%|████████████▏  | 186/230 [00:17<00:02, 16.31it/s]
Rescaling quality scores:  82%|████████████▎  | 189/230 [00:17<00:03, 11.80it/s]
Rescaling quality scores:  83%|████████████▍  | 191/230 [00:18<00:05,  7.36it/s]
Rescaling quality scores:  86%|████████████▊  | 197/230 [00:19<00:03,  8.80it/s]
Rescaling quality scores:  87%|████████████▉  | 199/230 [00:19<00:03,  7.86it/s]
Rescaling quality scores:  87%|█████████████  | 201/230 [00:19<00:03,  8.62it/s]
Rescaling quality scores:  91%|█████████████▋ | 210/230 [00:20<00:01, 10.59it/s]
Rescaling quality scores:  96%|██████████████▎| 220/230 [00:21<00:01,  9.54it/s]
Rescaling quality scores:  97%|██████████████▍| 222/230 [00:21<00:00,  9.94it/s]
Rescaling quality scores:  97%|██████████████▌| 224/230 [00:22<00:00,  9.53it/s]
Rescaling quality scores:  98%|██████████████▋| 226/230 [00:22<00:00,  8.48it/s]
Rescaling quality scores: 100%|███████████████| 230/230 [00:22<00:00, 10.19it/s]
Estimating and testing Damage
Computing alignment stats for entire reference

Compute damage for entire reference: 0it [00:00, ?it/s]
Compute damage for entire reference: 12492it [00:00, 124886.47it/s]
Compute damage for entire reference: 25169it [00:00, 125987.49it/s]
Compute damage for entire reference: 37768it [00:00, 125985.40it/s]
Compute damage for entire reference: 50446it [00:00, 126293.54it/s]
Compute damage for entire reference: 63076it [00:00, 126293.20it/s]
Compute damage for entire reference: 75883it [00:00, 126895.87it/s]
Compute damage for entire reference: 88573it [00:00, 126792.12it/s]
Compute damage for entire reference: 101505it [00:00, 127592.95it/s]
Compute damage for entire reference: 114265it [00:00, 127249.73it/s]
Compute damage for entire reference: 127123it [00:01, 127657.87it/s]
Compute damage for entire reference: 139890it [00:01, 127257.00it/s]
Compute damage for entire reference: 152617it [00:01, 126890.01it/s]
Compute damage for entire reference: 165382it [00:01, 127117.73it/s]
Compute damage for entire reference: 178095it [00:01, 127082.68it/s]
Compute damage for entire reference: 190862it [00:01, 127255.15it/s]
Compute damage for entire reference: 203698it [00:01, 127583.17it/s]
Compute damage for entire reference: 216497it [00:01, 127703.75it/s]
Compute damage for entire reference: 229268it [00:01, 127685.01it/s]
Compute damage for entire reference: 242037it [00:01, 127321.75it/s]
Compute damage for entire reference: 254820it [00:02, 127470.54it/s]
Compute damage for entire reference: 267573it [00:02, 127485.84it/s]
Compute damage for entire reference: 280322it [00:02, 127113.23it/s]
Compute damage for entire reference: 293034it [00:02, 125563.02it/s]
Compute damage for entire reference: 305595it [00:02, 124679.34it/s]
Compute damage for entire reference: 318067it [00:02, 123484.61it/s]
Compute damage for entire reference: 330420it [00:02, 122993.78it/s]
Compute damage for entire reference: 342722it [00:02, 122348.27it/s]
Compute damage for entire reference: 354961it [00:02, 122356.25it/s]
Compute damage for entire reference: 367292it [00:02, 122638.25it/s]
Compute damage for entire reference: 379601it [00:03, 122770.73it/s]
Compute damage for entire reference: 391879it [00:03, 122057.93it/s]
Compute damage for entire reference: 404125it [00:03, 122173.97it/s]
Compute damage for entire reference: 416541it [00:03, 122763.25it/s]
Compute damage for entire reference: 428871it [00:03, 122920.65it/s]
Compute damage for entire reference: 441203it [00:03, 123038.78it/s]
Compute damage for entire reference: 453556it [00:03, 123184.86it/s]
Compute damage for entire reference: 466021it [00:03, 123620.96it/s]
Compute damage for entire reference: 478492it [00:03, 123944.40it/s]
Compute damage for entire reference: 491258it [00:03, 125056.51it/s]
Compute damage for entire reference: 503950it [00:04, 125611.56it/s]
Compute damage for entire reference: 516582it [00:04, 125820.91it/s]
Compute damage for entire reference: 529165it [00:04, 125667.13it/s]
Compute damage for entire reference: 541732it [00:04, 125384.31it/s]
Compute damage for entire reference: 554271it [00:04, 125369.14it/s]
Compute damage for entire reference: 566860it [00:04, 125521.31it/s]
Compute damage for entire reference: 579464it [00:04, 125673.89it/s]
Compute damage for entire reference: 592182it [00:04, 126123.20it/s]
Compute damage for entire reference: 604868it [00:04, 126343.06it/s]
Compute damage for entire reference: 617521it [00:04, 126396.80it/s]
Compute damage for entire reference: 630161it [00:05, 126134.98it/s]
Compute damage for entire reference: 642948it [00:05, 126652.48it/s]
Compute damage for entire reference: 655644it [00:05, 126741.49it/s]
Compute damage for entire reference: 668319it [00:05, 126739.82it/s]
Compute damage for entire reference: 680994it [00:05, 126652.20it/s]
Compute damage for entire reference: 693689it [00:05, 126738.41it/s]
Compute damage for entire reference: 706477it [00:05, 127076.43it/s]
Compute damage for entire reference: 719291it [00:05, 127393.74it/s]
Compute damage for entire reference: 732031it [00:05, 127077.10it/s]
Compute damage for entire reference: 744739it [00:05, 126578.88it/s]
Compute damage for entire reference: 757458it [00:06, 126758.96it/s]
Compute damage for entire reference: 770172it [00:06, 126870.53it/s]
Compute damage for entire reference: 783105it [00:06, 127604.70it/s]
Compute damage for entire reference: 795866it [00:06, 126583.09it/s]
Compute damage for entire reference: 808527it [00:06, 125628.75it/s]
Compute damage for entire reference: 821202it [00:06, 125958.06it/s]
Compute damage for entire reference: 834270it [00:06, 127361.74it/s]
Compute damage for entire reference: 847301it [00:06, 128239.14it/s]
Compute damage for entire reference: 860141it [00:06, 128284.16it/s]
Compute damage for entire reference: 872971it [00:06, 127659.90it/s]
Compute damage for entire reference: 885739it [00:07, 125734.40it/s]
Compute damage for entire reference: 898320it [00:07, 125539.13it/s]
Compute damage for entire reference: 910902it [00:07, 125621.15it/s]
Compute damage for entire reference: 923468it [00:07, 125456.83it/s]
Compute damage for entire reference: 936036it [00:07, 125521.06it/s]
Compute damage for entire reference: 948590it [00:07, 123460.19it/s]
Compute damage for entire reference: 961074it [00:07, 123866.05it/s]
Compute damage for entire reference: 973603it [00:07, 124285.31it/s]
Compute damage for entire reference: 986510it [00:07, 125707.84it/s]
Compute damage for entire reference: 999086it [00:07, 125541.12it/s]
Compute damage for entire reference: 1011858it [00:08, 126188.38it/s]
Compute damage for entire reference: 1024705it [00:08, 126868.41it/s]
Compute damage for entire reference: 1037547it [00:08, 127330.68it/s]
Compute damage for entire reference: 1050428it [00:08, 127772.06it/s]
Compute damage for entire reference: 1063334it [00:08, 128155.38it/s]
Compute damage for entire reference: 1076151it [00:08, 127375.56it/s]
Compute damage for entire reference: 1088891it [00:08, 127239.07it/s]
Compute damage for entire reference: 1101616it [00:08, 127061.19it/s]
Compute damage for entire reference: 1114393it [00:08, 127271.13it/s]
Compute damage for entire reference: 1127147it [00:08, 127349.15it/s]
Compute damage for entire reference: 1139883it [00:09, 126805.06it/s]
Compute damage for entire reference: 1152565it [00:09, 126538.41it/s]
Compute damage for entire reference: 1165266it [00:09, 126676.21it/s]
Compute damage for entire reference: 1177935it [00:09, 126227.79it/s]
Compute damage for entire reference: 1190599it [00:09, 126346.76it/s]
Compute damage for entire reference: 1203235it [00:09, 126171.77it/s]
Compute damage for entire reference: 1215853it [00:09, 126139.20it/s]
Compute damage for entire reference: 1228702it [00:09, 126838.25it/s]
Compute damage for entire reference: 1241387it [00:09, 126748.78it/s]
Compute damage for entire reference: 1254063it [00:09, 126032.38it/s]
Compute damage for entire reference: 1266668it [00:10, 125737.43it/s]
Compute damage for entire reference: 1279379it [00:10, 126144.80it/s]
Compute damage for entire reference: 1292030it [00:10, 126252.82it/s]
Compute damage for entire reference: 1304656it [00:10, 126216.02it/s]
Compute damage for entire reference: 1317360it [00:10, 126461.38it/s]
Compute damage for entire reference: 1330007it [00:10, 126077.16it/s]
Compute damage for entire reference: 1342616it [00:10, 125998.84it/s]
Compute damage for entire reference: 1355217it [00:10, 125190.88it/s]
Compute damage for entire reference: 1367776it [00:10, 125307.48it/s]
Compute damage for entire reference: 1380349it [00:10, 125432.19it/s]
Compute damage for entire reference: 1393087it [00:11, 126012.84it/s]
Compute damage for entire reference: 1405870it [00:11, 126555.01it/s]
Compute damage for entire reference: 1418527it [00:11, 126471.74it/s]
Compute damage for entire reference: 1431175it [00:11, 126463.96it/s]
Compute damage for entire reference: 1443928it [00:11, 126781.17it/s]
Compute damage for entire reference: 1456607it [00:11, 126703.72it/s]
Compute damage for entire reference: 1469453it [00:11, 127225.55it/s]
Compute damage for entire reference: 1482198it [00:11, 127243.86it/s]
Compute damage for entire reference: 1494923it [00:11, 127104.39it/s]
Compute damage for entire reference: 1507634it [00:11, 126940.53it/s]
Compute damage for entire reference: 1520329it [00:12, 125546.48it/s]
Compute damage for entire reference: 1532887it [00:12, 124605.61it/s]
Compute damage for entire reference: 1545351it [00:12, 123672.91it/s]
Compute damage for entire reference: 1557761it [00:12, 123796.03it/s]
Compute damage for entire reference: 1570143it [00:12, 123781.26it/s]
Compute damage for entire reference: 1582523it [00:12, 123751.10it/s]
Compute damage for entire reference: 1594900it [00:12, 123395.39it/s]
Compute damage for entire reference: 1607241it [00:12, 122851.78it/s]
Compute damage for entire reference: 1619527it [00:12, 122680.26it/s]
Compute damage for entire reference: 1631796it [00:12, 122481.67it/s]
Compute damage for entire reference: 1644206it [00:13, 122962.02it/s]
Compute damage for entire reference: 1656701it [00:13, 123554.92it/s]
Compute damage for entire reference: 1669264it [00:13, 124172.58it/s]
Compute damage for entire reference: 1681682it [00:13, 123638.86it/s]
Compute damage for entire reference: 1694249it [00:13, 124243.57it/s]
Compute damage for entire reference: 1706675it [00:13, 123797.77it/s]
Compute damage for entire reference: 1719056it [00:13, 123645.39it/s]
Compute damage for entire reference: 1731422it [00:13, 123449.13it/s]
Compute damage for entire reference: 1743996it [00:13, 124131.79it/s]
Compute damage for entire reference: 1756568it [00:13, 124605.60it/s]
Compute damage for entire reference: 1769030it [00:14, 124515.02it/s]
Compute damage for entire reference: 1781482it [00:14, 124318.82it/s]
Compute damage for entire reference: 1794002it [00:14, 124581.13it/s]
Compute damage for entire reference: 1806694it [00:14, 125278.57it/s]
Compute damage for entire reference: 1819476it [00:14, 126037.94it/s]
Compute damage for entire reference: 1832081it [00:14, 125088.49it/s]
Compute damage for entire reference: 1844649it [00:14, 125263.68it/s]
Compute damage for entire reference: 1857177it [00:14, 121900.20it/s]
Compute damage for entire reference: 1869936it [00:14, 123568.57it/s]
Compute damage for entire reference: 1882585it [00:14, 124429.61it/s]
Compute damage for entire reference: 1895325it [00:15, 125307.55it/s]
Compute damage for entire reference: 1907867it [00:15, 125208.20it/s]
Compute damage for entire reference: 1920584it [00:15, 125792.02it/s]
Compute damage for entire reference: 1933330it [00:15, 126286.26it/s]
Compute damage for entire reference: 1946037it [00:15, 126516.20it/s]
Compute damage for entire reference: 1958692it [00:15, 126438.64it/s]
Compute damage for entire reference: 1971463it [00:15, 126818.06it/s]
Compute damage for entire reference: 1984147it [00:15, 126176.42it/s]
Compute damage for entire reference: 1996847it [00:15, 126417.99it/s]
Compute damage for entire reference: 2009561it [00:15, 126630.50it/s]
Compute damage for entire reference: 2022256it [00:16, 126723.46it/s]
Compute damage for entire reference: 2035095it [00:16, 127220.29it/s]
Compute damage for entire reference: 2048002it [00:16, 127770.86it/s]
Compute damage for entire reference: 2060849it [00:16, 127978.37it/s]
Compute damage for entire reference: 2073810it [00:16, 128465.77it/s]
Compute damage for entire reference: 2086657it [00:16, 127801.43it/s]
Compute damage for entire reference: 2099449it [00:16, 127834.89it/s]
Compute damage for entire reference: 2112300it [00:16, 128034.16it/s]
Compute damage for entire reference: 2125104it [00:16, 127854.50it/s]
Compute damage for entire reference: 2137890it [00:16, 127832.01it/s]
Compute damage for entire reference: 2150674it [00:17, 127731.84it/s]
Compute damage for entire reference: 2163448it [00:17, 126719.76it/s]
Compute damage for entire reference: 2176122it [00:17, 125491.88it/s]
Compute damage for entire reference: 2188819it [00:17, 125928.60it/s]
Compute damage for entire reference: 2201550it [00:17, 126336.89it/s]
Compute damage for entire reference: 2214286it [00:17, 126637.23it/s]
Compute damage for entire reference: 2227112it [00:17, 127120.95it/s]
Compute damage for entire reference: 2239918it [00:17, 127400.35it/s]
Compute damage for entire reference: 2252660it [00:17, 126998.15it/s]
Compute damage for entire reference: 2265361it [00:18, 126362.00it/s]
Compute damage for entire reference: 2277999it [00:18, 126350.96it/s]
Compute damage for entire reference: 2290727it [00:18, 126626.42it/s]
Compute damage for entire reference: 2303455it [00:18, 126818.59it/s]
Compute damage for entire reference: 2316141it [00:18, 126827.04it/s]
Compute damage for entire reference: 2328868it [00:18, 126957.49it/s]
Compute damage for entire reference: 2341565it [00:18, 126224.38it/s]
Compute damage for entire reference: 2354189it [00:18, 125815.42it/s]
Compute damage for entire reference: 2366842it [00:18, 126026.19it/s]
Compute damage for entire reference: 2379625it [00:18, 126563.59it/s]
Compute damage for entire reference: 2392446it [00:19, 127053.99it/s]
Compute damage for entire reference: 2405153it [00:19, 126885.27it/s]
Compute damage for entire reference: 2417955it [00:19, 127223.11it/s]
Compute damage for entire reference: 2430850it [00:19, 127738.45it/s]
Compute damage for entire reference: 2443625it [00:19, 127620.32it/s]
Compute damage for entire reference: 2456388it [00:19, 127528.08it/s]
Compute damage for entire reference: 2469142it [00:19, 127376.77it/s]
Compute damage for entire reference: 2481936it [00:19, 127544.26it/s]
Compute damage for entire reference: 2494754it [00:19, 127730.66it/s]
Compute damage for entire reference: 2507528it [00:19, 127288.09it/s]
Compute damage for entire reference: 2520258it [00:20, 126713.36it/s]
Compute damage for entire reference: 2532931it [00:20, 126690.69it/s]
Compute damage for entire reference: 2545744it [00:20, 127117.21it/s]
Compute damage for entire reference: 2558470it [00:20, 127157.97it/s]
Compute damage for entire reference: 2571275it [00:20, 127423.00it/s]
Compute damage for entire reference: 2584018it [00:20, 127197.18it/s]
Compute damage for entire reference: 2596738it [00:20, 127166.39it/s]
Compute damage for entire reference: 2609470it [00:20, 127210.16it/s]
Compute damage for entire reference: 2622256it [00:20, 127403.36it/s]
Compute damage for entire reference: 2634997it [00:20, 127379.81it/s]
Compute damage for entire reference: 2647820it [00:21, 127631.06it/s]
Compute damage for entire reference: 2660606it [00:21, 127696.64it/s]
Compute damage for entire reference: 2673477it [00:21, 127995.99it/s]
Compute damage for entire reference: 2686307it [00:21, 128081.98it/s]
Compute damage for entire reference: 2699138it [00:21, 128148.30it/s]
Compute damage for entire reference: 2711953it [00:21, 127648.88it/s]
Compute damage for entire reference: 2724755it [00:21, 127756.74it/s]
Compute damage for entire reference: 2737532it [00:21, 126893.19it/s]
Compute damage for entire reference: 2750235it [00:21, 126931.31it/s]
Compute damage for entire reference: 2762930it [00:21, 126932.41it/s]
Compute damage for entire reference: 2775624it [00:22, 126429.69it/s]
Compute damage for entire reference: 2788406it [00:22, 126843.49it/s]
Compute damage for entire reference: 2801092it [00:22, 126215.93it/s]
Compute damage for entire reference: 2813715it [00:22, 125239.83it/s]
Compute damage for entire reference: 2826280it [00:22, 125357.47it/s]
Compute damage for entire reference: 2838854it [00:22, 125466.50it/s]
Compute damage for entire reference: 2851402it [00:22, 123929.56it/s]
Compute damage for entire reference: 2863800it [00:22, 123534.14it/s]
Compute damage for entire reference: 2876157it [00:22, 123078.53it/s]
Compute damage for entire reference: 2888581it [00:22, 123421.55it/s]
Compute damage for entire reference: 2901437it [00:23, 124951.05it/s]
Compute damage for entire reference: 2914004it [00:23, 125164.09it/s]
Compute damage for entire reference: 2926756it [00:23, 125866.34it/s]
Compute damage for entire reference: 2939545it [00:23, 126470.35it/s]
Compute damage for entire reference: 2952194it [00:23, 126337.53it/s]
Compute damage for entire reference: 2965122it [00:23, 127215.83it/s]
Compute damage for entire reference: 2977914it [00:23, 127424.54it/s]
Compute damage for entire reference: 2990658it [00:23, 126786.36it/s]
Compute damage for entire reference: 3003338it [00:23, 126589.50it/s]
Compute damage for entire reference: 3016099it [00:23, 126891.55it/s]
Compute damage for entire reference: 3028831it [00:24, 127017.58it/s]
Compute damage for entire reference: 3041581it [00:24, 127158.69it/s]
Compute damage for entire reference: 3054463it [00:24, 127651.66it/s]
Compute damage for entire reference: 3067229it [00:24, 127621.28it/s]
Compute damage for entire reference: 3080073it [00:24, 127863.97it/s]
Compute damage for entire reference: 3092860it [00:24, 127801.23it/s]
Compute damage for entire reference: 3105641it [00:24, 126787.85it/s]
Compute damage for entire reference: 3118322it [00:24, 126550.70it/s]
Compute damage for entire reference: 3130979it [00:24, 126220.04it/s]
Compute damage for entire reference: 3143751it [00:24, 126664.92it/s]
Compute damage for entire reference: 3156419it [00:25, 126421.37it/s]
Compute damage for entire reference: 3169195it [00:25, 126818.49it/s]
Compute damage for entire reference: 3181878it [00:25, 126793.58it/s]
Compute damage for entire reference: 3194602it [00:25, 126924.43it/s]
Compute damage for entire reference: 3194672it [00:25, 126099.94it/s]

Rescaling quality scores:   0%|                         | 0/230 [00:00<?, ?it/s]
Rescaling quality scores:   0%|                 | 1/230 [00:00<02:24,  1.58it/s]
Rescaling quality scores:   1%|▏                | 3/230 [00:00<00:52,  4.29it/s]
Rescaling quality scores:   3%|▌                | 7/230 [00:00<00:20, 10.76it/s]
Rescaling quality scores:   6%|▉               | 13/230 [00:01<00:10, 20.34it/s]
Rescaling quality scores:   8%|█▎              | 19/230 [00:01<00:08, 24.83it/s]
Rescaling quality scores:  14%|██▏             | 32/230 [00:02<00:13, 14.76it/s]
Rescaling quality scores:  15%|██▍             | 35/230 [00:03<00:20,  9.41it/s]
Rescaling quality scores:  17%|██▋             | 38/230 [00:05<00:45,  4.25it/s]
Rescaling quality scores:  17%|██▊             | 40/230 [00:07<01:03,  3.01it/s]
Rescaling quality scores:  18%|██▊             | 41/230 [00:08<01:23,  2.25it/s]
Rescaling quality scores:  20%|███▏            | 46/230 [00:09<00:50,  3.63it/s]
Rescaling quality scores:  22%|███▍            | 50/230 [00:09<00:35,  5.12it/s]
Rescaling quality scores:  23%|███▋            | 53/230 [00:09<00:30,  5.73it/s]
Rescaling quality scores:  24%|███▊            | 55/230 [00:09<00:27,  6.44it/s]
Rescaling quality scores:  29%|████▌           | 66/230 [00:09<00:11, 14.22it/s]
Rescaling quality scores:  31%|████▉           | 71/230 [00:10<00:11, 14.40it/s]
Rescaling quality scores:  33%|█████▏          | 75/230 [00:10<00:14, 10.86it/s]
Rescaling quality scores:  35%|█████▌          | 80/230 [00:10<00:10, 13.91it/s]
Rescaling quality scores:  42%|██████▋         | 96/230 [00:11<00:06, 22.23it/s]
Rescaling quality scores:  44%|██████▌        | 101/230 [00:11<00:05, 22.10it/s]
Rescaling quality scores:  46%|██████▊        | 105/230 [00:11<00:05, 21.46it/s]
Rescaling quality scores:  48%|███████▏       | 111/230 [00:11<00:04, 26.17it/s]
Rescaling quality scores:  50%|███████▌       | 115/230 [00:12<00:09, 11.71it/s]
Rescaling quality scores:  51%|███████▋       | 118/230 [00:13<00:08, 12.72it/s]
Rescaling quality scores:  53%|███████▉       | 122/230 [00:13<00:06, 15.44it/s]
Rescaling quality scores:  54%|████████▏      | 125/230 [00:13<00:10, 10.48it/s]
Rescaling quality scores:  56%|████████▎      | 128/230 [00:14<00:11,  8.88it/s]
Rescaling quality scores:  57%|████████▍      | 130/230 [00:15<00:19,  5.22it/s]
Rescaling quality scores:  57%|████████▌      | 132/230 [00:15<00:15,  6.16it/s]
Rescaling quality scores:  58%|████████▋      | 134/230 [00:15<00:15,  6.14it/s]
Rescaling quality scores:  59%|████████▊      | 136/230 [00:16<00:15,  6.05it/s]
Rescaling quality scores:  61%|█████████▏     | 141/230 [00:17<00:16,  5.32it/s]
Rescaling quality scores:  65%|█████████▋     | 149/230 [00:17<00:07, 10.16it/s]
Rescaling quality scores:  67%|█████████▉     | 153/230 [00:19<00:16,  4.66it/s]
Rescaling quality scores:  70%|██████████▌    | 162/230 [00:19<00:08,  8.29it/s]
Rescaling quality scores:  73%|██████████▉    | 167/230 [00:19<00:06,  9.00it/s]
Rescaling quality scores:  76%|███████████▍   | 175/230 [00:20<00:04, 11.65it/s]
Rescaling quality scores:  81%|████████████▏  | 186/230 [00:20<00:02, 15.29it/s]
Rescaling quality scores:  82%|████████████▎  | 189/230 [00:21<00:03, 11.28it/s]
Rescaling quality scores:  83%|████████████▌  | 192/230 [00:22<00:04,  8.53it/s]
Rescaling quality scores:  86%|████████████▊  | 197/230 [00:22<00:04,  7.97it/s]
Rescaling quality scores:  87%|████████████▉  | 199/230 [00:23<00:04,  7.41it/s]
Rescaling quality scores:  87%|█████████████  | 201/230 [00:23<00:03,  8.13it/s]
Rescaling quality scores:  91%|█████████████▋ | 210/230 [00:25<00:03,  6.27it/s]
Rescaling quality scores:  96%|██████████████▎| 220/230 [00:26<00:01,  6.89it/s]
Rescaling quality scores:  96%|██████████████▍| 221/230 [00:27<00:01,  5.52it/s]
Rescaling quality scores:  97%|██████████████▌| 223/230 [00:27<00:01,  6.03it/s]
Rescaling quality scores:  98%|██████████████▋| 225/230 [00:27<00:00,  6.83it/s]
Rescaling quality scores:  99%|██████████████▊| 227/230 [00:27<00:00,  6.96it/s]
Rescaling quality scores: 100%|███████████████| 230/230 [00:27<00:00,  8.30it/s]
Estimating and testing Damage
Computing alignment stats for entire reference

Compute damage for entire reference: 0it [00:00, ?it/s]
Compute damage for entire reference: 12812it [00:00, 128094.47it/s]
Compute damage for entire reference: 25622it [00:00, 127196.47it/s]
Compute damage for entire reference: 38343it [00:00, 126626.90it/s]
Compute damage for entire reference: 51007it [00:00, 126221.93it/s]
Compute damage for entire reference: 63630it [00:00, 125897.36it/s]
Compute damage for entire reference: 76230it [00:00, 125927.95it/s]
Compute damage for entire reference: 88823it [00:00, 125880.85it/s]
Compute damage for entire reference: 101729it [00:00, 126886.80it/s]
Compute damage for entire reference: 114418it [00:00, 126626.61it/s]
Compute damage for entire reference: 127155it [00:01, 126852.55it/s]
Compute damage for entire reference: 139841it [00:01, 126824.20it/s]
Compute damage for entire reference: 152524it [00:01, 126036.81it/s]
Compute damage for entire reference: 165337it [00:01, 126666.26it/s]
Compute damage for entire reference: 178112it [00:01, 126990.22it/s]
Compute damage for entire reference: 190812it [00:01, 126955.34it/s]
Compute damage for entire reference: 203509it [00:01, 126542.63it/s]
Compute damage for entire reference: 216164it [00:01, 125972.72it/s]
Compute damage for entire reference: 228977it [00:01, 126614.82it/s]
Compute damage for entire reference: 241749it [00:01, 126943.72it/s]
Compute damage for entire reference: 254616it [00:02, 127456.66it/s]
Compute damage for entire reference: 267535it [00:02, 127973.01it/s]
Compute damage for entire reference: 280333it [00:02, 127913.63it/s]
Compute damage for entire reference: 293125it [00:02, 127508.98it/s]
Compute damage for entire reference: 305877it [00:02, 127176.47it/s]
Compute damage for entire reference: 318596it [00:02, 127155.10it/s]
Compute damage for entire reference: 331397it [00:02, 127409.04it/s]
Compute damage for entire reference: 344197it [00:02, 127581.91it/s]
Compute damage for entire reference: 356956it [00:02, 127456.20it/s]
Compute damage for entire reference: 369851it [00:02, 127901.69it/s]
Compute damage for entire reference: 382719it [00:03, 128131.46it/s]
Compute damage for entire reference: 395533it [00:03, 127914.94it/s]
Compute damage for entire reference: 408369it [00:03, 128044.60it/s]
Compute damage for entire reference: 421185it [00:03, 128076.92it/s]
Compute damage for entire reference: 434013it [00:03, 128134.35it/s]
Compute damage for entire reference: 446827it [00:03, 127808.29it/s]
Compute damage for entire reference: 459609it [00:03, 127730.43it/s]
Compute damage for entire reference: 472383it [00:03, 126720.16it/s]
Compute damage for entire reference: 485219it [00:03, 127205.91it/s]
Compute damage for entire reference: 498158it [00:03, 127854.96it/s]
Compute damage for entire reference: 510945it [00:04, 127727.21it/s]
Compute damage for entire reference: 523732it [00:04, 127766.39it/s]
Compute damage for entire reference: 536591it [00:04, 128011.87it/s]
Compute damage for entire reference: 549438it [00:04, 128146.93it/s]
Compute damage for entire reference: 562254it [00:04, 128043.30it/s]
Compute damage for entire reference: 575059it [00:04, 127967.19it/s]
Compute damage for entire reference: 587856it [00:04, 127872.90it/s]
Compute damage for entire reference: 600671it [00:04, 127952.84it/s]
Compute damage for entire reference: 613467it [00:04, 127912.06it/s]
Compute damage for entire reference: 626259it [00:04, 127886.97it/s]
Compute damage for entire reference: 639161it [00:05, 128224.62it/s]
Compute damage for entire reference: 652054it [00:05, 128432.47it/s]
Compute damage for entire reference: 664898it [00:05, 128182.38it/s]
Compute damage for entire reference: 677760it [00:05, 128311.37it/s]
Compute damage for entire reference: 690651it [00:05, 128488.31it/s]
Compute damage for entire reference: 703500it [00:05, 128449.38it/s]
Compute damage for entire reference: 716408it [00:05, 128635.05it/s]
Compute damage for entire reference: 729308it [00:05, 128743.31it/s]
Compute damage for entire reference: 742183it [00:05, 128404.76it/s]
Compute damage for entire reference: 755024it [00:05, 128251.39it/s]
Compute damage for entire reference: 767850it [00:06, 127855.13it/s]
Compute damage for entire reference: 780818it [00:06, 128397.43it/s]
Compute damage for entire reference: 793659it [00:06, 127788.30it/s]
Compute damage for entire reference: 806439it [00:06, 127100.10it/s]
Compute damage for entire reference: 819151it [00:06, 126611.87it/s]
Compute damage for entire reference: 831814it [00:06, 126505.46it/s]
Compute damage for entire reference: 844535it [00:06, 126713.93it/s]
Compute damage for entire reference: 857245it [00:06, 126825.31it/s]
Compute damage for entire reference: 869973it [00:06, 126958.80it/s]
Compute damage for entire reference: 882780it [00:06, 127290.11it/s]
Compute damage for entire reference: 895579it [00:07, 127495.70it/s]
Compute damage for entire reference: 908336it [00:07, 127515.54it/s]
Compute damage for entire reference: 921088it [00:07, 127387.18it/s]
Compute damage for entire reference: 933840it [00:07, 127423.64it/s]
Compute damage for entire reference: 946583it [00:07, 122998.84it/s]
Compute damage for entire reference: 958979it [00:07, 123278.33it/s]
Compute damage for entire reference: 971560it [00:07, 124023.40it/s]
Compute damage for entire reference: 984410it [00:07, 125347.75it/s]
Compute damage for entire reference: 996960it [00:07, 125241.22it/s]
Compute damage for entire reference: 1009495it [00:07, 125187.15it/s]
Compute damage for entire reference: 1022133it [00:08, 125540.87it/s]
Compute damage for entire reference: 1034960it [00:08, 126352.48it/s]
Compute damage for entire reference: 1047742it [00:08, 126789.87it/s]
Compute damage for entire reference: 1060620it [00:08, 127382.45it/s]
Compute damage for entire reference: 1073361it [00:08, 127231.25it/s]
Compute damage for entire reference: 1086086it [00:08, 126891.64it/s]
Compute damage for entire reference: 1098777it [00:08, 126763.49it/s]
Compute damage for entire reference: 1111455it [00:08, 126693.66it/s]
Compute damage for entire reference: 1124125it [00:08, 126658.09it/s]
Compute damage for entire reference: 1136792it [00:08, 126434.51it/s]
Compute damage for entire reference: 1149436it [00:09, 126331.83it/s]
Compute damage for entire reference: 1162150it [00:09, 126571.38it/s]
Compute damage for entire reference: 1174808it [00:09, 125959.98it/s]
Compute damage for entire reference: 1187405it [00:09, 125942.20it/s]
Compute damage for entire reference: 1200040it [00:09, 126061.03it/s]
Compute damage for entire reference: 1212647it [00:09, 125944.58it/s]
Compute damage for entire reference: 1225437it [00:09, 126526.64it/s]
Compute damage for entire reference: 1238303it [00:09, 127163.46it/s]
Compute damage for entire reference: 1251020it [00:09, 126615.83it/s]
Compute damage for entire reference: 1263720it [00:09, 126727.52it/s]
Compute damage for entire reference: 1276394it [00:10, 126434.84it/s]
Compute damage for entire reference: 1289038it [00:10, 126324.86it/s]
Compute damage for entire reference: 1301734it [00:10, 126512.78it/s]
Compute damage for entire reference: 1314386it [00:10, 126411.22it/s]
Compute damage for entire reference: 1327028it [00:10, 126141.17it/s]
Compute damage for entire reference: 1339742it [00:10, 126438.16it/s]
Compute damage for entire reference: 1352387it [00:10, 126057.55it/s]
Compute damage for entire reference: 1365073it [00:10, 126294.40it/s]
Compute damage for entire reference: 1377804it [00:10, 126595.45it/s]
Compute damage for entire reference: 1390510it [00:10, 126733.52it/s]
Compute damage for entire reference: 1403184it [00:11, 126426.71it/s]
Compute damage for entire reference: 1415927it [00:11, 126725.42it/s]
Compute damage for entire reference: 1428643it [00:11, 126851.43it/s]
Compute damage for entire reference: 1441462it [00:11, 127251.15it/s]
Compute damage for entire reference: 1454228it [00:11, 127370.63it/s]
Compute damage for entire reference: 1467480it [00:11, 128911.98it/s]
Compute damage for entire reference: 1480900it [00:11, 130497.11it/s]
Compute damage for entire reference: 1494014it [00:11, 130687.99it/s]
Compute damage for entire reference: 1507083it [00:11, 129409.29it/s]
Compute damage for entire reference: 1520027it [00:11, 128585.42it/s]
Compute damage for entire reference: 1532889it [00:12, 128010.83it/s]
Compute damage for entire reference: 1545693it [00:12, 127394.54it/s]
Compute damage for entire reference: 1558434it [00:12, 127220.94it/s]
Compute damage for entire reference: 1571247it [00:12, 127487.57it/s]
Compute damage for entire reference: 1583997it [00:12, 127444.37it/s]
Compute damage for entire reference: 1596792it [00:12, 127593.62it/s]
Compute damage for entire reference: 1609552it [00:12, 127316.30it/s]
Compute damage for entire reference: 1622341it [00:12, 127482.73it/s]
Compute damage for entire reference: 1635173it [00:12, 127729.84it/s]
Compute damage for entire reference: 1647968it [00:12, 127792.15it/s]
Compute damage for entire reference: 1660748it [00:13, 127604.13it/s]
Compute damage for entire reference: 1673509it [00:13, 127379.23it/s]
Compute damage for entire reference: 1686248it [00:13, 127056.37it/s]
Compute damage for entire reference: 1698968it [00:13, 127096.62it/s]
Compute damage for entire reference: 1711678it [00:13, 126804.20it/s]
Compute damage for entire reference: 1724359it [00:13, 126770.91it/s]
Compute damage for entire reference: 1737037it [00:13, 126446.75it/s]
Compute damage for entire reference: 1749682it [00:13, 126319.20it/s]
Compute damage for entire reference: 1762315it [00:13, 126121.23it/s]
Compute damage for entire reference: 1774928it [00:13, 126101.78it/s]
Compute damage for entire reference: 1787602it [00:14, 126291.45it/s]
Compute damage for entire reference: 1800232it [00:14, 125845.94it/s]
Compute damage for entire reference: 1812833it [00:14, 125893.22it/s]
Compute damage for entire reference: 1825424it [00:14, 125895.58it/s]
Compute damage for entire reference: 1838035it [00:14, 125958.39it/s]
Compute damage for entire reference: 1850705it [00:14, 126178.45it/s]
Compute damage for entire reference: 1863323it [00:14, 122543.18it/s]
Compute damage for entire reference: 1876046it [00:14, 123916.72it/s]
Compute damage for entire reference: 1888828it [00:14, 125062.65it/s]
Compute damage for entire reference: 1901509it [00:14, 125578.31it/s]
Compute damage for entire reference: 1914078it [00:15, 125534.95it/s]
Compute damage for entire reference: 1926699it [00:15, 125734.85it/s]
Compute damage for entire reference: 1939380it [00:15, 126052.21it/s]
Compute damage for entire reference: 1952088it [00:15, 126356.04it/s]
Compute damage for entire reference: 1964727it [00:15, 126014.60it/s]
Compute damage for entire reference: 1977331it [00:15, 125347.58it/s]
Compute damage for entire reference: 1989977it [00:15, 125677.44it/s]
Compute damage for entire reference: 2002766it [00:15, 126336.25it/s]
Compute damage for entire reference: 2015474it [00:15, 126557.03it/s]
Compute damage for entire reference: 2028172it [00:15, 126682.78it/s]
Compute damage for entire reference: 2040999it [00:16, 127156.46it/s]
Compute damage for entire reference: 2053764it [00:16, 127299.40it/s]
Compute damage for entire reference: 2066544it [00:16, 127446.50it/s]
Compute damage for entire reference: 2079289it [00:16, 127130.68it/s]
Compute damage for entire reference: 2092003it [00:16, 126645.12it/s]
Compute damage for entire reference: 2104813it [00:16, 127076.72it/s]
Compute damage for entire reference: 2117676it [00:16, 127539.37it/s]
Compute damage for entire reference: 2130431it [00:16, 127374.30it/s]
Compute damage for entire reference: 2143178it [00:16, 127399.16it/s]
Compute damage for entire reference: 2155919it [00:16, 127348.52it/s]
Compute damage for entire reference: 2168655it [00:17, 127010.74it/s]
Compute damage for entire reference: 2181357it [00:17, 126703.88it/s]
Compute damage for entire reference: 2194051it [00:17, 126770.96it/s]
Compute damage for entire reference: 2206791it [00:17, 126957.67it/s]
Compute damage for entire reference: 2219487it [00:17, 126815.81it/s]
Compute damage for entire reference: 2232392it [00:17, 127481.43it/s]
Compute damage for entire reference: 2245141it [00:17, 127184.19it/s]
Compute damage for entire reference: 2257860it [00:17, 127001.15it/s]
Compute damage for entire reference: 2270561it [00:17, 126599.34it/s]
Compute damage for entire reference: 2283292it [00:17, 126809.59it/s]
Compute damage for entire reference: 2295996it [00:18, 126876.82it/s]
Compute damage for entire reference: 2308684it [00:18, 126630.16it/s]
Compute damage for entire reference: 2321348it [00:18, 126592.33it/s]
Compute damage for entire reference: 2334013it [00:18, 126608.00it/s]
Compute damage for entire reference: 2346674it [00:18, 125550.91it/s]
Compute damage for entire reference: 2359372it [00:18, 125973.92it/s]
Compute damage for entire reference: 2372143it [00:18, 126488.18it/s]
Compute damage for entire reference: 2385025it [00:18, 127180.63it/s]
Compute damage for entire reference: 2397758it [00:18, 127223.10it/s]
Compute damage for entire reference: 2410518it [00:18, 127334.01it/s]
Compute damage for entire reference: 2423269it [00:19, 127382.78it/s]
Compute damage for entire reference: 2436082it [00:19, 127524.40it/s]
Compute damage for entire reference: 2448861it [00:19, 127602.03it/s]
Compute damage for entire reference: 2461628it [00:19, 127620.89it/s]
Compute damage for entire reference: 2474391it [00:19, 127349.90it/s]
Compute damage for entire reference: 2487151it [00:19, 127421.92it/s]
Compute damage for entire reference: 2499912it [00:19, 127475.66it/s]
Compute damage for entire reference: 2512660it [00:19, 127106.78it/s]
Compute damage for entire reference: 2525371it [00:19, 126963.60it/s]
Compute damage for entire reference: 2538068it [00:19, 126424.18it/s]
Compute damage for entire reference: 2550711it [00:20, 126378.64it/s]
Compute damage for entire reference: 2563384it [00:20, 126480.99it/s]
Compute damage for entire reference: 2576175it [00:20, 126906.18it/s]
Compute damage for entire reference: 2588866it [00:20, 126732.01it/s]
Compute damage for entire reference: 2601540it [00:20, 126109.40it/s]
Compute damage for entire reference: 2614336it [00:20, 126659.39it/s]
Compute damage for entire reference: 2627105it [00:20, 126965.16it/s]
Compute damage for entire reference: 2640029it [00:20, 127644.04it/s]
Compute damage for entire reference: 2652886it [00:20, 127919.64it/s]
Compute damage for entire reference: 2665740it [00:20, 128096.77it/s]
Compute damage for entire reference: 2678584it [00:21, 128195.47it/s]
Compute damage for entire reference: 2691494it [00:21, 128462.74it/s]
Compute damage for entire reference: 2704341it [00:21, 127600.98it/s]
Compute damage for entire reference: 2717103it [00:21, 126923.93it/s]
Compute damage for entire reference: 2729803it [00:21, 126942.75it/s]
Compute damage for entire reference: 2742499it [00:21, 126010.20it/s]
Compute damage for entire reference: 2755212it [00:21, 126339.29it/s]
Compute damage for entire reference: 2767848it [00:21, 126337.24it/s]
Compute damage for entire reference: 2780654it [00:21, 126849.31it/s]
Compute damage for entire reference: 2793443it [00:22, 127158.41it/s]
Compute damage for entire reference: 2806197it [00:22, 127271.22it/s]
Compute damage for entire reference: 2818925it [00:22, 127265.16it/s]
Compute damage for entire reference: 2831709it [00:22, 127435.46it/s]
Compute damage for entire reference: 2844453it [00:22, 127034.02it/s]
Compute damage for entire reference: 2857157it [00:22, 126817.12it/s]
Compute damage for entire reference: 2869850it [00:22, 126848.66it/s]
Compute damage for entire reference: 2882536it [00:22, 126631.94it/s]
Compute damage for entire reference: 2895522it [00:22, 127595.80it/s]
Compute damage for entire reference: 2908458it [00:22, 128120.96it/s]
Compute damage for entire reference: 2921369it [00:23, 128415.10it/s]
Compute damage for entire reference: 2934242it [00:23, 128506.39it/s]
Compute damage for entire reference: 2947093it [00:23, 128262.37it/s]
Compute damage for entire reference: 2960000it [00:23, 128503.24it/s]
Compute damage for entire reference: 2972882it [00:23, 128596.44it/s]
Compute damage for entire reference: 2985742it [00:23, 128333.97it/s]
Compute damage for entire reference: 2998592it [00:23, 128382.16it/s]
Compute damage for entire reference: 3011474it [00:23, 128511.70it/s]
Compute damage for entire reference: 3024326it [00:23, 128452.64it/s]
Compute damage for entire reference: 3037172it [00:23, 128276.25it/s]
Compute damage for entire reference: 3050012it [00:24, 128310.05it/s]
Compute damage for entire reference: 3062844it [00:24, 128281.73it/s]
Compute damage for entire reference: 3075673it [00:24, 128214.43it/s]
Compute damage for entire reference: 3088568it [00:24, 128432.88it/s]
Compute damage for entire reference: 3101439it [00:24, 128511.21it/s]
Compute damage for entire reference: 3114291it [00:24, 127699.43it/s]
Compute damage for entire reference: 3127063it [00:24, 126939.76it/s]
Compute damage for entire reference: 3139847it [00:24, 127205.11it/s]
Compute damage for entire reference: 3152569it [00:24, 127181.99it/s]
Compute damage for entire reference: 3165800it [00:24, 128712.05it/s]
Compute damage for entire reference: 3178847it [00:25, 129235.26it/s]
Compute damage for entire reference: 3191772it [00:25, 129046.81it/s]
Compute damage for entire reference: 3194672it [00:25, 127102.91it/s]

Rescaling quality scores:   0%|                         | 0/230 [00:00<?, ?it/s]
Rescaling quality scores:   0%|                 | 1/230 [00:01<05:04,  1.33s/it]
Rescaling quality scores:   1%|▏                | 3/230 [00:01<01:33,  2.43it/s]
Rescaling quality scores:   3%|▌                | 7/230 [00:01<00:33,  6.72it/s]
Rescaling quality scores:   6%|▉               | 13/230 [00:01<00:15, 14.04it/s]
Rescaling quality scores:   8%|█▎              | 19/230 [00:02<00:24,  8.52it/s]
Rescaling quality scores:  14%|██▏             | 32/230 [00:03<00:14, 13.81it/s]
Rescaling quality scores:  15%|██▍             | 35/230 [00:04<00:27,  7.21it/s]
Rescaling quality scores:  17%|██▋             | 38/230 [00:06<00:43,  4.45it/s]
Rescaling quality scores:  17%|██▊             | 40/230 [00:07<00:45,  4.17it/s]
Rescaling quality scores:  18%|██▊             | 41/230 [00:07<00:55,  3.39it/s]
Rescaling quality scores:  20%|███▏            | 46/230 [00:08<00:34,  5.36it/s]
Rescaling quality scores:  21%|███▍            | 49/230 [00:09<00:43,  4.15it/s]
Rescaling quality scores:  23%|███▌            | 52/230 [00:09<00:36,  4.89it/s]
Rescaling quality scores:  23%|███▊            | 54/230 [00:09<00:34,  5.04it/s]
Rescaling quality scores:  29%|████▌           | 66/230 [00:10<00:13, 12.52it/s]
Rescaling quality scores:  30%|████▊           | 70/230 [00:10<00:12, 12.99it/s]
Rescaling quality scores:  32%|█████           | 73/230 [00:10<00:13, 11.28it/s]
Rescaling quality scores:  33%|█████▎          | 76/230 [00:11<00:15, 10.05it/s]
Rescaling quality scores:  37%|█████▊          | 84/230 [00:11<00:08, 16.71it/s]
Rescaling quality scores:  42%|██████▋         | 96/230 [00:12<00:10, 12.43it/s]
Rescaling quality scores:  44%|██████▌        | 101/230 [00:13<00:15,  8.52it/s]
Rescaling quality scores:  46%|██████▊        | 105/230 [00:14<00:16,  7.62it/s]
Rescaling quality scores:  47%|██████▉        | 107/230 [00:14<00:14,  8.28it/s]
Rescaling quality scores:  49%|███████▎       | 113/230 [00:15<00:14,  7.92it/s]
Rescaling quality scores:  50%|███████▌       | 115/230 [00:15<00:15,  7.52it/s]
Rescaling quality scores:  51%|███████▋       | 118/230 [00:15<00:12,  9.12it/s]
Rescaling quality scores:  54%|████████       | 124/230 [00:15<00:07, 13.73it/s]
Rescaling quality scores:  55%|████████▎      | 127/230 [00:16<00:09, 10.49it/s]
Rescaling quality scores:  57%|████████▍      | 130/230 [00:16<00:11,  8.91it/s]
Rescaling quality scores:  58%|████████▋      | 134/230 [00:17<00:10,  9.51it/s]
Rescaling quality scores:  59%|████████▊      | 136/230 [00:17<00:09, 10.20it/s]
Rescaling quality scores:  61%|█████████▏     | 141/230 [00:17<00:06, 12.91it/s]
Rescaling quality scores:  65%|█████████▋     | 149/230 [00:17<00:03, 21.35it/s]
Rescaling quality scores:  67%|█████████▉     | 153/230 [00:18<00:06, 12.08it/s]
Rescaling quality scores:  71%|██████████▋    | 163/230 [00:18<00:03, 20.68it/s]
Rescaling quality scores:  73%|██████████▉    | 168/230 [00:18<00:03, 20.30it/s]
Rescaling quality scores:  76%|███████████▍   | 175/230 [00:19<00:04, 13.50it/s]
Rescaling quality scores:  81%|████████████▏  | 186/230 [00:20<00:02, 18.87it/s]
Rescaling quality scores:  83%|████████████▍  | 190/230 [00:20<00:02, 16.52it/s]
Rescaling quality scores:  84%|████████████▌  | 193/230 [00:21<00:03, 11.21it/s]
Rescaling quality scores:  86%|████████████▊  | 197/230 [00:21<00:02, 12.40it/s]
Rescaling quality scores:  87%|████████████▉  | 199/230 [00:22<00:03,  7.84it/s]
Rescaling quality scores:  87%|█████████████  | 201/230 [00:22<00:03,  8.67it/s]
Rescaling quality scores:  91%|█████████████▋ | 210/230 [00:22<00:01, 10.63it/s]
Rescaling quality scores:  93%|█████████████▉ | 213/230 [00:23<00:02,  7.32it/s]
Rescaling quality scores:  96%|██████████████▎| 220/230 [00:24<00:01,  7.90it/s]
Rescaling quality scores:  97%|██████████████▍| 222/230 [00:25<00:01,  6.33it/s]
Rescaling quality scores:  97%|██████████████▌| 223/230 [00:26<00:01,  3.85it/s]
Rescaling quality scores:  98%|██████████████▋| 225/230 [00:26<00:01,  4.62it/s]
Rescaling quality scores:  99%|██████████████▊| 227/230 [00:27<00:00,  4.85it/s]
Rescaling quality scores: 100%|███████████████| 230/230 [00:27<00:00,  8.50it/s]
Estimating and testing Damage
Computing alignment stats for entire reference

Compute damage for entire reference: 0it [00:00, ?it/s]
Compute damage for entire reference: 12578it [00:00, 125754.34it/s]
Compute damage for entire reference: 25193it [00:00, 125980.59it/s]
Compute damage for entire reference: 37990it [00:00, 126881.25it/s]
Compute damage for entire reference: 50679it [00:00, 126451.43it/s]
Compute damage for entire reference: 63325it [00:00, 125647.47it/s]
Compute damage for entire reference: 75967it [00:00, 125903.50it/s]
Compute damage for entire reference: 88559it [00:00, 125554.17it/s]
Compute damage for entire reference: 101336it [00:00, 126254.78it/s]
Compute damage for entire reference: 113963it [00:00, 126139.23it/s]
Compute damage for entire reference: 126648it [00:01, 126355.94it/s]
Compute damage for entire reference: 139284it [00:01, 126275.65it/s]
Compute damage for entire reference: 151912it [00:01, 125810.93it/s]
Compute damage for entire reference: 164550it [00:01, 125977.62it/s]
Compute damage for entire reference: 177237it [00:01, 126244.47it/s]
Compute damage for entire reference: 189898it [00:01, 126352.12it/s]
Compute damage for entire reference: 202593it [00:01, 126528.89it/s]
Compute damage for entire reference: 215278it [00:01, 126623.03it/s]
Compute damage for entire reference: 228063it [00:01, 126989.96it/s]
Compute damage for entire reference: 240763it [00:01, 126653.98it/s]
Compute damage for entire reference: 253587it [00:02, 127126.15it/s]
Compute damage for entire reference: 266300it [00:02, 126720.52it/s]
Compute damage for entire reference: 278973it [00:02, 126463.38it/s]
Compute damage for entire reference: 291620it [00:02, 125891.57it/s]
Compute damage for entire reference: 304210it [00:02, 125594.79it/s]
Compute damage for entire reference: 316862it [00:02, 125867.88it/s]
Compute damage for entire reference: 329604it [00:02, 126326.94it/s]
Compute damage for entire reference: 342347it [00:02, 126654.98it/s]
Compute damage for entire reference: 355096it [00:02, 126901.59it/s]
Compute damage for entire reference: 367882it [00:02, 127186.39it/s]
Compute damage for entire reference: 380758it [00:03, 127654.21it/s]
Compute damage for entire reference: 393524it [00:03, 127361.68it/s]
Compute damage for entire reference: 406261it [00:03, 127272.55it/s]
Compute damage for entire reference: 418989it [00:03, 127222.60it/s]
Compute damage for entire reference: 431747it [00:03, 127326.40it/s]
Compute damage for entire reference: 444480it [00:03, 127192.94it/s]
Compute damage for entire reference: 457200it [00:03, 126733.52it/s]
Compute damage for entire reference: 469874it [00:03, 126469.79it/s]
Compute damage for entire reference: 482522it [00:03, 125364.84it/s]
Compute damage for entire reference: 495203it [00:03, 125791.33it/s]
Compute damage for entire reference: 507784it [00:04, 125675.27it/s]
Compute damage for entire reference: 520353it [00:04, 125633.84it/s]
Compute damage for entire reference: 532927it [00:04, 125662.92it/s]
Compute damage for entire reference: 545533it [00:04, 125778.08it/s]
Compute damage for entire reference: 558160it [00:04, 125921.63it/s]
Compute damage for entire reference: 570753it [00:04, 125754.41it/s]
Compute damage for entire reference: 583363it [00:04, 125855.95it/s]
Compute damage for entire reference: 596026it [00:04, 126083.66it/s]
Compute damage for entire reference: 608648it [00:04, 126123.38it/s]
Compute damage for entire reference: 621327it [00:04, 126320.11it/s]
Compute damage for entire reference: 633960it [00:05, 126048.18it/s]
Compute damage for entire reference: 646624it [00:05, 126224.62it/s]
Compute damage for entire reference: 659340it [00:05, 126501.56it/s]
Compute damage for entire reference: 672047it [00:05, 126668.07it/s]
Compute damage for entire reference: 684751it [00:05, 126776.71it/s]
Compute damage for entire reference: 697429it [00:05, 126401.82it/s]
Compute damage for entire reference: 710119it [00:05, 126546.88it/s]
Compute damage for entire reference: 722795it [00:05, 126608.57it/s]
Compute damage for entire reference: 735457it [00:05, 126226.90it/s]
Compute damage for entire reference: 748081it [00:05, 126132.63it/s]
Compute damage for entire reference: 760695it [00:06, 126035.61it/s]
Compute damage for entire reference: 773325it [00:06, 126113.51it/s]
Compute damage for entire reference: 786051it [00:06, 126454.30it/s]
Compute damage for entire reference: 798697it [00:06, 125465.60it/s]
Compute damage for entire reference: 811246it [00:06, 124712.76it/s]
Compute damage for entire reference: 823805it [00:06, 124970.40it/s]
Compute damage for entire reference: 836372it [00:06, 125174.68it/s]
Compute damage for entire reference: 848932it [00:06, 125298.19it/s]
Compute damage for entire reference: 861496it [00:06, 125399.12it/s]
Compute damage for entire reference: 874037it [00:06, 125232.85it/s]
Compute damage for entire reference: 886738it [00:07, 125763.12it/s]
Compute damage for entire reference: 899315it [00:07, 125725.09it/s]
Compute damage for entire reference: 911888it [00:07, 125591.68it/s]
Compute damage for entire reference: 924448it [00:07, 125590.35it/s]
Compute damage for entire reference: 937008it [00:07, 123708.11it/s]
Compute damage for entire reference: 949510it [00:07, 124093.62it/s]
Compute damage for entire reference: 961925it [00:07, 123994.13it/s]
Compute damage for entire reference: 974328it [00:07, 122523.31it/s]
Compute damage for entire reference: 986897it [00:07, 123459.63it/s]
Compute damage for entire reference: 999414it [00:07, 123965.79it/s]
Compute damage for entire reference: 1012009it [00:08, 124556.08it/s]
Compute damage for entire reference: 1024653it [00:08, 125116.82it/s]
Compute damage for entire reference: 1037267it [00:08, 125420.44it/s]
Compute damage for entire reference: 1049867it [00:08, 125591.72it/s]
Compute damage for entire reference: 1062470it [00:08, 125721.06it/s]
Compute damage for entire reference: 1075066it [00:08, 125789.64it/s]
Compute damage for entire reference: 1087646it [00:08, 125400.06it/s]
Compute damage for entire reference: 1100187it [00:08, 125122.20it/s]
Compute damage for entire reference: 1112700it [00:08, 124782.06it/s]
Compute damage for entire reference: 1125179it [00:08, 124733.39it/s]
Compute damage for entire reference: 1137653it [00:09, 124338.84it/s]
Compute damage for entire reference: 1150139it [00:09, 124488.75it/s]
Compute damage for entire reference: 1162618it [00:09, 124518.23it/s]
Compute damage for entire reference: 1175071it [00:09, 124093.14it/s]
Compute damage for entire reference: 1187509it [00:09, 124177.19it/s]
Compute damage for entire reference: 1199941it [00:09, 124218.97it/s]
Compute damage for entire reference: 1212364it [00:09, 124158.41it/s]
Compute damage for entire reference: 1224942it [00:09, 124641.10it/s]
Compute damage for entire reference: 1237620it [00:09, 125280.01it/s]
Compute damage for entire reference: 1250149it [00:09, 124986.51it/s]
Compute damage for entire reference: 1262648it [00:10, 124719.70it/s]
Compute damage for entire reference: 1275125it [00:10, 124730.51it/s]
Compute damage for entire reference: 1287682it [00:10, 124977.82it/s]
Compute damage for entire reference: 1300444it [00:10, 125767.20it/s]
Compute damage for entire reference: 1313021it [00:10, 125260.47it/s]
Compute damage for entire reference: 1325584it [00:10, 125368.91it/s]
Compute damage for entire reference: 1338185it [00:10, 125559.17it/s]
Compute damage for entire reference: 1350742it [00:10, 125312.38it/s]
Compute damage for entire reference: 1363274it [00:10, 125064.44it/s]
Compute damage for entire reference: 1375837it [00:10, 125230.83it/s]
Compute damage for entire reference: 1388389it [00:11, 125313.93it/s]
Compute damage for entire reference: 1401026it [00:11, 125628.39it/s]
Compute damage for entire reference: 1413590it [00:11, 125323.81it/s]
Compute damage for entire reference: 1426123it [00:11, 125075.04it/s]
Compute damage for entire reference: 1438793it [00:11, 125558.15it/s]
Compute damage for entire reference: 1451445it [00:11, 125844.03it/s]
Compute damage for entire reference: 1464106it [00:11, 126070.44it/s]
Compute damage for entire reference: 1476880it [00:11, 126568.70it/s]
Compute damage for entire reference: 1489538it [00:11, 126129.34it/s]
Compute damage for entire reference: 1502152it [00:11, 125710.43it/s]
Compute damage for entire reference: 1514778it [00:12, 125871.82it/s]
Compute damage for entire reference: 1527439it [00:12, 126089.20it/s]
Compute damage for entire reference: 1540049it [00:12, 125574.74it/s]
Compute damage for entire reference: 1552608it [00:12, 125064.32it/s]
Compute damage for entire reference: 1565236it [00:12, 125425.19it/s]
Compute damage for entire reference: 1577830it [00:12, 125577.85it/s]
Compute damage for entire reference: 1590525it [00:12, 125986.34it/s]
Compute damage for entire reference: 1603133it [00:12, 126011.00it/s]
Compute damage for entire reference: 1615735it [00:12, 125835.43it/s]
Compute damage for entire reference: 1628391it [00:12, 126051.23it/s]
Compute damage for entire reference: 1641074it [00:13, 126272.21it/s]
Compute damage for entire reference: 1653789it [00:13, 126533.85it/s]
Compute damage for entire reference: 1666443it [00:13, 126331.58it/s]
Compute damage for entire reference: 1679077it [00:13, 125581.95it/s]
Compute damage for entire reference: 1691668it [00:13, 125678.62it/s]
Compute damage for entire reference: 1704326it [00:13, 125945.19it/s]
Compute damage for entire reference: 1716936it [00:13, 125988.31it/s]
Compute damage for entire reference: 1729536it [00:13, 125602.50it/s]
Compute damage for entire reference: 1742097it [00:13, 125388.94it/s]
Compute damage for entire reference: 1754637it [00:13, 125270.60it/s]
Compute damage for entire reference: 1767165it [00:14, 125235.05it/s]
Compute damage for entire reference: 1779689it [00:14, 125178.87it/s]
Compute damage for entire reference: 1792207it [00:14, 125081.22it/s]
Compute damage for entire reference: 1804716it [00:14, 124682.39it/s]
Compute damage for entire reference: 1817350it [00:14, 125176.47it/s]
Compute damage for entire reference: 1829873it [00:14, 125189.22it/s]
Compute damage for entire reference: 1842393it [00:14, 125171.21it/s]
Compute damage for entire reference: 1854911it [00:14, 121382.36it/s]
Compute damage for entire reference: 1867507it [00:14, 122721.21it/s]
Compute damage for entire reference: 1880099it [00:14, 123662.69it/s]
Compute damage for entire reference: 1892755it [00:15, 124520.24it/s]
Compute damage for entire reference: 1905220it [00:15, 124267.70it/s]
Compute damage for entire reference: 1917656it [00:15, 124176.70it/s]
Compute damage for entire reference: 1930185it [00:15, 124507.25it/s]
Compute damage for entire reference: 1942712it [00:15, 124732.00it/s]
Compute damage for entire reference: 1955368it [00:15, 125277.56it/s]
Compute damage for entire reference: 1967899it [00:15, 125285.25it/s]
Compute damage for entire reference: 1980430it [00:15, 124481.73it/s]
Compute damage for entire reference: 1992929it [00:15, 124631.01it/s]
Compute damage for entire reference: 2005475it [00:15, 124874.51it/s]
Compute damage for entire reference: 2017982it [00:16, 124930.71it/s]
Compute damage for entire reference: 2030675it [00:16, 125527.85it/s]
Compute damage for entire reference: 2043355it [00:16, 125905.42it/s]
Compute damage for entire reference: 2055985it [00:16, 126022.36it/s]
Compute damage for entire reference: 2068683it [00:16, 126308.32it/s]
Compute damage for entire reference: 2081315it [00:16, 126271.78it/s]
Compute damage for entire reference: 2093943it [00:16, 126256.95it/s]
Compute damage for entire reference: 2106599it [00:16, 126345.51it/s]
Compute damage for entire reference: 2119234it [00:16, 126138.91it/s]
Compute damage for entire reference: 2131849it [00:16, 125723.00it/s]
Compute damage for entire reference: 2144422it [00:17, 125469.76it/s]
Compute damage for entire reference: 2156970it [00:17, 125229.78it/s]
Compute damage for entire reference: 2169494it [00:17, 125069.28it/s]
Compute damage for entire reference: 2182073it [00:17, 125281.87it/s]
Compute damage for entire reference: 2194602it [00:17, 125137.76it/s]
Compute damage for entire reference: 2207256it [00:17, 125554.13it/s]
Compute damage for entire reference: 2219834it [00:17, 125620.18it/s]
Compute damage for entire reference: 2232470it [00:17, 125838.10it/s]
Compute damage for entire reference: 2245054it [00:17, 125620.75it/s]
Compute damage for entire reference: 2257617it [00:17, 125365.79it/s]
Compute damage for entire reference: 2270154it [00:18, 124831.33it/s]
Compute damage for entire reference: 2282653it [00:18, 124874.91it/s]
Compute damage for entire reference: 2295272it [00:18, 125265.52it/s]
Compute damage for entire reference: 2307839it [00:18, 125382.93it/s]
Compute damage for entire reference: 2320542it [00:18, 125872.82it/s]
Compute damage for entire reference: 2333201it [00:18, 126084.05it/s]
Compute damage for entire reference: 2345810it [00:18, 125154.72it/s]
Compute damage for entire reference: 2358400it [00:18, 125373.84it/s]
Compute damage for entire reference: 2371074it [00:18, 125780.17it/s]
Compute damage for entire reference: 2383771it [00:18, 126133.25it/s]
Compute damage for entire reference: 2396386it [00:19, 125856.30it/s]
Compute damage for entire reference: 2409047it [00:19, 126079.79it/s]
Compute damage for entire reference: 2421656it [00:19, 126062.01it/s]
Compute damage for entire reference: 2434402it [00:19, 126477.26it/s]
Compute damage for entire reference: 2447051it [00:19, 126312.08it/s]
Compute damage for entire reference: 2459685it [00:19, 126316.87it/s]
Compute damage for entire reference: 2472317it [00:19, 126197.49it/s]
Compute damage for entire reference: 2485028it [00:19, 126468.60it/s]
Compute damage for entire reference: 2497720it [00:19, 126599.75it/s]
Compute damage for entire reference: 2510381it [00:19, 126097.55it/s]
Compute damage for entire reference: 2522992it [00:20, 125783.17it/s]
Compute damage for entire reference: 2535571it [00:20, 125567.99it/s]
Compute damage for entire reference: 2548294it [00:20, 126062.79it/s]
Compute damage for entire reference: 2560969it [00:20, 126266.24it/s]
Compute damage for entire reference: 2573619it [00:20, 126333.74it/s]
Compute damage for entire reference: 2586253it [00:20, 125903.38it/s]
Compute damage for entire reference: 2598844it [00:20, 125577.42it/s]
Compute damage for entire reference: 2611570it [00:20, 126078.22it/s]
Compute damage for entire reference: 2624179it [00:20, 126027.67it/s]
Compute damage for entire reference: 2636842it [00:20, 126206.45it/s]
Compute damage for entire reference: 2649464it [00:21, 126207.21it/s]
Compute damage for entire reference: 2662085it [00:21, 126165.81it/s]
Compute damage for entire reference: 2674877it [00:21, 126687.83it/s]
Compute damage for entire reference: 2687546it [00:21, 126654.75it/s]
Compute damage for entire reference: 2700258it [00:21, 126791.63it/s]
Compute damage for entire reference: 2712938it [00:21, 126242.22it/s]
Compute damage for entire reference: 2725607it [00:21, 126373.43it/s]
Compute damage for entire reference: 2738245it [00:21, 125626.41it/s]
Compute damage for entire reference: 2750818it [00:21, 125655.38it/s]
Compute damage for entire reference: 2763401it [00:21, 125705.79it/s]
Compute damage for entire reference: 2775973it [00:22, 125075.14it/s]
Compute damage for entire reference: 2788692it [00:22, 125703.96it/s]
Compute damage for entire reference: 2801397it [00:22, 126102.90it/s]
Compute damage for entire reference: 2814009it [00:22, 125908.68it/s]
Compute damage for entire reference: 2826629it [00:22, 125993.06it/s]
Compute damage for entire reference: 2839257it [00:22, 126076.11it/s]
Compute damage for entire reference: 2851865it [00:22, 125589.48it/s]
Compute damage for entire reference: 2864482it [00:22, 125760.15it/s]
Compute damage for entire reference: 2877059it [00:22, 125377.38it/s]
Compute damage for entire reference: 2889827it [00:22, 126061.12it/s]
Compute damage for entire reference: 2902700it [00:23, 126857.56it/s]
Compute damage for entire reference: 2915520it [00:23, 127254.98it/s]
Compute damage for entire reference: 2928247it [00:23, 127185.12it/s]
Compute damage for entire reference: 2940966it [00:23, 127008.27it/s]
Compute damage for entire reference: 2953668it [00:23, 126894.69it/s]
Compute damage for entire reference: 2966445it [00:23, 127152.98it/s]
Compute damage for entire reference: 2979211it [00:23, 127300.81it/s]
Compute damage for entire reference: 2991942it [00:23, 127072.07it/s]
Compute damage for entire reference: 3004650it [00:23, 126786.05it/s]
Compute damage for entire reference: 3017329it [00:24, 126647.73it/s]
Compute damage for entire reference: 3030322it [00:24, 127627.26it/s]
Compute damage for entire reference: 3043582it [00:24, 129112.79it/s]
Compute damage for entire reference: 3056763it [00:24, 129919.54it/s]
Compute damage for entire reference: 3069756it [00:24, 129078.34it/s]
Compute damage for entire reference: 3082666it [00:24, 128458.95it/s]
Compute damage for entire reference: 3095514it [00:24, 128096.18it/s]
Compute damage for entire reference: 3108325it [00:24, 127119.17it/s]
Compute damage for entire reference: 3121039it [00:24, 125987.77it/s]
Compute damage for entire reference: 3133641it [00:24, 125489.51it/s]
Compute damage for entire reference: 3146212it [00:25, 125553.55it/s]
Compute damage for entire reference: 3158848it [00:25, 125790.40it/s]
Compute damage for entire reference: 3171592it [00:25, 126279.98it/s]
Compute damage for entire reference: 3184221it [00:25, 125990.67it/s]
Compute damage for entire reference: 3194672it [00:25, 125798.28it/s]

Rescaling quality scores:   0%|                         | 0/230 [00:00<?, ?it/s]
Rescaling quality scores:   0%|                 | 1/230 [00:00<02:32,  1.50it/s]
Rescaling quality scores:   1%|▏                | 3/230 [00:00<00:54,  4.19it/s]
Rescaling quality scores:   3%|▌                | 7/230 [00:00<00:20, 10.67it/s]
Rescaling quality scores:   6%|▉               | 13/230 [00:01<00:10, 20.57it/s]
Rescaling quality scores:   8%|█▎              | 19/230 [00:01<00:10, 19.76it/s]
Rescaling quality scores:  14%|██▏             | 32/230 [00:01<00:08, 22.30it/s]
Rescaling quality scores:  15%|██▍             | 35/230 [00:02<00:11, 16.84it/s]
Rescaling quality scores:  17%|██▋             | 38/230 [00:03<00:25,  7.55it/s]
Rescaling quality scores:  17%|██▊             | 40/230 [00:05<00:45,  4.18it/s]
Rescaling quality scores:  18%|██▉             | 42/230 [00:06<00:48,  3.85it/s]
Rescaling quality scores:  20%|███▏            | 46/230 [00:06<00:34,  5.40it/s]
Rescaling quality scores:  21%|███▍            | 49/230 [00:06<00:36,  5.00it/s]
Rescaling quality scores:  23%|███▌            | 52/230 [00:08<00:47,  3.73it/s]
Rescaling quality scores:  23%|███▊            | 54/230 [00:08<00:48,  3.66it/s]
Rescaling quality scores:  29%|████▌           | 66/230 [00:08<00:17,  9.40it/s]
Rescaling quality scores:  31%|████▉           | 71/230 [00:10<00:22,  7.19it/s]
Rescaling quality scores:  33%|█████▏          | 75/230 [00:10<00:24,  6.38it/s]
Rescaling quality scores:  35%|█████▌          | 80/230 [00:11<00:17,  8.55it/s]
Rescaling quality scores:  40%|██████▍         | 93/230 [00:11<00:09, 14.52it/s]
Rescaling quality scores:  42%|██████▋         | 96/230 [00:11<00:08, 15.02it/s]
Rescaling quality scores:  44%|██████▌        | 101/230 [00:11<00:09, 14.15it/s]
Rescaling quality scores:  46%|██████▊        | 105/230 [00:12<00:11, 10.72it/s]
Rescaling quality scores:  49%|███████▎       | 112/230 [00:12<00:07, 15.32it/s]
Rescaling quality scores:  50%|███████▌       | 115/230 [00:14<00:21,  5.38it/s]
Rescaling quality scores:  51%|███████▋       | 118/230 [00:15<00:17,  6.48it/s]
Rescaling quality scores:  53%|███████▉       | 121/230 [00:15<00:15,  7.07it/s]
Rescaling quality scores:  54%|████████▏      | 125/230 [00:16<00:16,  6.40it/s]
Rescaling quality scores:  55%|████████▎      | 127/230 [00:16<00:16,  6.35it/s]
Rescaling quality scores:  56%|████████▍      | 129/230 [00:16<00:17,  5.88it/s]
Rescaling quality scores:  57%|████████▌      | 131/230 [00:17<00:14,  6.74it/s]
Rescaling quality scores:  58%|████████▋      | 134/230 [00:17<00:19,  4.91it/s]
Rescaling quality scores:  59%|████████▊      | 135/230 [00:18<00:18,  5.12it/s]
Rescaling quality scores:  61%|█████████▏     | 141/230 [00:18<00:12,  6.88it/s]
Rescaling quality scores:  65%|█████████▋     | 149/230 [00:18<00:06, 12.69it/s]
Rescaling quality scores:  67%|█████████▉     | 153/230 [00:20<00:11,  6.78it/s]
Rescaling quality scores:  71%|██████████▋    | 163/230 [00:20<00:05, 12.37it/s]
Rescaling quality scores:  73%|██████████▉    | 168/230 [00:21<00:07,  8.73it/s]
Rescaling quality scores:  76%|███████████▍   | 175/230 [00:22<00:07,  7.20it/s]
Rescaling quality scores:  81%|████████████▏  | 186/230 [00:23<00:04,  9.58it/s]
Rescaling quality scores:  82%|████████████▎  | 189/230 [00:23<00:04,  8.64it/s]
Rescaling quality scores:  83%|████████████▍  | 191/230 [00:25<00:07,  5.37it/s]
Rescaling quality scores:  86%|████████████▊  | 197/230 [00:25<00:05,  6.20it/s]
Rescaling quality scores:  87%|████████████▉  | 199/230 [00:26<00:04,  6.49it/s]
Rescaling quality scores:  87%|█████████████  | 201/230 [00:26<00:03,  7.25it/s]
Rescaling quality scores:  88%|█████████████▏ | 203/230 [00:26<00:04,  6.09it/s]
Rescaling quality scores:  91%|█████████████▋ | 210/230 [00:27<00:02,  7.46it/s]
Rescaling quality scores:  93%|█████████████▉ | 213/230 [00:28<00:02,  6.35it/s]
Rescaling quality scores:  96%|██████████████▎| 220/230 [00:29<00:01,  5.55it/s]
Rescaling quality scores:  96%|██████████████▍| 221/230 [00:29<00:01,  5.72it/s]
Rescaling quality scores:  97%|██████████████▌| 223/230 [00:30<00:01,  5.04it/s]
Rescaling quality scores:  98%|██████████████▋| 225/230 [00:30<00:00,  5.99it/s]
Rescaling quality scores:  99%|██████████████▊| 227/230 [00:30<00:00,  6.29it/s]
Rescaling quality scores: 100%|███████████████| 230/230 [00:30<00:00,  7.47it/s]
1min 13s ± 1.6 s per loop (mean ± std. dev. of 3 runs, 1 loop each)
[3]:
<TimeitResult : 1min 13s ± 1.6 s per loop (mean ± std. dev. of 3 runs, 1 loop each)>
[4]:
res = _
res_dict = {
    "pydamage v0.80" : {
        "mean" : res.average,
        "std" : res.stdev
    }
}
[5]:
%%timeit -r 3 -o
! pydamage analyze --rescale -p 8 --force ../../tests/data/bigger_test_data.bam

Estimating and testing Damage:   0%|                    | 0/230 [00:00<?, ?it/s]
Estimating and testing Damage:   0%|            | 1/230 [00:01<06:09,  1.61s/it]
Estimating and testing Damage:   2%|▏           | 4/230 [00:01<01:20,  2.81it/s]
Estimating and testing Damage:   7%|▋          | 15/230 [00:02<00:20, 10.45it/s]
Estimating and testing Damage:  10%|█▏         | 24/230 [00:02<00:15, 13.39it/s]
Estimating and testing Damage:  24%|██▋        | 55/230 [00:03<00:07, 24.93it/s]
Estimating and testing Damage:  26%|██▊        | 60/230 [00:04<00:11, 15.31it/s]
Estimating and testing Damage:  32%|███▌       | 74/230 [00:05<00:09, 15.65it/s]
Estimating and testing Damage:  51%|█████▏    | 118/230 [00:05<00:03, 30.90it/s]
Estimating and testing Damage:  53%|█████▎    | 123/230 [00:06<00:04, 25.59it/s]
Estimating and testing Damage:  61%|██████    | 140/230 [00:07<00:03, 27.34it/s]
Estimating and testing Damage:  65%|██████▍   | 149/230 [00:07<00:03, 24.72it/s]
Estimating and testing Damage:  78%|███████▊  | 180/230 [00:09<00:02, 17.04it/s]
Estimating and testing Damage:  90%|█████████ | 208/230 [00:10<00:00, 23.33it/s]
Estimating and testing Damage: 100%|██████████| 230/230 [00:10<00:00, 21.99it/s]
230 contig(s) analyzed by Pydamage

Rescaling quality scores:   0%|                         | 0/230 [00:00<?, ?it/s]
Rescaling quality scores:   0%|                 | 1/230 [00:00<01:54,  2.00it/s]
Rescaling quality scores:   1%|▏                | 3/230 [00:00<00:42,  5.30it/s]
Rescaling quality scores:   6%|▉               | 13/230 [00:00<00:09, 23.01it/s]
Rescaling quality scores:  10%|█▌              | 22/230 [00:01<00:07, 29.51it/s]
Rescaling quality scores:  14%|██▏             | 32/230 [00:02<00:12, 15.95it/s]
Rescaling quality scores:  15%|██▍             | 35/230 [00:02<00:16, 11.58it/s]
Rescaling quality scores:  17%|██▋             | 38/230 [00:03<00:23,  8.24it/s]
Rescaling quality scores:  17%|██▊             | 40/230 [00:04<00:31,  6.12it/s]
Rescaling quality scores:  18%|██▉             | 42/230 [00:06<01:10,  2.65it/s]
Rescaling quality scores:  20%|███▏            | 46/230 [00:07<00:48,  3.82it/s]
Rescaling quality scores:  21%|███▍            | 49/230 [00:07<00:39,  4.53it/s]
Rescaling quality scores:  23%|███▌            | 52/230 [00:07<00:33,  5.29it/s]
Rescaling quality scores:  23%|███▊            | 54/230 [00:08<00:32,  5.38it/s]
Rescaling quality scores:  25%|███▉            | 57/230 [00:08<00:27,  6.34it/s]
Rescaling quality scores:  30%|████▊           | 70/230 [00:08<00:09, 16.12it/s]
Rescaling quality scores:  32%|█████▏          | 74/230 [00:09<00:12, 12.10it/s]
Rescaling quality scores:  33%|█████▎          | 77/230 [00:09<00:12, 12.53it/s]
Rescaling quality scores:  37%|█████▉          | 86/230 [00:09<00:07, 20.30it/s]
Rescaling quality scores:  42%|██████▋         | 96/230 [00:09<00:04, 28.71it/s]
Rescaling quality scores:  44%|██████▌        | 101/230 [00:11<00:12, 10.13it/s]
Rescaling quality scores:  46%|██████▊        | 105/230 [00:12<00:16,  7.67it/s]
Rescaling quality scores:  48%|███████▏       | 111/230 [00:12<00:12,  9.52it/s]
Rescaling quality scores:  50%|███████▍       | 114/230 [00:12<00:12,  9.06it/s]
Rescaling quality scores:  50%|███████▌       | 116/230 [00:13<00:15,  7.13it/s]
Rescaling quality scores:  54%|████████       | 124/230 [00:13<00:08, 12.15it/s]
Rescaling quality scores:  56%|████████▎      | 128/230 [00:15<00:15,  6.58it/s]
Rescaling quality scores:  57%|████████▌      | 131/230 [00:15<00:16,  5.85it/s]
Rescaling quality scores:  58%|████████▋      | 134/230 [00:16<00:16,  5.86it/s]
Rescaling quality scores:  59%|████████▊      | 136/230 [00:16<00:17,  5.28it/s]
Rescaling quality scores:  61%|█████████▏     | 141/230 [00:17<00:11,  7.57it/s]
Rescaling quality scores:  65%|█████████▊     | 150/230 [00:17<00:05, 13.99it/s]
Rescaling quality scores:  67%|██████████     | 154/230 [00:18<00:10,  7.53it/s]
Rescaling quality scores:  73%|██████████▉    | 167/230 [00:18<00:05, 12.51it/s]
Rescaling quality scores:  76%|███████████▍   | 175/230 [00:19<00:03, 15.22it/s]
Rescaling quality scores:  77%|███████████▌   | 178/230 [00:19<00:04, 11.50it/s]
Rescaling quality scores:  81%|████████████▏  | 186/230 [00:20<00:02, 15.10it/s]
Rescaling quality scores:  82%|████████████▎  | 189/230 [00:20<00:02, 14.34it/s]
Rescaling quality scores:  83%|████████████▌  | 192/230 [00:20<00:02, 13.68it/s]
Rescaling quality scores:  86%|████████████▊  | 197/230 [00:20<00:02, 13.41it/s]
Rescaling quality scores:  87%|████████████▉  | 199/230 [00:21<00:03,  7.81it/s]
Rescaling quality scores:  90%|█████████████▍ | 206/230 [00:21<00:01, 12.50it/s]
Rescaling quality scores:  91%|█████████████▋ | 209/230 [00:22<00:01, 12.81it/s]
Rescaling quality scores:  92%|█████████████▊ | 212/230 [00:23<00:03,  5.51it/s]
Rescaling quality scores:  94%|██████████████ | 216/230 [00:24<00:02,  6.27it/s]
Rescaling quality scores:  96%|██████████████▎| 220/230 [00:25<00:01,  5.14it/s]
Rescaling quality scores:  97%|██████████████▍| 222/230 [00:25<00:01,  5.77it/s]
Rescaling quality scores:  97%|██████████████▌| 224/230 [00:26<00:01,  5.10it/s]
Rescaling quality scores:  98%|██████████████▋| 226/230 [00:26<00:00,  5.53it/s]
Rescaling quality scores: 100%|███████████████| 230/230 [00:27<00:00,  5.43it/s]
Rescaling quality scores: 100%|███████████████| 230/230 [00:27<00:00,  8.51it/s]

Estimating and testing Damage:   0%|                    | 0/230 [00:00<?, ?it/s]
Estimating and testing Damage:   0%|            | 1/230 [00:01<06:18,  1.65s/it]
Estimating and testing Damage:   1%|            | 2/230 [00:02<03:36,  1.05it/s]
Estimating and testing Damage:   3%|▎           | 7/230 [00:05<02:36,  1.43it/s]
Estimating and testing Damage:  37%|████       | 85/230 [00:05<00:06, 22.84it/s]
Estimating and testing Damage:  53%|█████▎    | 122/230 [00:06<00:03, 31.80it/s]
Estimating and testing Damage:  56%|█████▌    | 129/230 [00:08<00:05, 18.70it/s]
Estimating and testing Damage:  66%|██████▌   | 151/230 [00:08<00:03, 25.09it/s]
Estimating and testing Damage:  69%|██████▊   | 158/230 [00:09<00:04, 17.63it/s]
Estimating and testing Damage:  90%|█████████ | 207/230 [00:10<00:00, 31.24it/s]
Estimating and testing Damage: 100%|██████████| 230/230 [00:10<00:00, 22.61it/s]
230 contig(s) analyzed by Pydamage

Rescaling quality scores:   0%|                         | 0/230 [00:00<?, ?it/s]
Rescaling quality scores:   0%|                 | 1/230 [00:00<01:26,  2.65it/s]
Rescaling quality scores:   1%|▏                | 3/230 [00:00<00:35,  6.41it/s]
Rescaling quality scores:   6%|▉               | 13/230 [00:00<00:08, 25.70it/s]
Rescaling quality scores:  10%|█▌              | 22/230 [00:01<00:16, 12.84it/s]
Rescaling quality scores:  14%|██▏             | 32/230 [00:02<00:13, 14.96it/s]
Rescaling quality scores:  15%|██▍             | 35/230 [00:02<00:16, 12.09it/s]
Rescaling quality scores:  17%|██▋             | 38/230 [00:03<00:17, 11.11it/s]
Rescaling quality scores:  17%|██▊             | 40/230 [00:04<00:35,  5.29it/s]
Rescaling quality scores:  18%|██▊             | 41/230 [00:06<01:07,  2.79it/s]
Rescaling quality scores:  20%|███▏            | 46/230 [00:06<00:40,  4.50it/s]
Rescaling quality scores:  22%|███▌            | 51/230 [00:06<00:26,  6.65it/s]
Rescaling quality scores:  23%|███▊            | 54/230 [00:08<00:39,  4.50it/s]
Rescaling quality scores:  29%|████▌           | 66/230 [00:08<00:16, 10.02it/s]
Rescaling quality scores:  31%|████▉           | 71/230 [00:09<00:22,  6.95it/s]
Rescaling quality scores:  33%|█████▏          | 75/230 [00:09<00:18,  8.17it/s]
Rescaling quality scores:  35%|█████▌          | 80/230 [00:09<00:14, 10.71it/s]
Rescaling quality scores:  42%|██████▋         | 96/230 [00:10<00:06, 20.96it/s]
Rescaling quality scores:  44%|██████▌        | 101/230 [00:10<00:08, 15.17it/s]
Rescaling quality scores:  46%|██████▊        | 105/230 [00:11<00:07, 16.01it/s]
Rescaling quality scores:  48%|███████▏       | 111/230 [00:11<00:07, 16.15it/s]
Rescaling quality scores:  50%|███████▍       | 114/230 [00:12<00:16,  7.06it/s]
Rescaling quality scores:  50%|███████▌       | 116/230 [00:13<00:14,  7.62it/s]
Rescaling quality scores:  54%|████████       | 124/230 [00:13<00:08, 12.67it/s]
Rescaling quality scores:  56%|████████▎      | 128/230 [00:15<00:21,  4.80it/s]
Rescaling quality scores:  57%|████████▌      | 131/230 [00:16<00:22,  4.45it/s]
Rescaling quality scores:  58%|████████▋      | 134/230 [00:17<00:22,  4.24it/s]
Rescaling quality scores:  59%|████████▊      | 136/230 [00:17<00:20,  4.63it/s]
Rescaling quality scores:  61%|█████████▏     | 141/230 [00:18<00:14,  6.17it/s]
Rescaling quality scores:  65%|█████████▊     | 150/230 [00:18<00:06, 11.52it/s]
Rescaling quality scores:  67%|██████████     | 154/230 [00:19<00:11,  6.88it/s]
Rescaling quality scores:  73%|██████████▉    | 167/230 [00:20<00:06, 10.16it/s]
Rescaling quality scores:  76%|███████████▍   | 175/230 [00:20<00:04, 12.63it/s]
Rescaling quality scores:  81%|████████████▏  | 186/230 [00:21<00:03, 13.85it/s]
Rescaling quality scores:  82%|████████████▎  | 189/230 [00:21<00:04, 10.12it/s]
Rescaling quality scores:  83%|████████████▍  | 191/230 [00:22<00:04,  8.84it/s]
Rescaling quality scores:  86%|████████████▊  | 197/230 [00:22<00:02, 11.32it/s]
Rescaling quality scores:  87%|████████████▉  | 199/230 [00:22<00:02, 11.07it/s]
Rescaling quality scores:  90%|█████████████▍ | 206/230 [00:22<00:01, 16.49it/s]
Rescaling quality scores:  91%|█████████████▋ | 210/230 [00:23<00:02,  9.18it/s]
Rescaling quality scores:  96%|██████████████▎| 220/230 [00:26<00:01,  6.08it/s]
Rescaling quality scores:  97%|██████████████▌| 223/230 [00:26<00:01,  6.64it/s]
Rescaling quality scores:  98%|██████████████▋| 226/230 [00:26<00:00,  7.24it/s]
Rescaling quality scores: 100%|███████████████| 230/230 [00:26<00:00,  8.58it/s]

Estimating and testing Damage:   0%|                    | 0/230 [00:00<?, ?it/s]
Estimating and testing Damage:   0%|            | 1/230 [00:01<06:12,  1.63s/it]
Estimating and testing Damage:   1%|            | 2/230 [00:04<09:14,  2.43s/it]
Estimating and testing Damage:  32%|███▌       | 74/230 [00:06<00:10, 14.37it/s]
Estimating and testing Damage:  48%|████▊     | 111/230 [00:07<00:05, 21.94it/s]
Estimating and testing Damage:  54%|█████▍    | 124/230 [00:09<00:07, 14.66it/s]
Estimating and testing Damage:  80%|███████▉  | 183/230 [00:09<00:01, 29.52it/s]
Estimating and testing Damage:  85%|████████▍ | 195/230 [00:11<00:01, 19.94it/s]
Estimating and testing Damage: 100%|█████████▉| 229/230 [00:11<00:00, 29.16it/s]
Estimating and testing Damage: 100%|██████████| 230/230 [00:11<00:00, 19.49it/s]
230 contig(s) analyzed by Pydamage

Rescaling quality scores:   0%|                         | 0/230 [00:00<?, ?it/s]
Rescaling quality scores:   0%|                 | 1/230 [00:00<03:14,  1.18it/s]
Rescaling quality scores:   1%|▏                | 3/230 [00:01<01:03,  3.59it/s]
Rescaling quality scores:   6%|▉               | 13/230 [00:01<00:12, 17.44it/s]
Rescaling quality scores:  10%|█▌              | 22/230 [00:01<00:12, 17.18it/s]
Rescaling quality scores:  14%|██▏             | 32/230 [00:02<00:10, 19.24it/s]
Rescaling quality scores:  15%|██▍             | 35/230 [00:03<00:24,  7.85it/s]
Rescaling quality scores:  17%|██▋             | 38/230 [00:04<00:30,  6.37it/s]
Rescaling quality scores:  17%|██▊             | 40/230 [00:05<00:34,  5.58it/s]
Rescaling quality scores:  18%|██▊             | 41/230 [00:05<00:45,  4.19it/s]
Rescaling quality scores:  20%|███▏            | 46/230 [00:06<00:27,  6.63it/s]
Rescaling quality scores:  21%|███▍            | 49/230 [00:06<00:24,  7.48it/s]
Rescaling quality scores:  23%|███▌            | 52/230 [00:06<00:27,  6.42it/s]
Rescaling quality scores:  25%|███▉            | 57/230 [00:07<00:18,  9.51it/s]
Rescaling quality scores:  30%|████▊           | 70/230 [00:07<00:09, 17.43it/s]
Rescaling quality scores:  32%|█████           | 73/230 [00:07<00:09, 16.99it/s]
Rescaling quality scores:  33%|█████▎          | 76/230 [00:07<00:09, 16.66it/s]
Rescaling quality scores:  37%|█████▉          | 86/230 [00:07<00:05, 27.23it/s]
Rescaling quality scores:  42%|██████▋         | 96/230 [00:08<00:03, 36.15it/s]
Rescaling quality scores:  44%|██████▋        | 102/230 [00:08<00:05, 24.34it/s]
Rescaling quality scores:  46%|██████▉        | 106/230 [00:08<00:05, 22.70it/s]
Rescaling quality scores:  48%|███████▏       | 111/230 [00:08<00:05, 22.68it/s]
Rescaling quality scores:  50%|███████▍       | 114/230 [00:09<00:06, 16.84it/s]
Rescaling quality scores:  51%|███████▋       | 117/230 [00:09<00:07, 14.98it/s]
Rescaling quality scores:  54%|████████       | 124/230 [00:09<00:05, 18.27it/s]
Rescaling quality scores:  55%|████████▎      | 127/230 [00:10<00:11,  8.84it/s]
Rescaling quality scores:  56%|████████▍      | 129/230 [00:11<00:11,  9.05it/s]
Rescaling quality scores:  57%|████████▌      | 131/230 [00:11<00:09, 10.03it/s]
Rescaling quality scores:  58%|████████▋      | 134/230 [00:11<00:12,  7.52it/s]
Rescaling quality scores:  60%|█████████      | 139/230 [00:12<00:08, 11.31it/s]
Rescaling quality scores:  62%|█████████▎     | 142/230 [00:12<00:07, 11.82it/s]
Rescaling quality scores:  67%|█████████▉     | 153/230 [00:13<00:06, 11.87it/s]
Rescaling quality scores:  73%|██████████▉    | 167/230 [00:13<00:03, 17.34it/s]
Rescaling quality scores:  76%|███████████▍   | 175/230 [00:14<00:03, 17.39it/s]
Rescaling quality scores:  81%|████████████▏  | 186/230 [00:14<00:02, 17.80it/s]
Rescaling quality scores:  82%|████████████▎  | 188/230 [00:15<00:03, 13.95it/s]
Rescaling quality scores:  83%|████████████▍  | 191/230 [00:15<00:03, 11.32it/s]
Rescaling quality scores:  86%|████████████▊  | 197/230 [00:15<00:02, 13.97it/s]
Rescaling quality scores:  87%|████████████▉  | 199/230 [00:16<00:02, 13.72it/s]
Rescaling quality scores:  90%|█████████████▍ | 206/230 [00:16<00:01, 19.90it/s]
Rescaling quality scores:  91%|█████████████▋ | 210/230 [00:17<00:01, 10.23it/s]
Rescaling quality scores:  94%|██████████████ | 216/230 [00:17<00:01, 13.17it/s]
Rescaling quality scores:  96%|██████████████▎| 220/230 [00:18<00:01,  7.69it/s]
Rescaling quality scores:  97%|██████████████▍| 222/230 [00:18<00:01,  7.25it/s]
Rescaling quality scores:  97%|██████████████▌| 224/230 [00:19<00:01,  5.30it/s]
Rescaling quality scores:  98%|██████████████▋| 226/230 [00:20<00:00,  4.62it/s]
Rescaling quality scores: 100%|███████████████| 230/230 [00:20<00:00, 11.25it/s]

Estimating and testing Damage:   0%|                    | 0/230 [00:00<?, ?it/s]
Estimating and testing Damage:   0%|            | 1/230 [00:02<07:59,  2.09s/it]
Estimating and testing Damage:   3%|▎           | 6/230 [00:04<02:22,  1.57it/s]
Estimating and testing Damage:   4%|▍           | 9/230 [00:04<01:24,  2.63it/s]
Estimating and testing Damage:  21%|██▎        | 48/230 [00:05<00:10, 17.26it/s]
Estimating and testing Damage:  23%|██▍        | 52/230 [00:07<00:20,  8.70it/s]
Estimating and testing Damage:  41%|████▌      | 95/230 [00:08<00:08, 16.26it/s]
Estimating and testing Damage:  60%|█████▉    | 137/230 [00:08<00:03, 29.67it/s]
Estimating and testing Damage:  67%|██████▋   | 154/230 [00:08<00:02, 35.27it/s]
Estimating and testing Damage:  79%|███████▉  | 182/230 [00:09<00:01, 31.36it/s]
Estimating and testing Damage:  88%|████████▊ | 203/230 [00:10<00:00, 34.89it/s]
Estimating and testing Damage:  98%|█████████▊| 225/230 [00:10<00:00, 41.79it/s]
Estimating and testing Damage: 100%|██████████| 230/230 [00:11<00:00, 20.08it/s]
230 contig(s) analyzed by Pydamage

Rescaling quality scores:   0%|                         | 0/230 [00:00<?, ?it/s]
Rescaling quality scores:   0%|                 | 1/230 [00:00<01:30,  2.53it/s]
Rescaling quality scores:   1%|▏                | 3/230 [00:00<00:39,  5.76it/s]
Rescaling quality scores:   3%|▍                | 6/230 [00:00<00:20, 11.17it/s]
Rescaling quality scores:   6%|▉               | 13/230 [00:00<00:08, 24.88it/s]
Rescaling quality scores:  10%|█▌              | 22/230 [00:00<00:05, 39.32it/s]
Rescaling quality scores:  14%|██▏             | 32/230 [00:01<00:06, 30.95it/s]
Rescaling quality scores:  16%|██▌             | 37/230 [00:01<00:10, 18.06it/s]
Rescaling quality scores:  18%|██▊             | 41/230 [00:04<00:32,  5.90it/s]
Rescaling quality scores:  20%|███▏            | 46/230 [00:04<00:23,  7.76it/s]
Rescaling quality scores:  21%|███▍            | 49/230 [00:05<00:31,  5.69it/s]
Rescaling quality scores:  23%|███▌            | 52/230 [00:05<00:28,  6.34it/s]
Rescaling quality scores:  23%|███▊            | 54/230 [00:06<00:27,  6.48it/s]
Rescaling quality scores:  25%|███▉            | 57/230 [00:06<00:23,  7.47it/s]
Rescaling quality scores:  30%|████▊           | 70/230 [00:06<00:09, 17.44it/s]
Rescaling quality scores:  32%|█████▏          | 74/230 [00:06<00:10, 15.20it/s]
Rescaling quality scores:  33%|█████▎          | 77/230 [00:07<00:10, 14.70it/s]
Rescaling quality scores:  37%|█████▉          | 86/230 [00:07<00:06, 23.24it/s]
Rescaling quality scores:  42%|██████▋         | 96/230 [00:07<00:04, 32.13it/s]
Rescaling quality scores:  44%|██████▋        | 102/230 [00:08<00:07, 16.52it/s]
Rescaling quality scores:  46%|██████▉        | 106/230 [00:08<00:07, 16.51it/s]
Rescaling quality scores:  48%|███████▏       | 111/230 [00:09<00:11, 10.80it/s]
Rescaling quality scores:  50%|███████▍       | 114/230 [00:10<00:16,  7.03it/s]
Rescaling quality scores:  50%|███████▌       | 116/230 [00:10<00:15,  7.28it/s]
Rescaling quality scores:  54%|████████       | 124/230 [00:10<00:08, 12.45it/s]
Rescaling quality scores:  56%|████████▎      | 128/230 [00:11<00:09, 11.06it/s]
Rescaling quality scores:  57%|████████▌      | 131/230 [00:11<00:09, 10.67it/s]
Rescaling quality scores:  58%|████████▋      | 134/230 [00:11<00:09, 10.42it/s]
Rescaling quality scores:  60%|█████████      | 139/230 [00:11<00:06, 14.16it/s]
Rescaling quality scores:  62%|█████████▎     | 142/230 [00:12<00:06, 13.80it/s]
Rescaling quality scores:  66%|█████████▉     | 152/230 [00:12<00:03, 22.62it/s]
Rescaling quality scores:  68%|██████████▏    | 156/230 [00:13<00:07,  9.64it/s]
Rescaling quality scores:  73%|██████████▉    | 167/230 [00:13<00:04, 13.95it/s]
Rescaling quality scores:  76%|███████████▍   | 175/230 [00:15<00:05, 10.42it/s]
Rescaling quality scores:  81%|████████████▏  | 186/230 [00:15<00:03, 11.83it/s]
Rescaling quality scores:  82%|████████████▎  | 188/230 [00:16<00:05,  8.34it/s]
Rescaling quality scores:  83%|████████████▍  | 191/230 [00:17<00:06,  6.35it/s]
Rescaling quality scores:  86%|████████████▊  | 197/230 [00:18<00:04,  7.70it/s]
Rescaling quality scores:  87%|████████████▉  | 199/230 [00:19<00:05,  5.52it/s]
Rescaling quality scores:  90%|█████████████▍ | 206/230 [00:19<00:02,  8.68it/s]
Rescaling quality scores:  91%|█████████████▋ | 210/230 [00:20<00:02,  7.78it/s]
Rescaling quality scores:  96%|██████████████▎| 220/230 [00:22<00:01,  6.14it/s]
Rescaling quality scores:  97%|██████████████▍| 222/230 [00:22<00:01,  5.88it/s]
Rescaling quality scores:  97%|██████████████▌| 224/230 [00:22<00:01,  5.72it/s]
Rescaling quality scores:  98%|██████████████▋| 226/230 [00:23<00:00,  5.26it/s]
Rescaling quality scores: 100%|███████████████| 230/230 [00:23<00:00,  9.77it/s]
43.4 s ± 1.43 s per loop (mean ± std. dev. of 3 runs, 1 loop each)
[5]:
<TimeitResult : 43.4 s ± 1.43 s per loop (mean ± std. dev. of 3 runs, 1 loop each)>
[6]:
res = _
res_dict["pydamage v0.80 - parallel"] = {
    "mean" : res.average,
    "std" : res.stdev
}
[7]:
! mapDamage --version
2.2.2
[8]:
%%timeit -r 3 -o
! mapDamage -i ../../tests/data/bigger_test_data.bam -r ../../tests/data/ref_genome.fa --rescale
Warning, results_bigger_test_data already exists
Started with the command: /home/maxime_borry/miniforge3/envs/pydamage_bench/bin/mapDamage -i ../../tests/data/bigger_test_data.bam -r ../../tests/data/ref_genome.fa --rescale
        Reading from '../../tests/data/bigger_test_data.bam'
        Writing results to 'results_bigger_test_data/'
pdf results_bigger_test_data/Fragmisincorporation_plot.pdf generated
additional results_bigger_test_data/Length_plot.pdf generated
Performing Bayesian estimates
Starting grid search, starting from random values
Adjusting the proposal variance iteration  1
Adjusting the proposal variance iteration  2
Adjusting the proposal variance iteration  3
Adjusting the proposal variance iteration  4
Adjusting the proposal variance iteration  5
Adjusting the proposal variance iteration  6
Adjusting the proposal variance iteration  7
Adjusting the proposal variance iteration  8
Adjusting the proposal variance iteration  9
Adjusting the proposal variance iteration  10
Done burning, starting the iterations
Done with the iterations, finishing up
Writing and plotting to files
Rescaling BAM: '../../tests/data/bigger_test_data.bam' -> 'results_bigger_test_data/bigger_test_data.rescaled.bam'
Warning! Assuming the pairs are non-overlapping, facing inwards and correctly paired.
Number of non-rescaled reads due to improper pairing:  845319
        The expected substition frequencies before and after scaling using the scaled qualities as probalities:
        CT      0.022074949825252405            0.012365374164447053
        TC      0.006143060440522095            0.006143060440522095
        GA      0.022384267009500677            0.012317144729004435
        AG      0.006157675379772034            0.006157675379772034
        Quality metrics before and after scaling
        CT-Q0   541379          541379
        CT-Q10  541379          259309
        CT-Q20  533542          255363
        CT-Q30  529743          253189
        CT-Q40  0               0
        GA-Q0   559491          559491
        GA-Q10  559491          262017
        GA-Q20  548446          257032
        GA-Q30  543260          254466
        GA-Q40  0               0
Successful run
Warning, results_bigger_test_data already exists
Started with the command: /home/maxime_borry/miniforge3/envs/pydamage_bench/bin/mapDamage -i ../../tests/data/bigger_test_data.bam -r ../../tests/data/ref_genome.fa --rescale
        Reading from '../../tests/data/bigger_test_data.bam'
        Writing results to 'results_bigger_test_data/'
pdf results_bigger_test_data/Fragmisincorporation_plot.pdf generated
additional results_bigger_test_data/Length_plot.pdf generated
Performing Bayesian estimates
Starting grid search, starting from random values
Adjusting the proposal variance iteration  1
Adjusting the proposal variance iteration  2
Adjusting the proposal variance iteration  3
Adjusting the proposal variance iteration  4
Adjusting the proposal variance iteration  5
Adjusting the proposal variance iteration  6
Adjusting the proposal variance iteration  7
Adjusting the proposal variance iteration  8
Adjusting the proposal variance iteration  9
Adjusting the proposal variance iteration  10
Done burning, starting the iterations
Done with the iterations, finishing up
Writing and plotting to files
Rescaling BAM: '../../tests/data/bigger_test_data.bam' -> 'results_bigger_test_data/bigger_test_data.rescaled.bam'
Warning! Assuming the pairs are non-overlapping, facing inwards and correctly paired.
Number of non-rescaled reads due to improper pairing:  845319
        The expected substition frequencies before and after scaling using the scaled qualities as probalities:
        CT      0.022074949825252405            0.012365282422660039
        TC      0.006143060440522095            0.006143060440522095
        GA      0.022384267009500677            0.012317048861071829
        AG      0.006157675379772034            0.006157675379772034
        Quality metrics before and after scaling
        CT-Q0   541379          541379
        CT-Q10  541379          259309
        CT-Q20  533542          255363
        CT-Q30  529743          253189
        CT-Q40  0               0
        GA-Q0   559491          559491
        GA-Q10  559491          262017
        GA-Q20  548446          257032
        GA-Q30  543260          254466
        GA-Q40  0               0
Successful run
Warning, results_bigger_test_data already exists
Started with the command: /home/maxime_borry/miniforge3/envs/pydamage_bench/bin/mapDamage -i ../../tests/data/bigger_test_data.bam -r ../../tests/data/ref_genome.fa --rescale
        Reading from '../../tests/data/bigger_test_data.bam'
        Writing results to 'results_bigger_test_data/'
pdf results_bigger_test_data/Fragmisincorporation_plot.pdf generated
additional results_bigger_test_data/Length_plot.pdf generated
Performing Bayesian estimates
Starting grid search, starting from random values
Adjusting the proposal variance iteration  1
Adjusting the proposal variance iteration  2
Adjusting the proposal variance iteration  3
Adjusting the proposal variance iteration  4
Adjusting the proposal variance iteration  5
Adjusting the proposal variance iteration  6
Adjusting the proposal variance iteration  7
Adjusting the proposal variance iteration  8
Adjusting the proposal variance iteration  9
Adjusting the proposal variance iteration  10
Done burning, starting the iterations
Done with the iterations, finishing up
Writing and plotting to files
Rescaling BAM: '../../tests/data/bigger_test_data.bam' -> 'results_bigger_test_data/bigger_test_data.rescaled.bam'
Warning! Assuming the pairs are non-overlapping, facing inwards and correctly paired.
Number of non-rescaled reads due to improper pairing:  845319
        The expected substition frequencies before and after scaling using the scaled qualities as probalities:
        CT      0.022074949825252405            0.012365388851336931
        TC      0.006143060440522095            0.006143060440522095
        GA      0.022384267009500677            0.012317157513671044
        AG      0.006157675379772034            0.006157675379772034
        Quality metrics before and after scaling
        CT-Q0   541379          541379
        CT-Q10  541379          259309
        CT-Q20  533542          255363
        CT-Q30  529743          253189
        CT-Q40  0               0
        GA-Q0   559491          559491
        GA-Q10  559491          262017
        GA-Q20  548446          257032
        GA-Q30  543260          254466
        GA-Q40  0               0
Successful run
Warning, results_bigger_test_data already exists
Started with the command: /home/maxime_borry/miniforge3/envs/pydamage_bench/bin/mapDamage -i ../../tests/data/bigger_test_data.bam -r ../../tests/data/ref_genome.fa --rescale
        Reading from '../../tests/data/bigger_test_data.bam'
        Writing results to 'results_bigger_test_data/'
pdf results_bigger_test_data/Fragmisincorporation_plot.pdf generated
additional results_bigger_test_data/Length_plot.pdf generated
Performing Bayesian estimates
Starting grid search, starting from random values
Adjusting the proposal variance iteration  1
Adjusting the proposal variance iteration  2
Adjusting the proposal variance iteration  3
Adjusting the proposal variance iteration  4
Adjusting the proposal variance iteration  5
Adjusting the proposal variance iteration  6
Adjusting the proposal variance iteration  7
Adjusting the proposal variance iteration  8
Adjusting the proposal variance iteration  9
Adjusting the proposal variance iteration  10
Done burning, starting the iterations
Done with the iterations, finishing up
Writing and plotting to files
Rescaling BAM: '../../tests/data/bigger_test_data.bam' -> 'results_bigger_test_data/bigger_test_data.rescaled.bam'
Warning! Assuming the pairs are non-overlapping, facing inwards and correctly paired.
Number of non-rescaled reads due to improper pairing:  845319
        The expected substition frequencies before and after scaling using the scaled qualities as probalities:
        CT      0.022074949825252405            0.012365272201902557
        TC      0.006143060440522095            0.006143060440522095
        GA      0.022384267009500677            0.012317043166668018
        AG      0.006157675379772034            0.006157675379772034
        Quality metrics before and after scaling
        CT-Q0   541379          541379
        CT-Q10  541379          259309
        CT-Q20  533542          255363
        CT-Q30  529743          253189
        CT-Q40  0               0
        GA-Q0   559491          559491
        GA-Q10  559491          262017
        GA-Q20  548446          257032
        GA-Q30  543260          254466
        GA-Q40  0               0
Successful run
10min 53s ± 4.72 s per loop (mean ± std. dev. of 3 runs, 1 loop each)
[8]:
<TimeitResult : 10min 53s ± 4.72 s per loop (mean ± std. dev. of 3 runs, 1 loop each)>
[9]:
res = _
res_dict["mapDamage v2.2.2"] = {
    "mean" : res.average,
    "std" : res.stdev
}
[10]:
runtimes = pd.DataFrame.from_dict(res_dict, orient="index")
[11]:
ggplot(runtimes, aes(x = runtimes.index, y = "mean")) + geom_point() + geom_errorbar(aes(ymin = "mean - std", ymax = "mean + std")) + theme_classic() + ylab("Time (s)") + xlab("Tool")
_images/rescaling_12_0.png

PyDamage provides a 10-15x speedup over mapDamage for the same dataset for damage rescaling.

[12]:
def get_phred_scores(bam):
    fwd = []
    rev = []
    with pysam.AlignmentFile(bam, "rb") as bam:
        for read in bam:
            if not read.is_reverse:
                fwd.append(np.array(read.query_qualities)[:13])
            else:
                rev.append(np.array(read.query_qualities)[::-1][:13])
            # quals.append(np.array(read.query_qualities)[:13])
            # quals.append(np.array(read.get_forward_qualities())[:20])
    return (np.stack(fwd), np.stack(rev))
[13]:
original_fwd, original_rev = get_phred_scores("../../tests/data/bigger_test_data.bam")
[14]:
pydamage_fwd, pydamage_rev = get_phred_scores("pydamage_results/pydamage_rescaled.bam")
[15]:
mapdamage_fwd, mapdamage_rev = get_phred_scores("results_bigger_test_data/bigger_test_data.rescaled.bam")
[16]:
columns = ['original', 'mapdamage v2.2.2', 'pydamage v0.80']
[17]:
df_fwd = (
    pd.DataFrame(
        [original_fwd.mean(axis=0), mapdamage_fwd.mean(axis=0), pydamage_fwd.mean(axis=0)],
    )
    .transpose()
    .set_axis(columns, axis=1)
    .rename_axis("position")
    .reset_index()
    .melt(id_vars = "position", var_name = "bam", value_name = "mean")
).merge(
    (
        pd.DataFrame(
        [original_fwd.std(axis=0), mapdamage_fwd.std(axis=0), pydamage_fwd.std(axis=0)],
    )
    .transpose()
    .set_axis(columns, axis=1)
    .rename_axis("position")
    .reset_index()
    .melt(id_vars = "position", var_name = "bam", value_name = "std")
    ), on=['position', 'bam']
)
[18]:
(ggplot(df_fwd, aes(x='position', y='mean', color='bam')) + geom_point() + geom_errorbar(aes(ymin = "mean - std", ymax = "mean + std")) + theme_classic() + ylab("Mean Phred score") + xlab("Position"))
_images/rescaling_20_0.png
[19]:
df_rev = (
    pd.DataFrame(
        [original_rev.mean(axis=0), mapdamage_rev.mean(axis=0), pydamage_rev.mean(axis=0)],
    )
    .transpose()
    .set_axis(columns, axis=1)
    .rename_axis("position")
    .reset_index()
    .melt(id_vars = "position", var_name = "bam", value_name = "mean")
).merge(
    (
        pd.DataFrame(
        [original_rev.std(axis=0), mapdamage_rev.std(axis=0), pydamage_rev.std(axis=0)],
    )
    .transpose()
    .set_axis(columns, axis=1)
    .rename_axis("position")
    .reset_index()
    .melt(id_vars = "position", var_name = "bam", value_name = "std")
    ), on=['position', 'bam']
)
(ggplot(df_rev, aes(x='position', y='mean', color='bam')) + geom_point() + geom_errorbar(aes(ymin = "mean - std", ymax = "mean + std")) + theme_classic() + ylab("Mean Phred score") + xlab("Position"))
_images/rescaling_21_0.png

mapDamage and PyDamage produce very similar results with regards to reads base quality rescaling