[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_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: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_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: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam.bai 0it [00:00, ?it/s] 146544it [00:00, 1465308.64it/s] 304495it [00:00, 1532310.23it/s] 465887it [00:00, 1569533.31it/s] 627505it [00:00, 1587918.43it/s] 790735it [00:00, 1603890.74it/s] 952149it [00:00, 1607352.40it/s] 1113365it [00:00, 1608806.68it/s] 1275473it [00:00, 1612689.63it/s] 1438140it [00:00, 1616969.92it/s] 1599837it [00:01, 1616671.77it/s] 1764413it [00:01, 1625469.93it/s] 1926961it [00:01, 1615733.28it/s] 2088548it [00:01, 1608061.60it/s] 2249369it [00:01, 1583849.23it/s] 2407832it [00:01, 1570810.22it/s] 2566228it [00:01, 1574679.53it/s] 2723745it [00:01, 1538958.67it/s] 2883507it [00:01, 1556137.33it/s] 3046167it [00:01, 1576914.09it/s] 3204314it [00:02, 1578080.79it/s] 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[00:05, 1592708.32it/s] 8094533it [00:05, 1605334.67it/s] 8255128it [00:05, 1604991.77it/s] 8417799it [00:05, 1611461.91it/s] 8581292it [00:05, 1618463.52it/s] 8745579it [00:05, 1625749.04it/s] 8908583it [00:05, 1627014.60it/s] 9071297it [00:05, 1619169.05it/s] 9234952it [00:05, 1624339.24it/s] 9398272it [00:05, 1626968.62it/s] 9561226it [00:06, 1627714.61it/s] 9724005it [00:06, 1627338.97it/s] 9886745it [00:06, 1619615.30it/s] 10048812it [00:06, 1619906.64it/s] 10210811it [00:06, 1611362.47it/s] 10371961it [00:06, 1608813.67it/s] 10532852it [00:06, 1593259.81it/s] 10693327it [00:06, 1596650.02it/s] 10853019it [00:06, 1580634.87it/s] 11011225it [00:06, 1581028.61it/s] 11170826it [00:07, 1585460.22it/s] 11329647it [00:07, 1586253.57it/s]done loading BEDs. 11488291it [00:07, 1579780.41it/s] 11648621it [00:07, 1586776.28it/s] 11808684it [00:07, 1590756.00it/s] 11967773it [00:07, 1589563.19it/s] 12128332it [00:07, 1594337.53it/s] 12289763it [00:07, 1600292.44it/s] 12449799it [00:07, 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1596221.26it/s] 21716962it [00:13, 1586767.53it/s] 21875659it [00:13, 1575603.03it/s] 22033246it [00:13, 1574496.23it/s] 22190714it [00:14, 1556383.28it/s] 22351491it [00:14, 1571579.75it/s] 22513006it [00:14, 1584511.49it/s] 22674107it [00:14, 1592388.71it/s] 22833386it [00:14, 1531717.13it/s] 22987060it [00:14, 1533125.90it/s] 23147202it [00:14, 1553160.11it/s] 23302989it [00:14, 1554528.23it/s] 23460819it [00:14, 1561561.71it/s] 23620624it [00:14, 1572401.70it/s] 23780961it [00:15, 1581623.89it/s] 23941002it [00:15, 1587211.23it/s] 24099785it [00:15, 1580918.51it/s] 24257925it [00:15, 1573764.51it/s] 24415340it [00:15, 1556840.60it/s] 24576713it [00:15, 1573675.06it/s] 24734142it [00:15, 1570832.93it/s] 24891267it [00:15, 1565611.90it/s] 25047858it [00:15, 1564670.35it/s] 25204346it [00:15, 1554491.07it/s] 25359819it [00:16, 1548443.39it/s] 25517975it [00:16, 1558206.45it/s] 25675367it [00:16, 1562867.27it/s] 25834395it [00:16, 1570892.33it/s] 25991500it [00:16, 1565953.41it/s] 26149160it [00:16, 1569113.63it/s] 26306082it [00:16, 1567182.51it/s] 26464789it [00:16, 1573099.61it/s] 26623655it [00:16, 1577733.37it/s] 26783379it [00:16, 1583519.26it/s] 26942629it [00:17, 1586154.34it/s] 27101315it [00:17, 1586345.92it/s] 27259953it [00:17, 1575237.79it/s] 27418008it [00:17, 1576798.77it/s] 27577485it [00:17, 1582150.18it/s] 27740516it [00:17, 1596403.51it/s][W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam.bai 27900169it [00:17, 1593786.24it/s] 28060998it [00:17, 1598081.34it/s] 28222026it [00:17, 1601715.47it/s] 28382204it [00:17, 1598778.35it/s] 28413003it [00:18, 1578380.46it/s] [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_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: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam.bai