[W::hts_idx_load3] The index file is older than the data file: 1029_1XX-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1XX-N1-BDNA-1_B23KGCJLT4_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_1XX-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1XX-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1029_1XX-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
The index file is older than the data file: 1029_1XX-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1XX-N1-BDNA-1_B23KGCJLT4_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_1XX-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1XX-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
0it [00:00, ?it/s]
143728it [00:00, 1436774.39it/s]
301679it [00:00, 1520684.69it/s]
456536it [00:00, 1533378.80it/s]
613037it [00:00, 1545834.13it/s]
773798it [00:00, 1567775.93it/s]
930576it [00:00, 1527098.89it/s]
1084931it [00:00, 1532357.61it/s]
1238307it [00:00, 1527741.86it/s]
1391409it [00:00, 1528729.13it/s]
1544348it [00:01, 1487811.11it/s]
1705809it [00:01, 1525554.80it/s]
1870001it [00:01, 1560222.50it/s]
2034887it [00:01, 1586724.58it/s]
2194556it [00:01, 1589582.92it/s]
2354481it [00:01, 1592309.57it/s]
2516758it [00:01, 1601413.90it/s]
2680799it [00:01, 1613084.03it/s]
2842164it [00:01, 1608673.35it/s]
3003073it [00:01, 1592352.54it/s]
3162370it [00:02, 1589520.93it/s]
3324992it [00:02, 1600416.89it/s]
3485072it [00:02, 1587015.79it/s]
3646522it [00:02, 1595154.07it/s]
3806078it [00:02, 1591861.30it/s]
3966769it [00:02, 1596324.40it/s]
4129058it [00:02, 1604195.64it/s]
4291165it [00:02, 1609091.27it/s]
4454050it [00:02, 1614983.04it/s]
4615560it [00:02, 1601861.00it/s]
4776945it [00:03, 1605394.86it/s]
4939466it [00:03, 1611196.65it/s]
5100606it [00:03, 1599463.36it/s]
5260582it [00:03, 1598280.27it/s]
5420430it [00:03, 1595928.75it/s]
5581884it [00:03, 1601463.36it/s]
5703088it [00:03, 1580413.73it/s]
[W::hts_idx_load3] The index file is older than the data file: 1029_1XX-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
done loading BEDs.
[W::hts_idx_load3] The index file is older than the data file: 1029_1XX-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1XX-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1XX-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1XX-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1XX-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1XX-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1XX-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1XX-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1XX-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1XX-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1XX-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1XX-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1XX-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1XX-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1XX-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1XX-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1XX-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1XX-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1XX-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1XX-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1XX-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1XX-N1-BDNA-1_B23KGCJLT4_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_1XX-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1XX-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1XX-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1XX-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1XX-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1XX-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1XX-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1XX-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1XX-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1XX-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1XX-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1XX-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1XX-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1XX-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1XX-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1XX-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1XX-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1XX-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1XX-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1XX-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1XX-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1XX-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1XX-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1XX-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai