[W::hts_idx_load3] The index file is older than the data file: 1136_87O-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_87O-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_87O-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_87O-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_87O-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_87O-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_87O-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_87O-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_87O-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai 0it [00:00, ?it/s] 145021it [00:00, 1450135.32it/s] 306014it [00:00, 1544096.42it/s] 470642it [00:00, 1590725.75it/s] 634573it [00:00, 1609886.69it/s] 797340it [00:00, 1616274.87it/s] 961353it [00:00, 1624226.64it/s] 1124999it [00:00, 1628204.62it/s] 1288168it [00:00, 1629294.84it/s] 1451098it [00:00, 1627776.83it/s] 1616629it [00:01, 1636158.45it/s] 1782250it [00:01, 1642275.77it/s] 1947973it [00:01, 1646804.70it/s] 2112655it [00:01, 1631028.58it/s] 2277938it [00:01, 1637548.84it/s] 2441722it [00:01, 1617972.94it/s] 2603584it [00:01, 1605272.05it/s] 2764165it [00:01, 1582126.54it/s] 2922461it [00:01, 1572065.36it/s] 3084942it [00:01, 1587582.85it/s] 3243767it [00:02, 1547693.34it/s] 3399990it [00:02, 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1506652.02it/s] 8328217it [00:05, 1479928.44it/s] 8486870it [00:05, 1510030.90it/s] 8652144it [00:05, 1551168.23it/s] 8821693it [00:05, 1593261.66it/s] 8989817it [00:05, 1619125.64it/s] 9157186it [00:05, 1635255.64it/s] 9324318it [00:05, 1645955.13it/s] 9491288it [00:05, 1653014.52it/s] 9659436it [00:06, 1661497.58it/s] 9828904it [00:06, 1671398.17it/s] 9999429it [00:06, 1681486.01it/s] 10170956it [00:06, 1691585.54it/s] 10342598it [00:06, 1699008.23it/s] 10513605it [00:06, 1702268.54it/s] 10683859it [00:06, 1679518.12it/s] 10853759it [00:06, 1685286.52it/s]done loading BEDs. 11022667it [00:06, 1686400.40it/s] 11191355it [00:06, 1682374.44it/s] 11360528it [00:07, 1685147.99it/s] 11529068it [00:07, 1682588.09it/s] 11697345it [00:07, 1678909.86it/s] 11865249it [00:07, 1677456.79it/s] 12033004it [00:07, 1668239.03it/s] 12199843it [00:07, 1667785.47it/s] 12367495it [00:07, 1670373.96it/s] 12536560it [00:07, 1676418.34it/s] 12704210it [00:07, 1668941.21it/s] 12872428it [00:07, 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17763680it [00:10, 1711473.27it/s] 17934839it [00:10, 1701050.84it/s] 18104966it [00:11, 1674508.35it/s] 18272514it [00:11, 1673951.14it/s] 18439977it [00:11, 1664946.93it/s] 18606521it [00:11, 1648377.42it/s] 18775070it [00:11, 1659312.47it/s] 18942790it [00:11, 1664605.44it/s] 19109562it [00:11, 1665515.68it/s] 19278596it [00:11, 1672908.35it/s] 19446575it [00:11, 1674951.52it/s] 19614089it [00:11, 1661007.38it/s] 19780277it [00:12, 1661248.77it/s] 19948117it [00:12, 1666217.62it/s] 20116275it [00:12, 1670784.17it/s] 20284198it [00:12, 1673173.13it/s] 20451887it [00:12, 1674257.81it/s] 20619322it [00:12, 1671381.34it/s] 20786467it [00:12, 1657815.88it/s] 20956562it [00:12, 1670644.14it/s] 21125519it [00:12, 1676273.29it/s] 21294065it [00:12, 1678998.41it/s] 21461982it [00:13, 1665918.91it/s] 21629774it [00:13, 1669371.56it/s] 21796969it [00:13, 1669997.81it/s] 21965412it [00:13, 1674293.03it/s] 22132856it [00:13, 1672889.80it/s] 22300155it [00:13, 1669707.07it/s] 22470073it [00:13, 1678467.60it/s] 22640323it [00:13, 1685639.48it/s] 22811039it [00:13, 1692067.03it/s] 22980252it [00:13, 1687057.49it/s] 23148965it [00:14, 1680181.89it/s] 23316993it [00:14, 1672873.15it/s] 23484291it [00:14, 1638414.62it/s] 23648279it [00:14, 1637332.15it/s] 23818687it [00:14, 1657053.96it/s] 23986789it [00:14, 1664148.55it/s] 24153280it [00:14, 1594146.47it/s] 24313337it [00:14, 1588673.35it/s] 24482487it [00:14, 1618647.62it/s] 24648469it [00:14, 1630736.31it/s] 24815029it [00:15, 1641027.32it/s] 24981964it [00:15, 1649324.15it/s] 25149441it [00:15, 1656885.98it/s] 25317789it [00:15, 1664808.42it/s][W::hts_idx_load3] The index file is older than the data file: 1136_87O-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai 25485296it [00:15, 1667861.48it/s] 25652145it [00:15, 1654686.81it/s] 25820835it [00:15, 1664259.59it/s] 25990508it [00:15, 1673931.08it/s] 26157943it [00:15, 1671771.59it/s] 26325150it [00:15, 1656968.38it/s] 26490893it [00:16, 1619712.43it/s] 26656224it [00:16, 1629549.38it/s] 26823931it [00:16, 1643497.57it/s] 26992347it [00:16, 1655547.23it/s] 27160132it [00:16, 1662169.50it/s] 27326428it [00:16, 1658697.11it/s] 27494468it [00:16, 1665153.56it/s] 27662022it [00:16, 1668238.07it/s] 27829791it [00:16, 1671047.57it/s] 27996918it [00:17, 1668092.15it/s] 28164645it [00:17, 1670616.05it/s] 28332631it [00:17, 1673274.57it/s] 28502515it [00:17, 1680912.56it/s] 28671443it [00:17, 1683400.40it/s] 28839789it [00:17, 1678623.06it/s] 29007658it [00:17, 1678049.73it/s] 29175468it [00:17, 1670683.07it/s] 29198876it [00:17, 1647485.27it/s] [W::hts_idx_load3] The index file is older than the data file: 1136_87O-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_87O-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_87O-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_87O-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_87O-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_87O-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_87O-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_87O-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_87O-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_87O-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_87O-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_87O-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_87O-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_87O-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_87O-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_87O-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_87O-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_87O-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_87O-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_87O-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_87O-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_87O-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_87O-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_87O-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_87O-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_87O-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_87O-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_87O-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_87O-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_87O-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_87O-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_87O-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_87O-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_87O-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_87O-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_87O-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_87O-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_87O-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_87O-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_87O-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_87O-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_87O-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_87O-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_87O-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_87O-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_87O-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai