+ mkdir aih-tih-sc-835699-R1_A23WJ53LT4_1
+ all_qc -bam aih-tih-sc-835699-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-835699-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-835699-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-835699-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-835699-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-835699-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-835699-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-835699-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-835699-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-835699-R1_A23WJ53LT4_1.md.bai

144522it [00:00, 1444994.00it/s]
307907it [00:00, 1556022.75it/s]
463510it [00:00, 1540461.17it/s]
625089it [00:00, 1569935.29it/s]
783124it [00:00, 1573646.97it/s]
940509it [00:00, 1544475.35it/s]
1104799it [00:00, 1576148.23it/s]
1273425it [00:00, 1610818.30it/s]
1443721it [00:00, 1639390.21it/s]
1610649it [00:01, 1648538.45it/s]
1779041it [00:01, 1659212.32it/s]
1945614it [00:01, 1661160.85it/s]
2117895it [00:01, 1679683.88it/s]
2287142it [00:01, 1683515.11it/s]
2462433it [00:01, 1704388.64it/s]
2635987it [00:01, 1713729.29it/s]
2807372it [00:01, 1707191.55it/s]
2978438it [00:01, 1708205.53it/s]
3151741it [00:01, 1715619.20it/s]
3323312it [00:02, 1690453.16it/s]
3493390it [00:02, 1693495.45it/s]
3662851it [00:02, 1693700.32it/s]
3832266it [00:02, 1687647.07it/s]
4001537it [00:02, 1689094.39it/s]
4170471it [00:02, 1688393.98it/s]
4340720it [00:02, 1692585.76it/s]
4513388it [00:02, 1702766.63it/s]
4683677it [00:02, 1702629.00it/s]
4853949it [00:02, 1700618.26it/s]
5024017it [00:03, 1690777.61it/s]
5196914it [00:03, 1702152.41it/s]
5369495it [00:03, 1709200.74it/s]
5541077it [00:03, 1711163.52it/s]
5719953it [00:03, 1734379.25it/s]
5893403it [00:03, 1734269.74it/s]
6066839it [00:03, 1719792.50it/s]
6238851it [00:03, 1707741.21it/s]
6409660it [00:03, 1694818.00it/s]
6579177it [00:03, 1691175.03it/s]
6748317it [00:04, 1686272.60it/s]
6919431it [00:04, 1693648.89it/s]
7090475it [00:04, 1698576.17it/s]
7262150it [00:04, 1703990.93it/s]
7435445it [00:04, 1712637.05it/s]
7607983it [00:04, 1716436.02it/s]
7779636it [00:04, 1715602.14it/s]
7951203it [00:04, 1702402.53it/s]
8121470it [00:04, 1701191.55it/s]
8291607it [00:04, 1700946.30it/s]
8461714it [00:05, 1681064.53it/s]
8629876it [00:05, 1644582.53it/s]
8802302it [00:05, 1667927.11it/s]
8972268it [00:05, 1677272.80it/s]
9144266it [00:05, 1689928.16it/s]
9317787it [00:05, 1703391.60it/s]
9491662it [00:05, 1713925.59it/s]
9663124it [00:05, 1705777.38it/s]
9833757it [00:05, 1705852.90it/s]
10004381it [00:05, 1701414.46it/s]
10177579it [00:06, 1710523.63it/s]
10349726it [00:06, 1713763.69it/s]
10521121it [00:06, 1697827.95it/s]
10691915it [00:06, 1700822.54it/s]
10863194it [00:06, 1704348.82it/s]
11033797it [00:06, 1704837.03it/s]
11204299it [00:06, 1704675.84it/s]
11374779it [00:06, 1701027.43it/s]
11546601it [00:06, 1706083.93it/s]
11717218it [00:06, 1706071.22it/s]
11888427it [00:07, 1707849.01it/s]
12059217it [00:07, 1705519.00it/s]
12231092it [00:07, 1709468.59it/s]
12402042it [00:07, 1706057.31it/s]
12468521it [00:07, 1687521.02it/s]
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-835699-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-835699-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-835699-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-835699-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-835699-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-835699-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-835699-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-835699-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-835699-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-835699-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-835699-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-835699-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-835699-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-835699-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-835699-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-835699-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-835699-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-835699-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-835699-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-835699-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-835699-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-835699-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-835699-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-835699-R1_A23WJ53LT4_1.md.bai
+ merge_qc -folders aih-tih-sc-835699-R1_A23WJ53LT4_1/aih-tih-sc-835699-R1_A23WJ53LT4_1.md -output aih-tih-sc-835699-R1_A23WJ53LT4_1/aih-tih-sc-835699-R1_A23WJ53LT4_1_full_basic_stats.tsv
+ head -n1 aih-tih-sc-835699-R1_A23WJ53LT4_1/aih-tih-sc-835699-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-835699-R1_A23WJ53LT4_1/aih-tih-sc-835699-R1_A23WJ53LT4_1_full_basic_stats.tsv