+ mkdir aih-tih-sc-b7f13b-R1_A23WJ53LT4_1
+ all_qc -bam aih-tih-sc-b7f13b-R1_A23WJ53LT4_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 aih-tih-sc-b7f13b-R1_A23WJ53LT4_1 -reference ref_genome.fa -region chr20
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b7f13b-R1_A23WJ53LT4_1.md.bai
[mpileup] 1 samples in 1 input files
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b7f13b-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b7f13b-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b7f13b-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b7f13b-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b7f13b-R1_A23WJ53LT4_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: aih-tih-sc-b7f13b-R1_A23WJ53LT4_1.md.bai
0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b7f13b-R1_A23WJ53LT4_1.md.bai
150455it [00:00, 1504085.25it/s]
310604it [00:00, 1561338.53it/s]
472718it [00:00, 1588617.66it/s]
637351it [00:00, 1611375.32it/s]
802081it [00:00, 1624304.82it/s]
969492it [00:00, 1641218.49it/s]
1136982it [00:00, 1652210.58it/s]
1302204it [00:00, 1651933.23it/s]
1471053it [00:00, 1663341.74it/s]
1640567it [00:01, 1673139.53it/s]
1810077it [00:01, 1679844.59it/s]
1978062it [00:01, 1676043.26it/s]
2145669it [00:01, 1661960.92it/s]
2311892it [00:01, 1661823.44it/s]
2479981it [00:01, 1667520.98it/s]
2653126it [00:01, 1686673.68it/s]
2821938it [00:01, 1687070.59it/s]
2990658it [00:01, 1686801.07it/s]
3159347it [00:01, 1665879.50it/s]
3325998it [00:02, 1633204.51it/s]
3493794it [00:02, 1646335.68it/s]
3660823it [00:02, 1653401.00it/s]
3826271it [00:02, 1643716.37it/s]
3994976it [00:02, 1656527.83it/s]
4161192it [00:02, 1658165.79it/s]
4329045it [00:02, 1664206.09it/s]
4500102it [00:02, 1678032.68it/s]
4668964it [00:02, 1681169.44it/s]
4837105it [00:02, 1615431.96it/s]
4999205it [00:03, 1613612.90it/s]
5162187it [00:03, 1618320.99it/s]
5324300it [00:03, 1574704.45it/s]
5486065it [00:03, 1587162.48it/s]
5645679it [00:03, 1589760.91it/s]
5804884it [00:03, 1544451.82it/s]
5959717it [00:03, 1501112.34it/s]
6117208it [00:03, 1522295.01it/s]
6271791it [00:03, 1529043.38it/s]
6424990it [00:03, 1510285.53it/s]
6590417it [00:04, 1552433.09it/s]
6758105it [00:04, 1589020.56it/s]
6924946it [00:04, 1612530.89it/s]
7092499it [00:04, 1631251.77it/s]
7259508it [00:04, 1642814.50it/s]
7425317it [00:04, 1647308.37it/s]
7594327it [00:04, 1660056.87it/s]
7762560it [00:04, 1666707.66it/s]
7931443it [00:04, 1673183.44it/s]
8100989it [00:04, 1679841.67it/s]
8271112it [00:05, 1686234.47it/s]
8439752it [00:05, 1685089.61it/s]
8611191it [00:05, 1693746.63it/s]
8780575it [00:05, 1668926.66it/s]
8952336it [00:05, 1683354.49it/s]
9120831it [00:05, 1683810.87it/s]
9290005it [00:05, 1686159.43it/s]
9458660it [00:05, 1678803.46it/s]
9626573it [00:05, 1669995.24it/s]
9795959it [00:05, 1676965.36it/s]
9965314it [00:06, 1681818.28it/s]
10135320it [00:06, 1687248.42it/s]
10304062it [00:06, 1650892.64it/s]
10470225it [00:06, 1654040.64it/s]
10638074it [00:06, 1661103.35it/s]
10805659it [00:06, 1665469.99it/s]
10973471it [00:06, 1669222.53it/s]
11144157it [00:06, 1680443.94it/s]
11312603it [00:06, 1681614.49it/s]
11480795it [00:06, 1606052.59it/s]
11649847it [00:07, 1630527.71it/s]
11813734it [00:07, 1632949.00it/s]
11979754it [00:07, 1640969.08it/s]
12145852it [00:07, 1646847.77it/s]
12311842it [00:07, 1650711.68it/s]
12480019it [00:07, 1659926.03it/s]
12646642it [00:07, 1661786.29it/s]
12814037it [00:07, 1665395.69it/s]
12980899it [00:07, 1666324.63it/s]
13147984it [00:07, 1667656.95it/s]
13315273it [00:08, 1669207.86it/s]
13482215it [00:08, 1652494.29it/s]
13649348it [00:08, 1658083.94it/s]
13815197it [00:08, 1637481.41it/s]
13984166it [00:08, 1652835.66it/s]
14154416it [00:08, 1667580.38it/s]
14321238it [00:08, 1665023.38it/s]
14489851it [00:08, 1671299.62it/s]
14657910it [00:08, 1674054.97it/s]
14825341it [00:09, 1668690.90it/s]
14993511it [00:09, 1672559.93it/s]
14993705it [00:09, 1646368.89it/s]
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b7f13b-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b7f13b-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b7f13b-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b7f13b-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b7f13b-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b7f13b-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b7f13b-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b7f13b-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b7f13b-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b7f13b-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b7f13b-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b7f13b-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b7f13b-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b7f13b-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b7f13b-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b7f13b-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b7f13b-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b7f13b-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b7f13b-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b7f13b-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b7f13b-R1_A23WJ53LT4_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: aih-tih-sc-b7f13b-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b7f13b-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b7f13b-R1_A23WJ53LT4_1.md.bai
+ merge_qc -folders aih-tih-sc-b7f13b-R1_A23WJ53LT4_1/aih-tih-sc-b7f13b-R1_A23WJ53LT4_1.md -output aih-tih-sc-b7f13b-R1_A23WJ53LT4_1/aih-tih-sc-b7f13b-R1_A23WJ53LT4_1_full_basic_stats.tsv
+ head -n1 aih-tih-sc-b7f13b-R1_A23WJ53LT4_1/aih-tih-sc-b7f13b-R1_A23WJ53LT4_1_full_basic_stats.tsv
++ basename Twist_rna_exome_AND_fusion_hg38.bed
+ grep -e Twist_rna_exome_AND_fusion_hg38.bed aih-tih-sc-b7f13b-R1_A23WJ53LT4_1/aih-tih-sc-b7f13b-R1_A23WJ53LT4_1_full_basic_stats.tsv