[W::hts_idx_load3] The index file is older than the data file: 1136_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5L2-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_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5L2-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_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
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[W::hts_idx_load3] The index file is older than the data file: 1136_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5L2-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_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai