[W::hts_idx_load3] The index file is older than the data file: 1136_00H-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_00H-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_00H-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1136_00H-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_00H-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai The index file is older than the data file: 1136_00H-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_00H-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_00H-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai 0it [00:00, ?it/s] 146880it [00:00, 1468500.30it/s][W::hts_idx_load3] The index file is older than the data file: 1136_00H-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai 306764it [00:00, 1545132.63it/s] 469721it [00:00, 1583657.70it/s] 632343it [00:00, 1600439.57it/s] 796586it [00:00, 1615563.56it/s] 958888it [00:00, 1618080.84it/s] 1121737it [00:00, 1621373.04it/s] 1285743it [00:00, 1627304.89it/s] 1450060it [00:00, 1632248.97it/s] 1613285it [00:01, 1622375.80it/s] 1777125it [00:01, 1627242.00it/s] 1940071it [00:01, 1627899.91it/s] 2102869it [00:01, 1609476.41it/s] 2263866it [00:01, 1598345.30it/s] 2424824it [00:01, 1601675.24it/s] 2585025it [00:01, 1578617.02it/s] 2742968it [00:01, 1562610.99it/s] 2905087it [00:01, 1579760.33it/s] 3070368it [00:01, 1601401.88it/s] 3233087it [00:02, 1608889.87it/s] 3398465it [00:02, 1622237.72it/s] 3560744it [00:02, 1615840.47it/s] 3725341it [00:02, 1624693.92it/s] 3887845it [00:02, 1562229.69it/s] 4045893it [00:02, 1567525.28it/s] 4203024it [00:02, 1547191.35it/s] 4360439it [00:02, 1554965.13it/s] 4519001it [00:02, 1563988.37it/s] 4681155it [00:02, 1581029.15it/s] 4842309it [00:03, 1590089.68it/s] 5001424it [00:03, 1566032.54it/s] 5161878it [00:03, 1577398.87it/s] 5323375it [00:03, 1588536.16it/s] 5486111it [00:03, 1600078.20it/s] 5646194it [00:03, 1594727.09it/s] 5805721it [00:03, 1551918.37it/s] 5962682it [00:03, 1557087.75it/s] 6121279it [00:03, 1565584.47it/s] 6282879it [00:03, 1580509.38it/s] 6442033it [00:04, 1583591.06it/s] 6603389it [00:04, 1592516.61it/s] 6765796it [00:04, 1601932.09it/s] 6926041it [00:04, 1550050.57it/s] 7081436it [00:04, 1458663.54it/s] 7228523it [00:04, 1452368.26it/s] 7387606it [00:04, 1491938.67it/s] 7551222it [00:04, 1533617.10it/s] 7716801it [00:04, 1569386.50it/s] 7881390it [00:04, 1591832.33it/s] 8044436it [00:05, 1603269.47it/s] 8207621it [00:05, 1611758.02it/s] 8370393it [00:05, 1616405.34it/s] 8535590it [00:05, 1627015.97it/s] 8700459it [00:05, 1633439.16it/s] 8866240it [00:05, 1640580.05it/s] 9033543it [00:05, 1650284.30it/s] 9201327it [00:05, 1658526.09it/s] 9371066it [00:05, 1670019.41it/s] 9538091it [00:05, 1663726.35it/s] 9704485it [00:06, 1661420.19it/s] 9871336it [00:06, 1663526.66it/s] 10037700it [00:06, 1657194.64it/s] 10203432it [00:06, 1654726.98it/s] 10368913it [00:06, 1651680.10it/s] 10534087it [00:06, 1645092.93it/s] 10698604it [00:06, 1631267.78it/s]done loading BEDs. 10861756it [00:06, 1628191.82it/s] 11024591it [00:06, 1625797.96it/s] 11188779it [00:06, 1630569.09it/s] 11352275it [00:07, 1631860.73it/s] 11515469it [00:07, 1629544.29it/s] 11679214it [00:07, 1631885.19it/s] 11843874it [00:07, 1636270.93it/s] 12008362it [00:07, 1638833.42it/s] 12172249it [00:07, 1638249.12it/s] 12336088it [00:07, 1638273.08it/s] 12500074it [00:07, 1638729.35it/s] 12663949it [00:07, 1637295.19it/s] 12827680it [00:07, 1635423.35it/s] 12991411it [00:08, 1635971.44it/s] 13156237it [00:08, 1639637.01it/s] 13323143it [00:08, 1648438.93it/s] 13490186it [00:08, 1654914.91it/s] 13655679it [00:08, 1647841.70it/s] 13820471it [00:08, 1641862.16it/s] 13984729it [00:08, 1642057.06it/s] 14149331it [00:08, 1643098.30it/s] 14313646it [00:08, 1640764.67it/s] 14477726it [00:09, 1589830.99it/s] 14642019it [00:09, 1605366.03it/s] 14808169it [00:09, 1621906.66it/s] 14971085it [00:09, 1624039.02it/s] 15133912it [00:09, 1625279.78it/s] 15299040it [00:09, 1633002.22it/s] 15462422it [00:09, 1619794.80it/s] 15631714it [00:09, 1641401.04it/s] 15799796it [00:09, 1653137.06it/s] 15968900it [00:09, 1664442.84it/s] 16136346it [00:10, 1667420.35it/s] 16303121it [00:10, 1665349.09it/s] 16471446it [00:10, 1670690.26it/s] 16639321it [00:10, 1673089.05it/s] 16807202it [00:10, 1674789.41it/s] 16974690it [00:10, 1665889.20it/s] 17141296it [00:10, 1643033.47it/s] 17305673it [00:10, 1631214.28it/s] 17469851it [00:10, 1634323.88it/s] 17633328it [00:10, 1623731.47it/s] 17797813it [00:11, 1629980.75it/s] 17962117it [00:11, 1633851.07it/s] 18125861it [00:11, 1634906.98it/s] 18290358it [00:11, 1637731.13it/s] 18454723it [00:11, 1639485.78it/s] 18618683it [00:11, 1629348.45it/s] 18781638it [00:11, 1628533.50it/s] 18945492it [00:11, 1631506.39it/s] 19109684it [00:11, 1634604.93it/s] 19273816it [00:11, 1636600.34it/s] 19437483it [00:12, 1635841.28it/s] 19601072it [00:12, 1633764.07it/s] 19764452it [00:12, 1631520.32it/s] 19928493it [00:12, 1634167.61it/s] 20094358it [00:12, 1641443.57it/s] 20260279it [00:12, 1646753.73it/s] 20424957it [00:12, 1639828.84it/s] 20588948it [00:12, 1631003.59it/s] 20752449it [00:12, 1632130.03it/s] 20916289it [00:12, 1633814.72it/s] 21080449it [00:13, 1635952.07it/s] 21244411it [00:13, 1637035.20it/s] 21408120it [00:13, 1633798.18it/s] 21571716it [00:13, 1634421.06it/s] 21737034it [00:13, 1640026.32it/s] 21902463it [00:13, 1644286.44it/s] 22068971it [00:13, 1650505.33it/s] 22234237it [00:13, 1651013.72it/s] 22399341it [00:13, 1648924.95it/s] 22564236it [00:13, 1640074.28it/s] 22728255it [00:14, 1618780.33it/s] 22890195it [00:14, 1600460.16it/s] 23054141it [00:14, 1611952.97it/s] 23220028it [00:14, 1625821.96it/s] 23386699it [00:14, 1637972.38it/s] 23550552it [00:14, 1635803.40it/s] 23714171it [00:14, 1556484.53it/s] 23880029it [00:14, 1585937.49it/s] 24044989it [00:14, 1604439.33it/s] 24207292it [00:14, 1609898.52it/s] 24369858it [00:15, 1614548.15it/s] 24532554it [00:15, 1618224.48it/s] 24695384it [00:15, 1621174.61it/s] 24859445it [00:15, 1626959.97it/s] 25023127it [00:15, 1629895.97it/s] 25186187it [00:15, 1620291.70it/s] 25351012it [00:15, 1628620.33it/s] 25517413it [00:15, 1639181.40it/s] 25681369it [00:15, 1638160.67it/s] 25845212it [00:15, 1626367.72it/s] 26007884it [00:16, 1600382.07it/s] 26168025it [00:16, 1599978.80it/s] 26332236it [00:16, 1612457.30it/s] 26495692it [00:16, 1619023.06it/s] 26660212it [00:16, 1626817.78it/s] 26824281it [00:16, 1630742.46it/s] 26987385it [00:16, 1624501.60it/s] 27151620it [00:16, 1629747.59it/s] 27315841it [00:16, 1633461.37it/s] 27479202it [00:16, 1632162.31it/s] 27643138it [00:17, 1634306.77it/s][W::hts_idx_load3] The index file is older than the data file: 1136_00H-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai 27806725it [00:17, 1634761.46it/s] 27971451it [00:17, 1638406.68it/s] 28137171it [00:17, 1644027.62it/s] 28302260it [00:17, 1646072.67it/s] 28466870it [00:17, 1641084.19it/s] 28630984it [00:17, 1639847.03it/s] 28787217it [00:17, 1619459.99it/s] [W::hts_idx_load3] The index file is older than the data file: 1136_00H-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_00H-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_00H-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_00H-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_00H-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_00H-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_00H-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_00H-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_00H-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_00H-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_00H-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_00H-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_00H-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_00H-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_00H-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_00H-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_00H-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_00H-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_00H-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_00H-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_00H-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_00H-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_00H-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_00H-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_00H-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_00H-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_00H-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_00H-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_00H-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_00H-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_00H-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_00H-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_00H-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_00H-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_00H-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_00H-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_00H-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_00H-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_00H-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_00H-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_00H-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_00H-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_00H-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_00H-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_00H-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_00H-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai