+ mkdir aih-tih-sc-3cac57-R1_A23WJ53LT4_1
+ all_qc -bam aih-tih-sc-3cac57-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-3cac57-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-3cac57-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-3cac57-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3cac57-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3cac57-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3cac57-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3cac57-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-3cac57-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3cac57-R1_A23WJ53LT4_1.md.bai
0it [00:00, ?it/s]
151796it [00:00, 1517874.59it/s]
303584it [00:00, 1509019.81it/s]
462453it [00:00, 1545256.61it/s]
628697it [00:00, 1591409.01it/s]
794512it [00:00, 1615295.52it/s]
959080it [00:00, 1625593.92it/s]
1125765it [00:00, 1638997.21it/s]
1289673it [00:00, 1636709.47it/s]
1456185it [00:00, 1645558.13it/s]
1621572it [00:01, 1647975.73it/s]
1789129it [00:01, 1656396.41it/s]
1957655it [00:01, 1665151.54it/s]
2124173it [00:01, 1657393.21it/s]
2291714it [00:01, 1662796.30it/s]
2458003it [00:01, 1660324.15it/s]
2624042it [00:01, 1641535.13it/s]
2788757it [00:01, 1643188.65it/s]
2959548it [00:01, 1662486.89it/s]
3125835it [00:01, 1617030.70it/s]
3287819it [00:02, 1611653.30it/s]
3451889it [00:02, 1620173.47it/s]
3621717it [00:02, 1643283.53it/s]
3793600it [00:02, 1665717.25it/s]
3960287it [00:02, 1505355.78it/s]
4125088it [00:02, 1544960.33it/s]
4293025it [00:02, 1583122.42it/s]
4460008it [00:02, 1608123.08it/s]
4624421it [00:02, 1618610.94it/s]
4793598it [00:02, 1640115.43it/s]
4962562it [00:03, 1654447.16it/s]
5128555it [00:03, 1627661.08it/s]
5298211it [00:03, 1647917.78it/s]
5463366it [00:03, 1639485.74it/s]
5627569it [00:03, 1631306.19it/s]
5796881it [00:03, 1649541.19it/s]
5964270it [00:03, 1656752.93it/s]
6132052it [00:03, 1662949.72it/s]
6300753it [00:03, 1670108.96it/s]
6467825it [00:03, 1655793.38it/s]
6633471it [00:04, 1619778.18it/s]
6795644it [00:04, 1460474.98it/s]
6944605it [00:04, 1372979.75it/s]
7093337it [00:04, 1403575.53it/s]
7261373it [00:04, 1480211.29it/s]
7429503it [00:04, 1537194.30it/s]
7598669it [00:04, 1581692.16it/s]
7764190it [00:04, 1603110.50it/s]
7933646it [00:04, 1629986.59it/s]
8097466it [00:05, 1518091.53it/s]
8251315it [00:05, 1490607.59it/s]
8420358it [00:05, 1547085.76it/s]
8576396it [00:05, 1535178.33it/s]
8743209it [00:05, 1573604.44it/s]
8911885it [00:05, 1606660.14it/s]
9079809it [00:05, 1628016.84it/s]
9247508it [00:05, 1642493.06it/s]
9412113it [00:05, 1622190.90it/s]
9584927it [00:05, 1653371.64it/s]
9756556it [00:06, 1672018.06it/s]
9929168it [00:06, 1688101.36it/s]
10100281it [00:06, 1694945.66it/s]
10269885it [00:06, 1693757.34it/s]
10439671it [00:06, 1694835.98it/s]
10609790it [00:06, 1696711.56it/s]
10779500it [00:06, 1691975.08it/s]
10949994it [00:06, 1695822.51it/s]
11119598it [00:06, 1691591.58it/s]
11289027it [00:06, 1692371.14it/s]
11459052it [00:07, 1694647.51it/s]
11629511it [00:07, 1697137.36it/s]
11802184it [00:07, 1705970.52it/s]
11972941it [00:07, 1706385.76it/s]
12144746it [00:07, 1709854.93it/s]
12316931it [00:07, 1713419.03it/s]
12488276it [00:07, 1707836.22it/s]
12659193it [00:07, 1708204.14it/s]
12830018it [00:07, 1707545.40it/s]
13000776it [00:07, 1698122.42it/s]
13171951it [00:08, 1702163.10it/s]
13343618it [00:08, 1706467.68it/s]
13514274it [00:08, 1702192.75it/s]
13684502it [00:08, 1688545.92it/s]
13853383it [00:08, 1688246.48it/s]
14022911it [00:08, 1690250.99it/s]
14192302it [00:08, 1691310.92it/s]
14361444it [00:08, 1686518.42it/s]
14530105it [00:08, 1680150.05it/s]
14698750it [00:08, 1682000.25it/s]
14866958it [00:09, 1675007.11it/s]
15036353it [00:09, 1680625.06it/s]
15205221it [00:09, 1682984.51it/s]
15373528it [00:09, 1682579.72it/s]
15544359it [00:09, 1690252.66it/s]
15713390it [00:09, 1689384.73it/s]
15882333it [00:09, 1662515.28it/s]
16048680it [00:09, 1648845.71it/s]
16214753it [00:09, 1652330.94it/s]
16380045it [00:10, 1648583.40it/s]
16479657it [00:10, 1638076.44it/s]
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3cac57-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3cac57-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3cac57-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3cac57-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3cac57-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3cac57-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3cac57-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3cac57-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3cac57-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3cac57-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3cac57-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3cac57-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3cac57-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3cac57-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3cac57-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3cac57-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3cac57-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3cac57-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3cac57-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3cac57-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3cac57-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-3cac57-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3cac57-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3cac57-R1_A23WJ53LT4_1.md.bai
+ merge_qc -folders aih-tih-sc-3cac57-R1_A23WJ53LT4_1/aih-tih-sc-3cac57-R1_A23WJ53LT4_1.md -output aih-tih-sc-3cac57-R1_A23WJ53LT4_1/aih-tih-sc-3cac57-R1_A23WJ53LT4_1_full_basic_stats.tsv
+ head -n1 aih-tih-sc-3cac57-R1_A23WJ53LT4_1/aih-tih-sc-3cac57-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-3cac57-R1_A23WJ53LT4_1/aih-tih-sc-3cac57-R1_A23WJ53LT4_1_full_basic_stats.tsv