+ mkdir aih-tih-sc-804b22-R1_A23WJ53LT4_1
+ all_qc -bam aih-tih-sc-804b22-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-804b22-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-804b22-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-804b22-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-804b22-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-804b22-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-804b22-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-804b22-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-804b22-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-804b22-R1_A23WJ53LT4_1.md.bai

141319it [00:00, 1412830.92it/s]
300727it [00:00, 1519401.50it/s]
457885it [00:00, 1542930.70it/s]
622296it [00:00, 1582736.88it/s]
785509it [00:00, 1600522.81it/s]
952073it [00:00, 1622637.10it/s]
1115665it [00:00, 1626959.44it/s]
1282104it [00:00, 1638852.87it/s]
1451339it [00:00, 1655538.22it/s]
1618847it [00:01, 1661552.99it/s]
1785003it [00:01, 1660990.86it/s]
1951262it [00:01, 1661458.41it/s]
2117408it [00:01, 1660590.00it/s]
2283468it [00:01, 1654773.92it/s]
2454606it [00:01, 1671769.09it/s]
2623741it [00:01, 1677529.28it/s]
2791501it [00:01, 1669663.13it/s]
2958480it [00:01, 1669327.65it/s]
3128354it [00:01, 1678096.84it/s]
3296173it [00:02, 1653905.64it/s]
3461644it [00:02, 1652611.17it/s]
3630254it [00:02, 1662551.94it/s]
3800338it [00:02, 1673947.82it/s]
3967773it [00:02, 1669137.04it/s]
4134716it [00:02, 1668977.90it/s]
4301635it [00:02, 1618942.14it/s]
4463856it [00:02, 1584841.51it/s]
4626969it [00:02, 1598217.10it/s]
4787058it [00:02, 1580151.72it/s]
4945270it [00:03, 1577476.76it/s]
5103150it [00:03, 1535649.80it/s]
5256986it [00:03, 1516445.48it/s]
5421794it [00:03, 1554675.12it/s]
5577517it [00:03, 1541284.73it/s]
5731824it [00:03, 1530702.79it/s]
5900412it [00:03, 1576271.51it/s]
6058218it [00:03, 1540298.60it/s]
6214957it [00:03, 1548099.95it/s]
6382560it [00:03, 1585737.59it/s]
6544771it [00:04, 1596421.79it/s]
6713002it [00:04, 1621920.96it/s]
6880580it [00:04, 1637950.45it/s]
7045439it [00:04, 1640937.71it/s]
7211995it [00:04, 1648197.13it/s]
7378486it [00:04, 1653067.55it/s]
7543834it [00:04, 1637150.71it/s]
7709118it [00:04, 1641795.84it/s]
7876668it [00:04, 1651810.75it/s]
8044953it [00:04, 1661051.81it/s]
8216552it [00:05, 1677467.43it/s]
8384325it [00:05, 1677190.94it/s]
8555326it [00:05, 1686998.05it/s]
8724040it [00:05, 1682862.79it/s]
8892339it [00:05, 1682865.32it/s]
9060634it [00:05, 1673039.72it/s]
9229473it [00:05, 1677600.43it/s]
9397305it [00:05, 1677792.06it/s]
9565211it [00:05, 1678146.78it/s]
9733172it [00:05, 1678562.64it/s]
9901034it [00:06, 1674023.16it/s]
10068443it [00:06, 1673579.30it/s]
10235805it [00:06, 1666055.62it/s]
10402962it [00:06, 1667678.93it/s]
10569737it [00:06, 1628332.79it/s]
10732770it [00:06, 1545728.86it/s]
10899209it [00:06, 1579551.86it/s]
11065168it [00:06, 1602698.55it/s]
11134598it [00:06, 1628730.83it/s]
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-804b22-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-804b22-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-804b22-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-804b22-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-804b22-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-804b22-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-804b22-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-804b22-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-804b22-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-804b22-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-804b22-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-804b22-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-804b22-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-804b22-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-804b22-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-804b22-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-804b22-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-804b22-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-804b22-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-804b22-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-804b22-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-804b22-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-804b22-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-804b22-R1_A23WJ53LT4_1.md.bai
+ merge_qc -folders aih-tih-sc-804b22-R1_A23WJ53LT4_1/aih-tih-sc-804b22-R1_A23WJ53LT4_1.md -output aih-tih-sc-804b22-R1_A23WJ53LT4_1/aih-tih-sc-804b22-R1_A23WJ53LT4_1_full_basic_stats.tsv
+ head -n1 aih-tih-sc-804b22-R1_A23WJ53LT4_1/aih-tih-sc-804b22-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-804b22-R1_A23WJ53LT4_1/aih-tih-sc-804b22-R1_A23WJ53LT4_1_full_basic_stats.tsv