+ mkdir tih_rna_sample_00574_B23MVV7LT4_1
+ all_qc -bam tih_rna_sample_00574_B23MVV7LT4_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 tih_rna_sample_00574_B23MVV7LT4_1 -reference ref_genome.fa -region chr20
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai
[mpileup] 1 samples in 1 input files
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_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: tih_rna_sample_00574_B23MVV7LT4_1.md.bai
0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai
148000it [00:00, 1479772.09it/s]
309041it [00:00, 1556578.99it/s]
475903it [00:00, 1607714.85it/s]
640799it [00:00, 1623978.12it/s]
809277it [00:00, 1645756.46it/s]
976571it [00:00, 1654982.59it/s]
1147404it [00:00, 1672229.70it/s]
1317740it [00:00, 1682004.13it/s]
1488544it [00:00, 1690127.61it/s]
1658047it [00:01, 1691626.49it/s]
1827896it [00:01, 1693711.35it/s]
1998314it [00:01, 1696880.33it/s]
2170880it [00:01, 1705582.77it/s]
2341439it [00:01, 1687593.58it/s]
2513601it [00:01, 1697721.30it/s]
2685456it [00:01, 1703845.38it/s]
2860653it [00:01, 1718251.08it/s]
3032504it [00:01, 1714721.96it/s]
3203996it [00:01, 1707206.54it/s]
3374736it [00:02, 1687732.64it/s]
3546238it [00:02, 1695812.88it/s]
3719786it [00:02, 1707601.27it/s]
3890920it [00:02, 1708705.00it/s]
4061873it [00:02, 1708941.06it/s]
4233578it [00:02, 1711354.15it/s]
4407085it [00:02, 1718444.68it/s]
4578942it [00:02, 1678597.80it/s]
4747011it [00:02, 1604089.37it/s]
4918614it [00:02, 1636183.67it/s]
5086511it [00:03, 1648598.18it/s]
5256435it [00:03, 1663414.10it/s]
5423166it [00:03, 1641595.31it/s]
5594542it [00:03, 1662773.23it/s]
5768184it [00:03, 1684528.15it/s]
5941194it [00:03, 1698045.50it/s]
6115271it [00:03, 1710755.92it/s]
6290087it [00:03, 1721900.46it/s]
6462370it [00:03, 1714889.29it/s]
6634099it [00:03, 1715586.55it/s]
6805707it [00:04, 1705963.98it/s]
6976347it [00:04, 1703970.91it/s]
7148358it [00:04, 1708692.71it/s]
7320646it [00:04, 1712914.38it/s]
7494770it [00:04, 1721374.39it/s]
7667635it [00:04, 1723538.57it/s]
7840000it [00:04, 1553709.77it/s]
8011180it [00:04, 1597677.88it/s]
8180528it [00:04, 1624914.72it/s]
8350026it [00:04, 1645151.94it/s]
8520132it [00:05, 1661473.46it/s]
8691324it [00:05, 1676064.82it/s]
8862029it [00:05, 1685224.56it/s]
9031096it [00:05, 1677442.44it/s]
9201941it [00:05, 1686634.96it/s]
9372731it [00:05, 1692951.91it/s]
9542226it [00:05, 1691848.79it/s]
9713864it [00:05, 1699165.12it/s]
9884283it [00:05, 1700654.00it/s]
10056933it [00:05, 1708238.34it/s]
10230822it [00:06, 1717368.68it/s]
10402596it [00:06, 1714368.06it/s]
10580031it [00:06, 1732310.41it/s]
10753285it [00:06, 1721029.13it/s]
10925420it [00:06, 1716521.40it/s]
11099850it [00:06, 1724786.34it/s]
11274692it [00:06, 1731830.80it/s]
11447893it [00:06, 1730136.39it/s]
11620919it [00:06, 1726329.37it/s]
11793562it [00:06, 1717318.88it/s]
11965309it [00:07, 1708980.27it/s]
12136222it [00:07, 1702820.40it/s]
12309745it [00:07, 1712452.12it/s]
12481006it [00:07, 1691236.67it/s]
12650189it [00:07, 1687939.16it/s]
12821451it [00:07, 1695250.90it/s]
12993221it [00:07, 1701920.49it/s]
13165031it [00:07, 1706735.60it/s]
13337167it [00:07, 1711091.90it/s]
13508294it [00:07, 1702882.85it/s]
13678602it [00:08, 1701595.74it/s]
13848775it [00:08, 1679679.80it/s]
14023322it [00:08, 1699162.01it/s]
14194669it [00:08, 1703400.66it/s]
14365061it [00:08, 1701022.18it/s]
14539214it [00:08, 1713094.95it/s]
14710555it [00:08, 1708754.58it/s]
14881666it [00:08, 1709442.78it/s]
15053807it [00:08, 1713005.34it/s]
15225121it [00:09, 1701783.25it/s]
15395323it [00:09, 1696562.15it/s]
15465894it [00:09, 1690357.73it/s]
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_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: tih_rna_sample_00574_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00574_B23MVV7LT4_1.md.bai
+ merge_qc -folders tih_rna_sample_00574_B23MVV7LT4_1/tih_rna_sample_00574_B23MVV7LT4_1.md -output tih_rna_sample_00574_B23MVV7LT4_1/tih_rna_sample_00574_B23MVV7LT4_1_full_basic_stats.tsv
+ head -n1 tih_rna_sample_00574_B23MVV7LT4_1/tih_rna_sample_00574_B23MVV7LT4_1_full_basic_stats.tsv
++ basename Twist_rna_exome_AND_fusion_hg38.bed
+ grep -e Twist_rna_exome_AND_fusion_hg38.bed tih_rna_sample_00574_B23MVV7LT4_1/tih_rna_sample_00574_B23MVV7LT4_1_full_basic_stats.tsv