+ mkdir tih_rna_sample_00136_B23WHTKLT4_1
+ all_qc -bam tih_rna_sample_00136_B23WHTKLT4_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_00136_B23WHTKLT4_1 -reference ref_genome.fa -region chr20
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00136_B23WHTKLT4_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_00136_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00136_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00136_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00136_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00136_B23WHTKLT4_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_00136_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00136_B23WHTKLT4_1.md.bai

0it [00:00, ?it/s]
141641it [00:00, 1416306.67it/s]
294787it [00:00, 1484005.26it/s]
450843it [00:00, 1518918.39it/s]
613087it [00:00, 1559758.83it/s]
775055it [00:00, 1581334.03it/s]
940808it [00:00, 1607214.26it/s]
1108142it [00:00, 1628802.89it/s]
1273695it [00:00, 1637285.62it/s]
1438630it [00:00, 1641029.36it/s]
1602733it [00:01, 1640364.79it/s]
1769615it [00:01, 1649036.49it/s]
1936323it [00:01, 1654491.15it/s]
2101773it [00:01, 1640480.04it/s]
2269456it [00:01, 1651375.84it/s]
2434619it [00:01, 1637627.45it/s]
2599447it [00:01, 1640785.04it/s]
2771856it [00:01, 1665619.56it/s]
2938454it [00:01, 1661135.29it/s]
3104812it [00:01, 1661712.43it/s]
3271002it [00:02, 1642654.37it/s]
3437902it [00:02, 1650457.23it/s]
3605644it [00:02, 1658464.90it/s]
3771530it [00:02, 1638607.00it/s]
3938609it [00:02, 1648034.39it/s]
4107534it [00:02, 1660273.12it/s]
4274686it [00:02, 1663604.04it/s]
4443787it [00:02, 1671769.50it/s]
4610996it [00:02, 1666851.74it/s]
4777705it [00:02, 1655936.29it/s]
4946816it [00:03, 1666324.34it/s]
5113477it [00:03, 1649399.36it/s]
5278468it [00:03, 1646908.79it/s]
5443193it [00:03, 1631550.64it/s]
5609975it [00:03, 1642268.10it/s]
5779087it [00:03, 1656593.46it/s]
5944957it [00:03, 1657106.46it/s]
6110699it [00:03, 1548706.58it/s]
6274590it [00:03, 1574396.35it/s]
6437962it [00:03, 1591537.30it/s]
6603610it [00:04, 1610449.10it/s]
6771965it [00:04, 1631945.48it/s]
6938621it [00:04, 1642172.80it/s]
7107785it [00:04, 1656856.05it/s]
7275373it [00:04, 1662501.28it/s]
7445498it [00:04, 1674047.27it/s]
7613039it [00:04, 1673599.66it/s]
7781455it [00:04, 1676732.81it/s]
7951606it [00:04, 1684124.50it/s]
8121067it [00:04, 1687237.78it/s]
8289826it [00:05, 1683687.30it/s]
8458221it [00:05, 1679677.21it/s]
8626208it [00:05, 1675343.27it/s]
8793758it [00:05, 1665153.97it/s]
8960295it [00:05, 1660164.51it/s]
9126326it [00:05, 1657838.35it/s]
9294438it [00:05, 1664757.79it/s]
9460925it [00:05, 1660705.12it/s]
9630632it [00:05, 1671524.86it/s]
9798884it [00:05, 1674664.99it/s]
9969816it [00:06, 1685001.31it/s]
10138481it [00:06, 1685418.55it/s][W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00136_B23WHTKLT4_1.md.bai

10307029it [00:06, 1673378.89it/s]
10474390it [00:06, 1672508.78it/s]
10641657it [00:06, 1652474.79it/s]
10806962it [00:06, 1644814.06it/s]
10971483it [00:06, 1643480.53it/s]
11136883it [00:06, 1646585.03it/s]
11301563it [00:06, 1644196.13it/s]
11466668it [00:06, 1646088.44it/s]
11632554it [00:07, 1649721.32it/s]
11798772it [00:07, 1653282.92it/s]
11966256it [00:07, 1659709.26it/s]
12132234it [00:07, 1650977.59it/s]
12299421it [00:07, 1657131.54it/s]
12465238it [00:07, 1657412.98it/s]
12632098it [00:07, 1660735.65it/s]
12654606it [00:07, 1647566.31it/s]
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00136_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00136_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00136_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00136_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00136_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00136_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00136_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00136_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00136_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00136_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00136_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00136_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00136_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00136_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00136_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00136_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00136_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00136_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00136_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00136_B23WHTKLT4_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_00136_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00136_B23WHTKLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00136_B23WHTKLT4_1.md.bai
+ merge_qc -folders tih_rna_sample_00136_B23WHTKLT4_1/tih_rna_sample_00136_B23WHTKLT4_1.md -output tih_rna_sample_00136_B23WHTKLT4_1/tih_rna_sample_00136_B23WHTKLT4_1_full_basic_stats.tsv
+ head -n1 tih_rna_sample_00136_B23WHTKLT4_1/tih_rna_sample_00136_B23WHTKLT4_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_00136_B23WHTKLT4_1/tih_rna_sample_00136_B23WHTKLT4_1_full_basic_stats.tsv