[W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-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: 659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-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: 659_cfy-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: 659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai 145422it [00:00, 1454152.05it/s] 306550it [00:00, 1546542.47it/s] 469691it [00:00, 1585265.22it/s] 632468it [00:00, 1601971.94it/s] 795693it [00:00, 1612869.69it/s] 959011it [00:00, 1619751.84it/s] 1124097it [00:00, 1629835.60it/s] 1289596it [00:00, 1637657.14it/s] 1453362it [00:00, 1631820.01it/s] 1618357it [00:01, 1637329.99it/s] 1782789it [00:01, 1639446.81it/s] 1946738it [00:01, 1614091.94it/s] 2108234it [00:01, 1613200.79it/s] 2269614it [00:01, 1612302.20it/s] 2433055it [00:01, 1618881.33it/s] 2594976it [00:01, 1559808.43it/s] 2757756it [00:01, 1579644.04it/s] 2924144it [00:01, 1604419.91it/s] 3089969it [00:01, 1620169.29it/s] 3252934it [00:02, 1622644.54it/s] 3417732it [00:02, 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1609454.76it/s] 8262530it [00:05, 1620729.79it/s] 8426660it [00:05, 1626841.12it/s] 8589906it [00:05, 1628499.10it/s] 8757881it [00:05, 1643751.57it/s] 8925159it [00:05, 1652419.97it/s] 9093075it [00:05, 1660412.95it/s] 9262248it [00:05, 1669780.22it/s] 9432828it [00:05, 1680560.39it/s] 9600910it [00:05, 1667799.08it/s] 9768815it [00:06, 1671137.46it/s] 9935959it [00:06, 1670161.14it/s] 10102996it [00:06, 1666478.21it/s] 10269659it [00:06, 1665782.27it/s] 10436248it [00:06, 1661843.89it/s] 10602441it [00:06, 1657668.70it/s] 10768215it [00:06, 1647331.26it/s]done loading BEDs. 10932964it [00:06, 1646072.54it/s] 11097815it [00:06, 1646784.78it/s] 11262965it [00:06, 1648114.22it/s] 11427783it [00:07, 1642747.39it/s] 11593071it [00:07, 1645756.96it/s] 11758998it [00:07, 1649752.01it/s] 11925628it [00:07, 1654654.28it/s] 12091099it [00:07, 1651490.49it/s] 12256253it [00:07, 1649110.04it/s] 12421168it [00:07, 1647964.57it/s] 12587697it [00:07, 1653133.76it/s] 12753014it [00:07, 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17588486it [00:10, 1643060.76it/s] 17754204it [00:10, 1647267.28it/s] 17919391it [00:11, 1648529.98it/s] 18084253it [00:11, 1634090.59it/s] 18249765it [00:11, 1640278.88it/s] 18416093it [00:11, 1647120.38it/s] 18582048it [00:11, 1650819.64it/s] 18747845it [00:11, 1652905.47it/s] 18913149it [00:11, 1648478.57it/s] 19078008it [00:11, 1642845.46it/s] 19245925it [00:11, 1653662.28it/s] 19412482it [00:11, 1657183.27it/s] 19579891it [00:12, 1662219.20it/s] 19746121it [00:12, 1660894.16it/s] 19912216it [00:12, 1654440.01it/s] 20077669it [00:12, 1638728.11it/s] 20243255it [00:12, 1643803.45it/s] 20408235it [00:12, 1645573.44it/s] 20572814it [00:12, 1640022.50it/s] 20736834it [00:12, 1638252.45it/s] 20902635it [00:12, 1644132.22it/s] 21070699it [00:12, 1655030.89it/s] 21238961it [00:13, 1663269.75it/s] 21406709it [00:13, 1667507.23it/s] 21573468it [00:13, 1664234.30it/s] 21739898it [00:13, 1657404.48it/s] 21905648it [00:13, 1650522.56it/s] 22070711it [00:13, 1606931.64it/s] 22237156it [00:13, 1623777.92it/s] 22403237it [00:13, 1634689.68it/s] 22571357it [00:13, 1648465.38it/s] 22736718it [00:13, 1649973.53it/s] 22901807it [00:14, 1574834.16it/s] 23063435it [00:14, 1586799.71it/s] 23230393it [00:14, 1610975.04it/s] 23396374it [00:14, 1625313.60it/s] 23560361it [00:14, 1629607.91it/s] 23725169it [00:14, 1635073.54it/s] 23889762it [00:14, 1638225.37it/s] 24055153it [00:14, 1642835.34it/s] 24220495it [00:14, 1645967.13it/s] 24385158it [00:14, 1633821.64it/s] 24553086it [00:15, 1647329.18it/s] 24720110it [00:15, 1654151.08it/s] 24885567it [00:15, 1640286.50it/s] 25049832it [00:15, 1640859.78it/s] 25213955it [00:15, 1616989.90it/s] 25375746it [00:15, 1616518.26it/s] 25540312it [00:15, 1625152.88it/s] 25705374it [00:15, 1632715.49it/s] 25870476it [00:15, 1638159.22it/s] 26034325it [00:15, 1631360.74it/s][W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai 26197489it [00:16, 1631090.65it/s] 26362208it [00:16, 1635881.81it/s] 26527443it [00:16, 1640690.67it/s] 26691992it [00:16, 1642104.59it/s] 26856212it [00:16, 1641847.51it/s] 27021786it [00:16, 1645987.55it/s] 27189029it [00:16, 1653895.56it/s] 27355206it [00:16, 1656236.91it/s] 27520833it [00:16, 1652225.02it/s] 27686152it [00:16, 1652457.79it/s] 27821163it [00:17, 1629763.21it/s] [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-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: 659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai