[W::hts_idx_load3] The index file is older than the data file: 1136_86S-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_86S-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_86S-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_86S-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_86S-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_86S-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_86S-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_86S-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai 0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: 1136_86S-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai 150353it [00:00, 1503402.40it/s] 314447it [00:00, 1584247.16it/s] 481150it [00:00, 1621992.06it/s] 650342it [00:00, 1649547.01it/s] 817432it [00:00, 1657127.59it/s] 985004it [00:00, 1663411.31it/s] 1152586it [00:00, 1667330.50it/s] 1322878it [00:00, 1678620.36it/s] 1492881it [00:00, 1685275.58it/s] 1661409it [00:01, 1668336.34it/s] 1830825it [00:01, 1676149.27it/s] 1998472it [00:01, 1673605.22it/s] 2165854it [00:01, 1643325.70it/s] 2330311it [00:01, 1622804.52it/s] 2497317it [00:01, 1636720.61it/s] 2661098it [00:01, 1618873.56it/s] 2823082it [00:01, 1571735.69it/s] 2989948it [00:01, 1599871.05it/s] 3160614it [00:01, 1631160.58it/s] 3328249it [00:02, 1644229.27it/s] 3499780it [00:02, 1665276.98it/s] 3667861it [00:02, 1669859.44it/s] 3834977it [00:02, 1664262.53it/s] 4004878it [00:02, 1674580.44it/s] 4172408it [00:02, 1578308.81it/s] 4332917it [00:02, 1585875.43it/s] 4496397it [00:02, 1600054.54it/s] 4657041it [00:02, 1572925.84it/s] 4819522it [00:02, 1587854.40it/s] 4979137it [00:03, 1590265.83it/s] 5147299it [00:03, 1617248.11it/s] 5314579it [00:03, 1633718.45it/s] 5479838it [00:03, 1639265.13it/s] 5643895it [00:03, 1602898.88it/s] 5814654it [00:03, 1633670.75it/s] 5982636it [00:03, 1647295.86it/s] 6150950it [00:03, 1657761.46it/s] 6316867it [00:03, 1649843.54it/s] 6481954it [00:03, 1575094.77it/s] 6643393it [00:04, 1586201.51it/s] 6802575it [00:04, 1584535.93it/s] 6968319it [00:04, 1605670.42it/s] 7130431it [00:04, 1610208.78it/s] 7296501it [00:04, 1624982.85it/s] 7463931it [00:04, 1639638.04it/s] 7628028it [00:04, 1591232.59it/s] 7787538it [00:04, 1492092.68it/s] 7938111it [00:04, 1481200.75it/s] 8087143it [00:05, 1471961.70it/s] 8255178it [00:05, 1531853.43it/s] 8427051it [00:05, 1586235.95it/s] 8600072it [00:05, 1628497.71it/s] 8770650it [00:05, 1651211.89it/s] 8940455it [00:05, 1665082.51it/s] 9109581it [00:05, 1672834.90it/s] 9279054it [00:05, 1679337.85it/s] 9450923it [00:05, 1691073.53it/s] 9623270it [00:05, 1700736.65it/s] 9796176it [00:06, 1709059.02it/s] 9969627it [00:06, 1716656.49it/s] 10144088it [00:06, 1725008.05it/s] 10316619it [00:06, 1713467.62it/s] 10489481it [00:06, 1717962.09it/s] 10661307it [00:06, 1713487.14it/s] 10832678it [00:06, 1710893.38it/s] 11003900it [00:06, 1711257.28it/s]done loading BEDs. 11175037it [00:06, 1709504.24it/s] 11345995it [00:06, 1703270.80it/s] 11516331it [00:07, 1694411.13it/s] 11685785it [00:07, 1692283.71it/s] 11855022it [00:07, 1692083.69it/s] 12025986it [00:07, 1697303.02it/s] 12195723it [00:07, 1687880.87it/s] 12366222it [00:07, 1692947.68it/s] 12536880it [00:07, 1696895.17it/s] 12707530it [00:07, 1699674.02it/s] 12877506it [00:07, 1698994.48it/s] 13047412it [00:07, 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18008594it [00:10, 1668278.73it/s] 18178795it [00:10, 1678211.16it/s] 18348758it [00:11, 1684538.49it/s] 18517267it [00:11, 1682865.90it/s] 18687154it [00:11, 1687504.15it/s] 18857877it [00:11, 1693364.34it/s] 19027237it [00:11, 1673244.48it/s] 19195968it [00:11, 1677387.11it/s] 19366457it [00:11, 1685498.59it/s] 19537452it [00:11, 1692764.96it/s] 19709036it [00:11, 1699627.46it/s] 19879764it [00:11, 1701881.36it/s] 20049971it [00:12, 1698527.10it/s] 20219838it [00:12, 1692795.90it/s] 20392778it [00:12, 1703699.32it/s] 20564456it [00:12, 1707578.16it/s] 20735225it [00:12, 1704557.20it/s] 20905689it [00:12, 1702407.59it/s] 21075936it [00:12, 1678634.32it/s] 21245877it [00:12, 1684620.24it/s] 21415362it [00:12, 1687625.73it/s] 21585246it [00:12, 1690934.66it/s] 21754372it [00:13, 1683763.12it/s] 21923253it [00:13, 1685013.53it/s] 22094850it [00:13, 1694215.67it/s] 22266650it [00:13, 1701293.69it/s][W::hts_idx_load3] The index file is older than the data file: 1136_86S-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai 22439292it [00:13, 1708728.33it/s] 22610177it [00:13, 1706486.25it/s] 22780835it [00:13, 1702601.33it/s] 22951103it [00:13, 1700962.36it/s] 23121205it [00:13, 1669702.51it/s] 23288300it [00:13, 1647315.74it/s] 23458000it [00:14, 1661748.93it/s] 23630752it [00:14, 1681174.37it/s] 23803445it [00:14, 1694732.50it/s] 23973009it [00:14, 1668215.14it/s] 24139971it [00:14, 1567144.08it/s] 24311841it [00:14, 1610114.04it/s] 24483134it [00:14, 1639619.97it/s] 24651271it [00:14, 1651769.48it/s] 24819994it [00:14, 1662170.39it/s] 24988316it [00:15, 1668368.86it/s] 25157369it [00:15, 1674919.34it/s] 25328848it [00:15, 1686657.52it/s] 25499787it [00:15, 1693414.85it/s] 25669260it [00:15, 1688729.75it/s] 25843226it [00:15, 1703909.53it/s] 26014593it [00:15, 1706715.78it/s] 26185316it [00:15, 1689479.27it/s] 26354337it [00:15, 1688777.47it/s] 26523265it [00:15, 1653068.27it/s] 26688755it [00:16, 1651551.61it/s] 26858442it [00:16, 1664924.76it/s] 27028882it [00:16, 1676477.78it/s] 27196617it [00:16, 1675570.88it/s] 27366933it [00:16, 1683618.62it/s] 27536990it [00:16, 1688652.93it/s] 27706020it [00:16, 1689119.64it/s] 27874957it [00:16, 1688756.28it/s] 28046336it [00:16, 1696142.45it/s] 28216555it [00:16, 1697771.97it/s] 28386342it [00:17, 1695902.72it/s] 28555940it [00:17, 1688978.91it/s] 28581249it [00:17, 1666170.23it/s] [W::hts_idx_load3] The index file is older than the data file: 1136_86S-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_86S-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_86S-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_86S-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_86S-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_86S-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_86S-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_86S-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_86S-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_86S-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_86S-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_86S-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_86S-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_86S-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_86S-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_86S-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_86S-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_86S-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_86S-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_86S-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_86S-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_86S-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_86S-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_86S-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_86S-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_86S-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_86S-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_86S-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_86S-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_86S-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_86S-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_86S-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_86S-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_86S-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_86S-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_86S-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_86S-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_86S-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_86S-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_86S-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_86S-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_86S-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_86S-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_86S-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_86S-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_86S-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai