+ mkdir 659_bCu-T1-TRNA-1_A23MVY2LT4_1
+ all_qc -bam 659_bCu-T1-TRNA-1_A23MVY2LT4_1.md.bam -beds Twist_rna_exome_AND_fusion_hg38.bed -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz -contamination_bed dbsnp_hg38_contam_sites.bed -output_folder 659_bCu-T1-TRNA-1_A23MVY2LT4_1 -reference ref_genome.fa -region chr20
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_A23MVY2LT4_1.md.bai
[mpileup] 1 samples in 1 input files
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_A23MVY2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_A23MVY2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_A23MVY2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_A23MVY2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_A23MVY2LT4_1.md.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: 659_bCu-T1-TRNA-1_A23MVY2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_A23MVY2LT4_1.md.bai

0it [00:00, ?it/s]
155517it [00:00, 1555101.04it/s]
321794it [00:00, 1618394.62it/s]
492820it [00:00, 1660219.12it/s]
660428it [00:00, 1666336.79it/s]
835299it [00:00, 1696014.21it/s]
1007644it [00:00, 1705176.44it/s]
1180646it [00:00, 1713273.97it/s]
1355674it [00:00, 1725032.18it/s]
1531759it [00:00, 1736068.69it/s]
1707083it [00:01, 1741313.37it/s]
1881964it [00:01, 1743583.83it/s]
2056323it [00:01, 1715684.48it/s]
2230037it [00:01, 1722088.03it/s]
2408532it [00:01, 1740903.56it/s]
2587084it [00:01, 1754258.30it/s]
2762565it [00:01, 1747315.74it/s]
2937339it [00:01, 1744614.68it/s]
3111830it [00:01, 1631645.26it/s]
3279326it [00:01, 1643988.79it/s]
3444812it [00:02, 1634258.81it/s]
3608982it [00:02, 1635742.86it/s]
3778818it [00:02, 1654084.55it/s]
3951307it [00:02, 1674966.65it/s]
4127185it [00:02, 1699815.59it/s]
4297417it [00:02, 1665304.04it/s]
4464258it [00:02, 1605198.50it/s]
4625369it [00:02, 1561668.07it/s]
4785350it [00:02, 1572529.68it/s]
4950743it [00:02, 1596062.11it/s]
5113861it [00:03, 1606313.02it/s]
5274783it [00:03, 1603384.87it/s]
5442159it [00:03, 1624188.10it/s]
5609484it [00:03, 1638620.73it/s]
5773478it [00:03, 1632078.30it/s]
5944592it [00:03, 1655547.92it/s]
6121177it [00:03, 1688427.14it/s]
6296930it [00:03, 1709053.81it/s]
6470456it [00:03, 1716866.89it/s]
6642188it [00:03, 1714759.15it/s]
6816166it [00:04, 1722224.50it/s]
6991049it [00:04, 1730169.34it/s]
7167818it [00:04, 1741346.30it/s]
7345252it [00:04, 1751072.98it/s]
7520370it [00:04, 1740385.71it/s]
7694431it [00:04, 1736761.43it/s]
7869445it [00:04, 1740728.97it/s]
8043531it [00:04, 1738415.38it/s]
8219128it [00:04, 1743510.70it/s]
8395090it [00:04, 1748233.93it/s][W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_A23MVY2LT4_1.md.bai

8569920it [00:05, 1745320.62it/s]
8744458it [00:05, 1735092.42it/s]
8917983it [00:05, 1658601.36it/s]
9084533it [00:05, 1492748.53it/s]
9237103it [00:05, 1466959.08it/s]
9401550it [00:05, 1515641.54it/s]
9556209it [00:05, 1524326.12it/s]
9718208it [00:05, 1551727.13it/s]
9881555it [00:05, 1575456.98it/s]
10054466it [00:06, 1620513.72it/s]
10217231it [00:06, 1598703.74it/s][W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_A23MVY2LT4_1.md.bai

10389973it [00:06, 1636466.44it/s]
10554080it [00:06, 1636892.01it/s]
10728193it [00:06, 1667788.67it/s]
10895232it [00:06, 1623542.81it/s]
11062158it [00:06, 1636894.56it/s]
11227365it [00:06, 1641335.92it/s]
11391733it [00:06, 1640503.31it/s]
11469948it [00:06, 1662986.40it/s]
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_A23MVY2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_A23MVY2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_A23MVY2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_A23MVY2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_A23MVY2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_A23MVY2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_A23MVY2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_A23MVY2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_A23MVY2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_A23MVY2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_A23MVY2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_A23MVY2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_A23MVY2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_A23MVY2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_A23MVY2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_A23MVY2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_A23MVY2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_A23MVY2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_A23MVY2LT4_1.md.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: 659_bCu-T1-TRNA-1_A23MVY2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_A23MVY2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_A23MVY2LT4_1.md.bai
+ merge_qc -folders 659_bCu-T1-TRNA-1_A23MVY2LT4_1/659_bCu-T1-TRNA-1_A23MVY2LT4_1.md -output 659_bCu-T1-TRNA-1_A23MVY2LT4_1/659_bCu-T1-TRNA-1_A23MVY2LT4_1_full_basic_stats.tsv
+ head -n1 659_bCu-T1-TRNA-1_A23MVY2LT4_1/659_bCu-T1-TRNA-1_A23MVY2LT4_1_full_basic_stats.tsv
++ basename Twist_rna_exome_AND_fusion_hg38.bed
+ grep -e Twist_rna_exome_AND_fusion_hg38.bed 659_bCu-T1-TRNA-1_A23MVY2LT4_1/659_bCu-T1-TRNA-1_A23MVY2LT4_1_full_basic_stats.tsv