[W::hts_idx_load3] The index file is older than the data file: 1136_3LU-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_3LU-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_3LU-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_3LU-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_3LU-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_3LU-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_3LU-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_3LU-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_3LU-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai 0it [00:00, ?it/s] 137462it [00:00, 1374572.15it/s] 296929it [00:00, 1504015.15it/s] 459597it [00:00, 1560005.87it/s] 615829it [00:00, 1560903.87it/s] 777909it [00:00, 1582455.39it/s] 936155it [00:00, 1573594.91it/s] 1093835it [00:00, 1574547.54it/s] 1251297it [00:00, 1565212.78it/s] 1413215it [00:00, 1581970.63it/s] 1575944it [00:01, 1595894.36it/s] 1735553it [00:01, 1585490.10it/s] 1894128it [00:01, 1584653.37it/s] 2052611it [00:01, 1566456.40it/s] 2209874it [00:01, 1568287.80it/s] 2369247it [00:01, 1575880.70it/s] 2527896it [00:01, 1579042.92it/s] 2685825it [00:01, 1556182.80it/s] 2841527it [00:01, 1507340.23it/s] 2998141it [00:01, 1524436.80it/s] 3150877it [00:02, 1495609.46it/s] 3300709it [00:02, 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1619442.87it/s] 31565507it [00:19, 1629519.54it/s] 31730068it [00:19, 1634299.28it/s] 31895143it [00:19, 1639197.26it/s] 32060326it [00:19, 1642962.98it/s] 32224641it [00:19, 1638022.65it/s] 32388696it [00:20, 1638766.65it/s] 32553653it [00:20, 1641935.90it/s] 32719096it [00:20, 1645518.64it/s] 32883655it [00:20, 1642053.78it/s] 33049658it [00:20, 1647256.19it/s] 33214518it [00:20, 1647647.31it/s] 33380668it [00:20, 1651759.32it/s][W::hts_idx_load3] The index file is older than the data file: 1136_3LU-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai 33547364it [00:20, 1656303.99it/s] 33713289it [00:20, 1657175.85it/s] 33879009it [00:20, 1646330.36it/s] 34043660it [00:21, 1642983.89it/s] 34207971it [00:21, 1634311.68it/s] 34323631it [00:21, 1619277.26it/s] [W::hts_idx_load3] The index file is older than the data file: 1136_3LU-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_3LU-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_3LU-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_3LU-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_3LU-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_3LU-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_3LU-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_3LU-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_3LU-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_3LU-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_3LU-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_3LU-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_3LU-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_3LU-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_3LU-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_3LU-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_3LU-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_3LU-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_3LU-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_3LU-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_3LU-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_3LU-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_3LU-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_3LU-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_3LU-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_3LU-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_3LU-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_3LU-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 1136_3LU-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older 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