+ mkdir tih_rna_sample_00588_B23MVV7LT4_1
+ all_qc -bam tih_rna_sample_00588_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_00588_B23MVV7LT4_1 -reference ref_genome.fa -region chr20
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00588_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_00588_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00588_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00588_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00588_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00588_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_00588_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00588_B23MVV7LT4_1.md.bai

0it [00:00, ?it/s]
154359it [00:00, 1543367.01it/s]
321657it [00:00, 1619565.44it/s]
492623it [00:00, 1660607.54it/s]
658684it [00:00, 1524547.06it/s]
814290it [00:00, 1535269.98it/s]
980318it [00:00, 1576211.22it/s]
1153202it [00:00, 1624719.97it/s]
1316359it [00:00, 1624270.72it/s]
1488548it [00:00, 1654346.48it/s]
1661009it [00:01, 1675775.85it/s]
1830344it [00:01, 1681100.51it/s]
2000385it [00:01, 1686929.95it/s]
2174393it [00:01, 1702961.30it/s]
2347122it [00:01, 1710255.13it/s]
2518218it [00:01, 1603466.65it/s]
2679955it [00:01, 1557534.71it/s]
2836805it [00:01, 1529659.36it/s]
2991354it [00:01, 1534039.42it/s]
3154493it [00:01, 1561967.94it/s]
3327496it [00:02, 1611084.13it/s]
3495897it [00:02, 1632531.06it/s]
3660699it [00:02, 1637077.69it/s]
3832720it [00:02, 1661759.99it/s]
4005791it [00:02, 1682276.17it/s]
4177368it [00:02, 1692126.17it/s]
4346697it [00:02, 1635119.24it/s]
4510693it [00:02, 1500458.74it/s]
4680587it [00:02, 1555271.23it/s]
4849385it [00:03, 1592844.80it/s]
5019415it [00:03, 1623702.35it/s]
5191455it [00:03, 1651870.02it/s]
5362295it [00:03, 1668467.40it/s]
5534996it [00:03, 1685759.03it/s]
5710711it [00:03, 1706938.35it/s]
5885721it [00:03, 1719764.79it/s]
6057982it [00:03, 1719597.57it/s]
6232190it [00:03, 1726228.45it/s]
6407151it [00:03, 1733089.62it/s]
6580561it [00:04, 1704032.75it/s]
6751141it [00:04, 1687340.17it/s]
6925655it [00:04, 1704371.31it/s]
7099379it [00:04, 1713967.18it/s]
7275481it [00:04, 1727925.36it/s]
7448650it [00:04, 1728881.54it/s]
7624238it [00:04, 1736926.12it/s]
7799912it [00:04, 1742827.56it/s]
7974639it [00:04, 1744131.94it/s]
8149075it [00:04, 1739571.36it/s]
8323051it [00:05, 1739574.94it/s]
8497022it [00:05, 1734950.74it/s]
8670986it [00:05, 1736331.10it/s]
8844628it [00:05, 1707378.98it/s]
9018443it [00:05, 1716470.53it/s]
9190178it [00:05, 1702747.08it/s]
9360528it [00:05, 1662682.02it/s]
9528343it [00:05, 1667181.40it/s]
9698731it [00:05, 1677975.40it/s]
9869445it [00:05, 1686595.30it/s]
10044076it [00:06, 1704331.69it/s]
10222154it [00:06, 1727101.22it/s]
10397485it [00:06, 1734910.34it/s]
10575661it [00:06, 1748900.27it/s]
10753795it [00:06, 1758462.39it/s]
10929675it [00:06, 1755795.46it/s]
11106042it [00:06, 1758130.54it/s]
11281873it [00:06, 1745946.83it/s]
11456498it [00:06, 1735414.18it/s]
11630069it [00:06, 1734702.99it/s]
11803560it [00:07, 1730520.34it/s]
11976626it [00:07, 1725783.85it/s]
12153672it [00:07, 1739084.32it/s]
12328204it [00:07, 1740930.02it/s]
12502309it [00:07, 1738151.68it/s]
12676133it [00:07, 1733290.20it/s]
12849470it [00:07, 1728249.49it/s]
13022302it [00:07, 1726850.39it/s]
13194992it [00:07, 1724835.99it/s]
13367479it [00:07, 1717395.92it/s]
13541333it [00:08, 1723683.19it/s]
13715951it [00:08, 1730382.69it/s]
13889569it [00:08, 1732015.01it/s]
14062777it [00:08, 1730959.97it/s]
14236105it [00:08, 1731635.43it/s]
14409272it [00:08, 1709436.67it/s]
14580280it [00:08, 1707577.34it/s]
14751082it [00:08, 1700780.13it/s]
14921192it [00:08, 1688071.01it/s]
15032975it [00:08, 1685011.40it/s]
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00588_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00588_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00588_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00588_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00588_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00588_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00588_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00588_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00588_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00588_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00588_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00588_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00588_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00588_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00588_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00588_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00588_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00588_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00588_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00588_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00588_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_00588_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00588_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00588_B23MVV7LT4_1.md.bai
+ merge_qc -folders tih_rna_sample_00588_B23MVV7LT4_1/tih_rna_sample_00588_B23MVV7LT4_1.md -output tih_rna_sample_00588_B23MVV7LT4_1/tih_rna_sample_00588_B23MVV7LT4_1_full_basic_stats.tsv
+ head -n1 tih_rna_sample_00588_B23MVV7LT4_1/tih_rna_sample_00588_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_00588_B23MVV7LT4_1/tih_rna_sample_00588_B23MVV7LT4_1_full_basic_stats.tsv