[W::hts_idx_load3] The index file is older than the data file: 659_d0M-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_d0M-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: 659_d0M-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_d0M-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_d0M-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_d0M-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_d0M-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: 659_d0M-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_d0M-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai 0it [00:00, ?it/s] 149381it [00:00, 1493462.48it/s] 312156it [00:00, 1572413.17it/s] 478074it [00:00, 1612008.08it/s] 643195it [00:00, 1627463.00it/s] 809330it [00:00, 1639660.44it/s] 974800it [00:00, 1644642.28it/s] 1142108it [00:00, 1653921.00it/s] 1309509it [00:00, 1660293.82it/s] 1475539it [00:00, 1652682.88it/s] 1641734it [00:01, 1655518.13it/s] 1807292it [00:01, 1654802.59it/s] 1972777it [00:01, 1635131.85it/s] 2136342it [00:01, 1623178.95it/s] 2303064it [00:01, 1636305.14it/s] 2466742it [00:01, 1602639.76it/s] 2627168it [00:01, 1592407.31it/s] 2794781it [00:01, 1617092.51it/s] 2963984it [00:01, 1639294.39it/s] 3134700it [00:01, 1659345.46it/s] 3300735it [00:02, 1651375.27it/s] 3466115it [00:02, 1652080.05it/s] 3631376it [00:02, 1639475.93it/s] 3795376it [00:02, 1590128.64it/s] 3960651it [00:02, 1608191.09it/s] 4121747it [00:02, 1587925.25it/s] 4280755it [00:02, 1583614.77it/s] 4446823it [00:02, 1606295.16it/s] 4612559it [00:02, 1621401.26it/s] 4777672it [00:02, 1630225.51it/s] 4940787it [00:03, 1595006.35it/s] 5107668it [00:03, 1616485.72it/s] 5273438it [00:03, 1628661.04it/s] 5436858it [00:03, 1630290.64it/s] 5599996it [00:03, 1592035.42it/s] 5760475it [00:03, 1595671.67it/s] 5920227it [00:03, 1592732.43it/s] 6079627it [00:03, 1520140.52it/s] 6235290it [00:03, 1530622.02it/s] 6399771it [00:03, 1563870.02it/s] 6563166it [00:04, 1584394.88it/s] 6721987it [00:04, 1517209.00it/s] 6874511it [00:04, 1490246.35it/s] 7024944it [00:04, 1494280.83it/s] 7190434it [00:04, 1540973.20it/s] 7360120it [00:04, 1586736.66it/s] 7530859it [00:04, 1622380.21it/s] 7700604it [00:04, 1644649.79it/s] 7867531it [00:04, 1651965.61it/s] 8034437it [00:04, 1656955.91it/s] 8200461it [00:05, 1657873.02it/s] 8369264it [00:05, 1666882.82it/s] 8537581it [00:05, 1671745.02it/s] 8707308it [00:05, 1679376.36it/s] 8878974it [00:05, 1690534.89it/s] 9051639it [00:05, 1701246.22it/s] 9224821it [00:05, 1710202.77it/s] 9395855it [00:05, 1696209.86it/s] 9567286it [00:05, 1701592.96it/s] 9737473it [00:05, 1698313.63it/s] 9907324it [00:06, 1693172.30it/s] 10076657it [00:06, 1688074.22it/s] 10245476it [00:06, 1681522.89it/s] 10413639it [00:06, 1675654.46it/s] 10581213it [00:06, 1670959.11it/s] 10748574it [00:06, 1671732.65it/s] 10915752it [00:06, 1663840.34it/s]done loading BEDs. 11082144it [00:06, 1661210.39it/s] 11248409it [00:06, 1661622.49it/s] 11415703it [00:07, 1664986.45it/s] 11583438it [00:07, 1668669.79it/s] 11750445it [00:07, 1669071.61it/s] 11917701it [00:07, 1669981.13it/s] 12084788it [00:07, 1670232.47it/s] 12251813it [00:07, 1669411.34it/s] 12419117it [00:07, 1670482.76it/s] 12586893it [00:07, 1672649.52it/s] 12754159it [00:07, 1672540.74it/s] 12925414it [00:07, 1684522.90it/s] 13094622it [00:08, 1686775.46it/s] 13263301it [00:08, 1682266.54it/s] 13431531it [00:08, 1680682.62it/s] 13599602it [00:08, 1678950.02it/s] 13767499it [00:08, 1676617.12it/s] 13935163it [00:08, 1676525.16it/s] 14102817it [00:08, 1624620.45it/s] 14272255it [00:08, 1645050.10it/s] 14442317it [00:08, 1661434.62it/s] 14610167it [00:08, 1666479.48it/s] 14776981it [00:09, 1663082.66it/s] 14945520it [00:09, 1669711.15it/s] 15112577it [00:09, 1657940.10it/s] 15284756it [00:09, 1676914.76it/s] 15457774it [00:09, 1692730.53it/s] 15631014it [00:09, 1704565.14it/s] 15801952it [00:09, 1705895.04it/s] 15974911it [00:09, 1712971.61it/s] 16146232it [00:09, 1712886.92it/s] 16317538it [00:09, 1699523.27it/s] 16487525it [00:10, 1678171.32it/s] 16655415it [00:10, 1663627.25it/s] 16821840it [00:10, 1648040.85it/s] 16988663it [00:10, 1653979.41it/s] 17155626it [00:10, 1658602.05it/s] 17322104it [00:10, 1660312.73it/s] 17489613it [00:10, 1664642.31it/s][W::hts_idx_load3] The index file is older than the data file: 659_d0M-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai 17656836it [00:10, 1666891.44it/s] 17823543it [00:10, 1656778.04it/s] 17989367it [00:10, 1657201.34it/s] 18156955it [00:11, 1662763.64it/s] 18325069it [00:11, 1668069.32it/s] 18492306it [00:11, 1669321.31it/s] 18660699it [00:11, 1673681.76it/s] 18828074it [00:11, 1670872.33it/s] 18995167it [00:11, 1666352.11it/s] 19166307it [00:11, 1679659.65it/s] 19335576it [00:11, 1683544.34it/s] 19504881it [00:11, 1686313.50it/s] 19673859it [00:11, 1687330.98it/s] 19842785it [00:12, 1687883.14it/s] 20011576it [00:12, 1671640.67it/s] 20178777it [00:12, 1670422.61it/s] 20345845it [00:12, 1668757.48it/s] 20513515it [00:12, 1671109.41it/s] 20680639it [00:12, 1670376.08it/s] 20847686it [00:12, 1656480.54it/s] 21017760it [00:12, 1669645.11it/s] 21188131it [00:12, 1679668.99it/s] 21359838it [00:12, 1690826.24it/s] 21531801it [00:13, 1699430.00it/s] 21701763it [00:13, 1694693.98it/s] 21871248it [00:13, 1690042.31it/s] 22040265it [00:13, 1684412.53it/s] 22208717it [00:13, 1644762.63it/s] 22374555it [00:13, 1648635.96it/s] 22542860it [00:13, 1658798.39it/s] 22712983it [00:13, 1671384.41it/s] 22883690it [00:13, 1682001.45it/s] 23051964it [00:13, 1679547.27it/s] 23219970it [00:14, 1601927.09it/s] 23386448it [00:14, 1620090.56it/s] 23555321it [00:14, 1640147.38it/s] 23720394it [00:14, 1643249.34it/s] 23886893it [00:14, 1649675.37it/s] 24053026it [00:14, 1653124.67it/s] 24218513it [00:14, 1618092.27it/s] 24380593it [00:14, 1616060.34it/s] 24546951it [00:14, 1630086.44it/s] 24710111it [00:14, 1623794.89it/s] 24880274it [00:15, 1646892.11it/s] 25049608it [00:15, 1660589.61it/s] 25215942it [00:15, 1661396.79it/s] 25382137it [00:15, 1651855.01it/s] 25547371it [00:15, 1632606.92it/s] 25711331it [00:15, 1634552.53it/s] 25875770it [00:15, 1637458.84it/s] 26042581it [00:15, 1646457.84it/s] 26208990it [00:15, 1651707.48it/s] 26374187it [00:15, 1648336.00it/s] 26539040it [00:16, 1646925.08it/s] 26706114it [00:16, 1654029.39it/s] 26871709it [00:16, 1654581.13it/s] 27039455it [00:16, 1661417.73it/s] 27205604it [00:16, 1660362.74it/s] 27375472it [00:16, 1671828.63it/s] 27544686it [00:16, 1677901.61it/s] 27713602it [00:16, 1681260.70it/s] 27881731it [00:16, 1673649.07it/s] 28049106it [00:16, 1671756.53it/s] 28210344it [00:17, 1650653.41it/s] [W::hts_idx_load3] The index file is older than the data file: 659_d0M-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_d0M-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_d0M-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_d0M-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_d0M-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_d0M-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_d0M-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_d0M-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_d0M-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_d0M-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_d0M-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_d0M-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_d0M-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_d0M-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_d0M-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_d0M-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_d0M-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_d0M-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_d0M-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_d0M-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_d0M-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_d0M-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: 659_d0M-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_d0M-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_d0M-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_d0M-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_d0M-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_d0M-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_d0M-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_d0M-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_d0M-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_d0M-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_d0M-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_d0M-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_d0M-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_d0M-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_d0M-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_d0M-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_d0M-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_d0M-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_d0M-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_d0M-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_d0M-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_d0M-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_d0M-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_d0M-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai