[W::hts_idx_load3] The index file is older than the data file: 1029_IYD-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IYD-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_IYD-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IYD-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IYD-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IYD-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IYD-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_IYD-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IYD-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
0it [00:00, ?it/s]
150441it [00:00, 1504128.13it/s]
316009it [00:00, 1592906.19it/s]
479790it [00:00, 1613277.57it/s]
641264it [00:00, 1613784.06it/s]
810063it [00:00, 1640517.96it/s]
974115it [00:00, 1609031.79it/s]
1137358it [00:00, 1616510.93it/s]
1299095it [00:00, 1612878.33it/s]
1461479it [00:00, 1616164.00it/s]
1623138it [00:01, 1560299.68it/s]
1791297it [00:01, 1596363.94it/s]
1960657it [00:01, 1625308.90it/s]
2132339it [00:01, 1652628.97it/s]
2298372it [00:01, 1654853.88it/s]
2465773it [00:01, 1660569.01it/s]
2633888it [00:01, 1666714.44it/s]
2801331it [00:01, 1669006.90it/s]
2970812it [00:01, 1676727.02it/s]
3138535it [00:01, 1666644.91it/s]
3305247it [00:02, 1664976.03it/s]
3477065it [00:02, 1680779.03it/s]
3647145it [00:02, 1686741.00it/s]
3815842it [00:02, 1672489.77it/s]
3983132it [00:02, 1669315.18it/s]
4152198it [00:02, 1675659.36it/s]
4322328it [00:02, 1683293.92it/s]
4490914it [00:02, 1684040.13it/s]
4660492it [00:02, 1687530.48it/s]
4829256it [00:02, 1680421.33it/s]
4997312it [00:03, 1670155.61it/s]
5164348it [00:03, 1657303.89it/s]
5332435it [00:03, 1664278.07it/s]
5500529it [00:03, 1669219.14it/s]
5667474it [00:03, 1663664.22it/s]
5835317it [00:03, 1667996.83it/s]
6003647it [00:03, 1672521.26it/s]
6171648it [00:03, 1674737.79it/s]
6182343it [00:03, 1653419.08it/s]
[W::hts_idx_load3] The index file is older than the data file: 1029_IYD-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_IYD-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IYD-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IYD-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IYD-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IYD-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IYD-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IYD-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IYD-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IYD-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IYD-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IYD-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IYD-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IYD-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IYD-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IYD-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IYD-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IYD-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IYD-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IYD-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IYD-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IYD-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IYD-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_IYD-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IYD-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IYD-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IYD-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IYD-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IYD-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IYD-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IYD-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IYD-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IYD-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IYD-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IYD-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IYD-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IYD-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IYD-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IYD-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IYD-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IYD-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IYD-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IYD-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IYD-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IYD-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IYD-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IYD-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai