[W::hts_idx_load3] The index file is older than the data file: 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_HTI-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: 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_HTI-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: 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai 0it [00:00, ?it/s] 142237it [00:00, 1422310.32it/s] 306249it [00:00, 1550321.43it/s] 469407it [00:00, 1587239.83it/s] 632555it [00:00, 1604607.57it/s] 799388it [00:00, 1627559.38it/s] 962144it [00:00, 1617669.57it/s] 1129282it [00:00, 1635136.10it/s] 1292811it [00:00, 1634970.14it/s] 1457048it [00:00, 1637259.72it/s] 1624445it [00:01, 1648557.92it/s] 1792009it [00:01, 1656812.09it/s] 1960039it [00:01, 1663869.61it/s] 2127334it [00:01, 1666600.17it/s] 2293998it [00:01, 1641269.47it/s] 2461263it [00:01, 1650603.31it/s] 2626866it [00:01, 1652208.21it/s] 2792138it [00:01, 1651593.89it/s] 2957333it [00:01, 1600434.71it/s] 3120660it [00:01, 1610033.75it/s] 3281934it [00:02, 1566249.07it/s] 3447911it [00:02, 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1677506.58it/s] 22306280it [00:13, 1683440.54it/s] 22475101it [00:13, 1684851.04it/s] 22645402it [00:14, 1690271.62it/s] 22814644it [00:14, 1690825.15it/s] 22983751it [00:14, 1661520.13it/s] 23150032it [00:14, 1635112.22it/s] 23313697it [00:14, 1635327.42it/s] 23477338it [00:14, 1620457.61it/s] 23643924it [00:14, 1633783.28it/s] 23807386it [00:14, 1612069.92it/s] 23973769it [00:14, 1627243.28it/s] 24139992it [00:14, 1637592.89it/s] 24307451it [00:15, 1648557.93it/s] 24472374it [00:15, 1645471.97it/s] 24639720it [00:15, 1653717.39it/s] 24806404it [00:15, 1657624.53it/s] 24973182it [00:15, 1660646.40it/s] 25139267it [00:15, 1656235.33it/s] 25304907it [00:15, 1619027.00it/s] 25470945it [00:15, 1631179.75it/s] 25637473it [00:15, 1641263.37it/s] 25804906it [00:15, 1651075.98it/s] 25970107it [00:16, 1649931.27it/s] 26137297it [00:16, 1656413.77it/s] 26303210it [00:16, 1657210.85it/s] 26468966it [00:16, 1656872.51it/s] 26634678it [00:16, 1652251.53it/s] 26799922it [00:16, 1652244.75it/s] 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35917797it [00:22, 1644505.84it/s] 36083085it [00:22, 1646987.42it/s] 36247869it [00:22, 1638781.52it/s] 36413558it [00:22, 1644161.86it/s] 36579721it [00:22, 1649296.36it/s] 36746054it [00:22, 1653476.13it/s] 36911663it [00:22, 1654240.15it/s] 37077107it [00:22, 1652321.61it/s] 37243354it [00:22, 1655215.42it/s] 37409084it [00:23, 1655820.29it/s] 37575822it [00:23, 1659265.08it/s] 37743800it [00:23, 1665332.39it/s] 37912310it [00:23, 1671243.30it/s] 38079438it [00:23, 1662923.68it/s] 38245793it [00:23, 1663090.01it/s] 38412382it [00:23, 1663836.87it/s] 38578772it [00:23, 1653737.23it/s] 38687569it [00:23, 1623464.15it/s] [W::hts_idx_load3] The index file is older than the data file: 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_HTI-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: 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1029_HTI-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai