[W::hts_idx_load3] The index file is older than the data file: 1136_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_76X-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_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_76X-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_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
0it [00:00, ?it/s]
146628it [00:00, 1466141.58it/s]
305167it [00:00, 1536223.36it/s]
466776it [00:00, 1572658.74it/s]
630114it [00:00, 1596591.43it/s]
792714it [00:00, 1607134.33it/s]
957541it [00:00, 1621083.50it/s]
1124631it [00:00, 1637336.20it/s]
1292142it [00:00, 1649325.21it/s]
1457075it [00:00, 1638049.14it/s]
1624687it [00:01, 1649566.78it/s]
1789973it [00:01, 1650540.53it/s]
1955040it [00:01, 1598871.49it/s]
2115271it [00:01, 1548612.78it/s]
2270615it [00:01, 1544115.73it/s]
2425350it [00:01, 1457792.69it/s]
2577490it [00:01, 1475748.97it/s]
2736296it [00:01, 1508032.72it/s]
2889968it [00:01, 1516246.84it/s]
3045377it [00:01, 1527337.47it/s]
3198511it [00:02, 1488142.61it/s]
3347780it [00:02, 1436802.23it/s]
3492043it [00:02, 1430755.73it/s]
3640542it [00:02, 1446417.43it/s]
3795780it [00:02, 1477379.58it/s]
3955364it [00:02, 1512258.52it/s]
4115756it [00:02, 1539373.20it/s]
4269925it [00:02, 1474499.61it/s]
4430123it [00:02, 1511167.21it/s]
4584818it [00:02, 1521603.68it/s]
4737446it [00:03, 1508401.61it/s]
4888620it [00:03, 1430597.11it/s]
5037990it [00:03, 1448548.27it/s]
5183614it [00:03, 1439614.32it/s]
5336356it [00:03, 1465100.06it/s]
5489463it [00:03, 1484428.01it/s]
5638571it [00:03, 1486366.22it/s]
5796806it [00:03, 1514825.24it/s]
5948496it [00:03, 1413028.64it/s]
6091277it [00:04, 1332608.88it/s]
6226230it [00:04, 1318001.15it/s]
6376494it [00:04, 1369668.61it/s]
6533682it [00:04, 1427411.40it/s]
6694311it [00:04, 1479181.22it/s]
6853361it [00:04, 1511680.55it/s]
7012041it [00:04, 1533809.07it/s]
7177098it [00:04, 1568389.79it/s]
7341070it [00:04, 1589584.33it/s]
7506981it [00:04, 1610294.98it/s]
7670172it [00:05, 1616728.78it/s]
7833033it [00:05, 1620261.22it/s]
8000457it [00:05, 1636391.60it/s]
8165015it [00:05, 1639116.48it/s]
8328988it [00:05, 1623383.00it/s]
8491403it [00:05, 1619460.62it/s]
8653402it [00:05, 1612942.75it/s]
8814735it [00:05, 1610302.17it/s]
8975792it [00:05, 1604791.14it/s]
9136291it [00:05, 1602106.56it/s]
9296515it [00:06, 1597235.23it/s]
9458292it [00:06, 1603332.25it/s]
9621384it [00:06, 1611546.07it/s]
9783585it [00:06, 1614652.62it/s]
9949323it [00:06, 1627418.00it/s]
10112074it [00:06, 1616590.85it/s]
10276281it [00:06, 1624101.88it/s]
10440260it [00:06, 1628757.01it/s]
10603151it [00:06, 1612894.54it/s]
10764483it [00:06, 1603021.18it/s]done loading BEDs.
10924820it [00:07, 1599029.77it/s]
11086429it [00:07, 1604070.54it/s]
11246857it [00:07, 1596499.24it/s]
11408116it [00:07, 1601260.56it/s]
11569697it [00:07, 1605464.67it/s]
11731510it [00:07, 1609068.65it/s]
11892428it [00:07, 1591937.26it/s]
12054024it [00:07, 1599050.23it/s]
12219727it [00:07, 1616308.12it/s]
12387022it [00:07, 1633191.40it/s]
12552952it [00:08, 1640975.26it/s]
12717077it [00:08, 1567561.93it/s]
12883110it [00:08, 1594432.13it/s]
13048574it [00:08, 1612003.22it/s]
13210225it [00:08, 1613270.76it/s]
13373667it [00:08, 1619516.22it/s]
13535849it [00:08, 1585710.90it/s]
13695920it [00:08, 1590096.55it/s]
13856605it [00:08, 1595020.30it/s]
14016266it [00:09, 1590446.62it/s]
14178335it [00:09, 1599407.29it/s]
14338849it [00:09, 1601012.63it/s]
14499012it [00:09, 1597940.57it/s]
14658849it [00:09, 1565464.44it/s]
14815560it [00:09, 1546096.99it/s]
14972568it [00:09, 1553112.16it/s]
15127991it [00:09, 1539790.30it/s]
15286392it [00:09, 1552813.63it/s]
15447835it [00:09, 1571009.82it/s]
15606251it [00:10, 1574901.44it/s]
15767348it [00:10, 1585632.44it/s]
15928908it [00:10, 1594489.83it/s]
16088394it [00:10, 1563575.52it/s]
16247501it [00:10, 1571666.96it/s]
16408147it [00:10, 1581830.90it/s]
16567343it [00:10, 1584823.75it/s]
16725894it [00:10, 1582197.34it/s]
16884162it [00:10, 1581354.97it/s]
17042331it [00:10, 1573529.28it/s]
17199714it [00:11, 1568225.89it/s]
17361626it [00:11, 1583364.39it/s]
17520228it [00:11, 1584129.51it/s]
17678659it [00:11, 1579232.93it/s]
17843254it [00:11, 1599130.02it/s]
18008773it [00:11, 1615865.78it/s]
18176875it [00:11, 1635342.71it/s]
18341899it [00:11, 1639718.60it/s]
18509140it [00:11, 1649485.74it/s]
18679896it [00:11, 1666864.45it/s]
18850455it [00:12, 1678359.41it/s]
19020170it [00:12, 1683963.19it/s]
19188572it [00:12, 1677318.53it/s]
19356314it [00:12, 1650551.01it/s]
19521465it [00:12, 1598010.36it/s]
19681639it [00:12, 1569658.68it/s]
19843597it [00:12, 1584064.17it/s]
20002262it [00:12, 1583878.78it/s]
20160830it [00:12, 1505474.77it/s]
20312211it [00:12, 1455957.42it/s]
20471907it [00:13, 1495788.47it/s]
20633339it [00:13, 1529851.79it/s]
20796764it [00:13, 1560226.33it/s]
20961946it [00:13, 1587112.02it/s]
21129420it [00:13, 1612993.29it/s]
21297752it [00:13, 1633661.72it/s]
21464029it [00:13, 1642303.09it/s]
21628455it [00:13, 1635504.39it/s]
21797352it [00:13, 1651408.38it/s]
21963455it [00:13, 1654253.41it/s]
22128959it [00:14, 1634008.82it/s]
22292465it [00:14, 1579333.56it/s]
22450820it [00:14, 1573588.75it/s]
22609589it [00:14, 1577686.32it/s]
22772833it [00:14, 1593786.47it/s]
22934748it [00:14, 1601273.27it/s]
23095008it [00:14, 1598292.76it/s]
23254929it [00:14, 1596794.85it/s]
23414672it [00:14, 1589315.80it/s]
23575318it [00:15, 1594248.04it/s]
23741345it [00:15, 1613919.39it/s]
23902774it [00:15, 1611308.52it/s]
24068348it [00:15, 1624557.90it/s]
24233527it [00:15, 1632681.28it/s]
24399384it [00:15, 1640360.86it/s]
24563435it [00:15, 1635575.31it/s]
24727006it [00:15, 1629573.47it/s]
24741812it [00:15, 1573259.38it/s]
[W::hts_idx_load3] The index file is older than the data file: 1136_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_76X-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_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_76X-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai