[W::hts_idx_load3] The index file is older than the data file: 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[mpileup] 1 samples in 1 input files
loading BEDs...
[W::hts_idx_load3] The index file is older than the data file: 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
/opt/conda/lib/python3.9/site-packages/pyranges/__init__.py:8: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
import pkg_resources
/opt/conda/lib/python3.9/site-packages/pyranges/__init__.py:8: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
import pkg_resources
[W::hts_idx_load3] The index file is older than the data file: 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
0it [00:00, ?it/s]
147870it [00:00, 1478493.43it/s]
314262it [00:00, 1587526.88it/s]
482916it [00:00, 1632708.67it/s]
651144it [00:00, 1652247.68it/s]
819888it [00:00, 1664719.44it/s]
989598it [00:00, 1675705.10it/s]
1162084it [00:00, 1691609.39it/s]
1331245it [00:00, 1686687.00it/s]
1499917it [00:00, 1686374.19it/s]
1671656it [00:01, 1695918.62it/s]
1842980it [00:01, 1701197.16it/s]
2015109it [00:01, 1707275.69it/s]
2185839it [00:01, 1678784.68it/s]
2355877it [00:01, 1685212.34it/s]
2524480it [00:01, 1684962.53it/s]
2693033it [00:01, 1679782.20it/s]
2861052it [00:01, 1643465.26it/s]
3025580it [00:01, 1634040.13it/s]
3189106it [00:01, 1625336.17it/s]
3356028it [00:02, 1638052.19it/s]
3519911it [00:02, 1577297.66it/s]
3678122it [00:02, 1563164.58it/s]
3844217it [00:02, 1591469.30it/s]
4015725it [00:02, 1627723.09it/s]
4186196it [00:02, 1650346.54it/s]
4358678it [00:02, 1672427.44it/s]
4527620it [00:02, 1677471.09it/s]
4695510it [00:02, 1667803.38it/s]
4865028it [00:02, 1675901.29it/s]
5032701it [00:03, 1647778.35it/s]
5197629it [00:03, 1563560.44it/s]
5356207it [00:03, 1569870.06it/s]
5516827it [00:03, 1580385.99it/s]
5675368it [00:03, 1553684.25it/s]
5835417it [00:03, 1567225.95it/s]
5992460it [00:03, 1563894.32it/s]
6160620it [00:03, 1598606.48it/s]
6325915it [00:03, 1614705.22it/s]
6492204it [00:03, 1628871.25it/s]
6655220it [00:04, 1622531.70it/s]
6817566it [00:04, 1587462.02it/s]
6983524it [00:04, 1608643.36it/s]
7152227it [00:04, 1631709.32it/s]
7320170it [00:04, 1645780.84it/s]
7484880it [00:04, 1639628.96it/s]
7649638it [00:04, 1641979.92it/s]
7813904it [00:04, 1551129.84it/s]
7976321it [00:04, 1572082.81it/s]
8138035it [00:04, 1585171.93it/s]
8298612it [00:05, 1591088.83it/s]
8468376it [00:05, 1622551.42it/s]
8630995it [00:05, 1603365.69it/s]
8801296it [00:05, 1632627.50it/s]
8966140it [00:05, 1637297.36it/s]
9133518it [00:05, 1648138.71it/s]
9298468it [00:05, 1635527.15it/s]
9462132it [00:05, 1518722.44it/s]
9615678it [00:05, 1460713.37it/s]
9763148it [00:06, 1458155.00it/s]
9909927it [00:06, 1458538.55it/s]
10076823it [00:06, 1519213.17it/s]
10245895it [00:06, 1569175.29it/s]
10418268it [00:06, 1614629.47it/s]
10589462it [00:06, 1643397.50it/s]done loading BEDs.
10757891it [00:06, 1655456.62it/s]
10927000it [00:06, 1666056.99it/s]
11096143it [00:06, 1673617.68it/s]
11265837it [00:06, 1680484.87it/s]
11435052it [00:07, 1683928.48it/s]
11605353it [00:07, 1689626.85it/s]
11776525it [00:07, 1696225.58it/s]
11949647it [00:07, 1706694.82it/s]
12122149it [00:07, 1712172.44it/s]
12296508it [00:07, 1721559.72it/s]
12470480it [00:07, 1726975.73it/s]
12645484it [00:07, 1733880.27it/s]
12818880it [00:07, 1724853.22it/s]
12991382it [00:07, 1720351.99it/s]
13165007it [00:08, 1725083.26it/s]
13337527it [00:08, 1722576.30it/s]
13509793it [00:08, 1719843.01it/s]
13681783it [00:08, 1716275.93it/s]
13853438it [00:08, 1716339.98it/s]
14025076it [00:08, 1712704.39it/s]
14196350it [00:08, 1707173.55it/s]
14367072it [00:08, 1704562.99it/s]
14537532it [00:08, 1697484.38it/s]
14707287it [00:08, 1689828.15it/s]
14876371it [00:09, 1690115.56it/s]
15046477it [00:09, 1693261.99it/s]
15216020it [00:09, 1693892.39it/s]
15387756it [00:09, 1700899.30it/s]
15557851it [00:09, 1686438.60it/s]
15727978it [00:09, 1690837.10it/s]
15899462it [00:09, 1697982.53it/s]
16070298it [00:09, 1701066.95it/s]
16242011it [00:09, 1705730.66it/s]
16412596it [00:09, 1702297.01it/s]
16582835it [00:10, 1700801.50it/s]
16752922it [00:10, 1698412.33it/s]
16922901it [00:10, 1698778.93it/s]
17092783it [00:10, 1698152.86it/s]
17262601it [00:10, 1691388.09it/s]
17432782it [00:10, 1694487.15it/s]
17602743it [00:10, 1696003.31it/s]
17775630it [00:10, 1705830.04it/s]
17950016it [00:10, 1717209.22it/s]
18121743it [00:10, 1703453.72it/s]
18292139it [00:11, 1703438.05it/s]
18463126it [00:11, 1705217.40it/s]
18633663it [00:11, 1704421.39it/s]
18804456it [00:11, 1705446.19it/s]
18975483it [00:11, 1706876.55it/s]
19146176it [00:11, 1706035.10it/s]
19316784it [00:11, 1672733.02it/s]
19484202it [00:11, 1620982.43it/s]
19656405it [00:11, 1650306.75it/s]
19827558it [00:11, 1668241.13it/s]
19996758it [00:12, 1675238.41it/s]
20164504it [00:12, 1669708.16it/s]
20335471it [00:12, 1681554.57it/s]
20503747it [00:12, 1668751.21it/s]
20670720it [00:12, 1668722.18it/s]
20846018it [00:12, 1693700.50it/s]
21018273it [00:12, 1702270.46it/s]
21192984it [00:12, 1715526.32it/s]
21367330it [00:12, 1723868.16it/s]
21541824it [00:12, 1730162.08it/s]
21714863it [00:13, 1726411.74it/s]
21888986it [00:13, 1730829.37it/s]
22062644it [00:13, 1732534.72it/s]
22237127it [00:13, 1736200.65it/s]
22410755it [00:13, 1735433.69it/s]
22584304it [00:13, 1711420.95it/s]
22755523it [00:13, 1686725.50it/s]
22924307it [00:13, 1668265.97it/s]
23094110it [00:13, 1676916.55it/s]
23261885it [00:14, 1660981.21it/s]
23430799it [00:14, 1669271.82it/s]
23601071it [00:14, 1679174.56it/s]
23770362it [00:14, 1683244.90it/s]
23941270it [00:14, 1690936.49it/s]
24110399it [00:14, 1690059.01it/s]
24280897it [00:14, 1694504.27it/s]
24452213it [00:14, 1700021.91it/s]
24622230it [00:14, 1699996.34it/s]
24792240it [00:14, 1670055.62it/s]
24961798it [00:15, 1677595.58it/s]
25132266it [00:15, 1685630.30it/s]
25303975it [00:15, 1694992.57it/s]
25474420it [00:15, 1697801.55it/s]
25645597it [00:15, 1701953.59it/s]
25816088it [00:15, 1702821.97it/s]
25986392it [00:15, 1701675.00it/s]
26156575it [00:15, 1697625.63it/s]
26326350it [00:15, 1688274.59it/s]
26499309it [00:15, 1700582.72it/s]
26671486it [00:16, 1706890.20it/s]
26842192it [00:16, 1706813.66it/s]
27012885it [00:16, 1706524.97it/s]
27184285it [00:16, 1708742.45it/s]
27355166it [00:16, 1690074.96it/s]
27524841it [00:16, 1692039.41it/s]
27694757it [00:16, 1694144.09it/s]
27864736it [00:16, 1695808.32it/s]
28035509it [00:16, 1699191.83it/s]
28205443it [00:16, 1698394.19it/s]
28375293it [00:17, 1693118.59it/s]
28545791it [00:17, 1696649.40it/s]
28718502it [00:17, 1705629.45it/s]
28891545it [00:17, 1713042.28it/s]
29065358it [00:17, 1720542.52it/s]
29239212it [00:17, 1725923.95it/s]
29411809it [00:17, 1720959.78it/s]
29583912it [00:17, 1716399.86it/s]
29755558it [00:17, 1707337.28it/s]
29926304it [00:17, 1705932.58it/s]
30096906it [00:18, 1667714.72it/s]
30263857it [00:18, 1637195.17it/s]
30433376it [00:18, 1654116.19it/s]
30605200it [00:18, 1672976.98it/s]
30778317it [00:18, 1690151.33it/s]
30948568it [00:18, 1693806.95it/s]
31118050it [00:18, 1670533.27it/s]
31285233it [00:18, 1546651.86it/s]
31455464it [00:18, 1590392.64it/s]
31627057it [00:18, 1626344.41it/s]
31798199it [00:19, 1651038.29it/s]
31966167it [00:19, 1659420.03it/s]
32135277it [00:19, 1668758.06it/s]
32305116it [00:19, 1677532.00it/s]
32474907it [00:19, 1683579.86it/s]
32644806it [00:19, 1688114.18it/s]
32816293it [00:19, 1696093.17it/s]
32986449it [00:19, 1697564.53it/s]
33157057it [00:19, 1700022.35it/s][W::hts_idx_load3] The index file is older than the data file: 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
33327124it [00:19, 1685048.92it/s]
33499975it [00:20, 1697854.44it/s]
33673855it [00:20, 1710057.08it/s]
33845115it [00:20, 1710783.55it/s]
34016228it [00:20, 1705414.99it/s]
34186797it [00:20, 1683049.40it/s]
34357512it [00:20, 1690050.78it/s]
34526580it [00:20, 1639868.71it/s]
34693488it [00:20, 1648377.94it/s]
34864058it [00:20, 1665231.37it/s]
35034631it [00:20, 1677201.98it/s]
35205057it [00:21, 1685223.03it/s]
35373703it [00:21, 1679738.12it/s]
35541764it [00:21, 1664286.40it/s]
35708277it [00:21, 1646269.97it/s]
35877861it [00:21, 1660889.61it/s]
36047572it [00:21, 1671620.34it/s]
36217619it [00:21, 1680192.76it/s]
36387218it [00:21, 1684858.52it/s]
36556699it [00:21, 1687701.86it/s]
36725500it [00:21, 1687139.87it/s]
36897504it [00:22, 1696902.66it/s]
37070300it [00:22, 1706183.71it/s]
37241264it [00:22, 1707101.63it/s]
37411984it [00:22, 1701997.37it/s]
37582851it [00:22, 1703978.46it/s]
37753257it [00:22, 1699709.03it/s]
37900093it [00:22, 1670156.30it/s]
[W::hts_idx_load3] The index file is older than the data file: 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi
[W::hts_idx_load3] The index file is older than the data file: 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5TB-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai