[W::hts_idx_load3] The index file is older than the data file: 1029_1BK-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1BK-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_1BK-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1BK-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1BK-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1BK-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1BK-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_1BK-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1BK-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
0it [00:00, ?it/s]
141037it [00:00, 1410206.60it/s]
282058it [00:00, 1403964.00it/s]
422457it [00:00, 1356673.89it/s]
576319it [00:00, 1426815.25it/s]
731323it [00:00, 1470568.34it/s]
894509it [00:00, 1524835.14it/s]
1048344it [00:00, 1529186.39it/s]
1202858it [00:00, 1534193.43it/s]
1359084it [00:00, 1542842.46it/s]
1513439it [00:01, 1523456.45it/s]
1671050it [00:01, 1539349.30it/s]
1825070it [00:01, 1468584.82it/s]
1979898it [00:01, 1491771.77it/s]
2134223it [00:01, 1506863.92it/s]
2291740it [00:01, 1527027.63it/s]
2449016it [00:01, 1540459.42it/s]
2603910it [00:01, 1542951.13it/s]
2758390it [00:01, 1535889.81it/s]
2912112it [00:01, 1515896.95it/s]
3063840it [00:02, 1492859.25it/s]
3213271it [00:02, 1492405.72it/s]
3364365it [00:02, 1497786.83it/s]
3516543it [00:02, 1504864.09it/s]
3667093it [00:02, 1491360.22it/s]
3816546it [00:02, 1492258.34it/s]
3975009it [00:02, 1519702.76it/s]
4129754it [00:02, 1527940.34it/s]
4282591it [00:02, 1510388.31it/s]
4433699it [00:02, 1507782.32it/s]
4584757it [00:03, 1508574.94it/s]
4735648it [00:03, 1496140.47it/s]
4889165it [00:03, 1507676.33it/s]
5044050it [00:03, 1519866.24it/s]
5196073it [00:03, 1505378.55it/s]
5346662it [00:03, 1479862.14it/s]
5494757it [00:03, 1433731.10it/s]
5638446it [00:03, 1388822.74it/s]
5777723it [00:03, 1375552.77it/s]
5921942it [00:03, 1394620.42it/s]
6066614it [00:04, 1409756.28it/s]
6211859it [00:04, 1422261.95it/s]
6354267it [00:04, 1419914.16it/s]
6497963it [00:04, 1424923.89it/s]
6641985it [00:04, 1429440.29it/s]
6786732it [00:04, 1434692.12it/s]
6931774it [00:04, 1439353.71it/s]
7075858it [00:04, 1439756.63it/s]
7078061it [00:04, 1477922.23it/s]
[W::hts_idx_load3] The index file is older than the data file: 1029_1BK-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_1BK-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1BK-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1BK-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1BK-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1BK-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1BK-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1BK-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1BK-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1BK-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1BK-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1BK-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1BK-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1BK-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1BK-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1BK-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1BK-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1BK-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1BK-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1BK-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1BK-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1BK-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1BK-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_1BK-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1BK-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_1BK-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
The index file is older than the data file: 1029_1BK-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1BK-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1BK-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1BK-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1BK-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1BK-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1BK-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1BK-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1BK-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1BK-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1BK-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1BK-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1BK-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1BK-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1BK-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1BK-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1BK-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1BK-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1BK-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1BK-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_1BK-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai