+ mkdir BVT_FFPE_TRNA_utn_04_A23WKFTLT4_3 + all_qc -bam BVT_FFPE_TRNA_utn_04_A23WKFTLT4_3.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 BVT_FFPE_TRNA_utn_04_A23WKFTLT4_3 -reference ref_genome.fa -region chr20 [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_utn_04_A23WKFTLT4_3.md.bai [mpileup] 1 samples in 1 input files [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_utn_04_A23WKFTLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_utn_04_A23WKFTLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_utn_04_A23WKFTLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_utn_04_A23WKFTLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_utn_04_A23WKFTLT4_3.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: BVT_FFPE_TRNA_utn_04_A23WKFTLT4_3.md.bai 0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_utn_04_A23WKFTLT4_3.md.bai 161236it [00:00, 1612219.32it/s] 336534it [00:00, 1694963.02it/s] 513037it [00:00, 1726917.17it/s] 692276it [00:00, 1752723.60it/s] 871262it [00:00, 1765963.54it/s] 1049089it [00:00, 1770112.11it/s] 1229746it [00:00, 1781998.85it/s] 1407946it [00:00, 1759668.35it/s] 1583972it [00:00, 1742824.98it/s] 1759404it [00:01, 1746299.95it/s] 1936642it [00:01, 1754178.56it/s] 2112100it [00:01, 1751854.51it/s] 2288588it [00:01, 1755752.24it/s] 2470360it [00:01, 1774373.77it/s] 2647819it [00:01, 1654297.42it/s] 2818960it [00:01, 1670601.60it/s] 2987638it [00:01, 1675217.41it/s] 3159382it [00:01, 1687558.73it/s] 3337168it [00:01, 1714092.64it/s] 3509073it [00:02, 1700886.71it/s] 3689416it [00:02, 1731175.81it/s] 3871271it [00:02, 1757099.84it/s] 4047215it [00:02, 1741906.47it/s] 4227211it [00:02, 1759098.17it/s] 4405061it [00:02, 1764841.78it/s] 4586377it [00:02, 1779183.56it/s] 4765936it [00:02, 1784053.58it/s] 4946430it [00:02, 1790132.83it/s] 5126301it [00:02, 1792670.61it/s] 5305720it [00:03, 1793098.12it/s] 5485052it [00:03, 1780404.03it/s] 5663128it [00:03, 1764472.30it/s] 5839624it [00:03, 1744558.25it/s] 6014146it [00:03, 1722331.82it/s] 6190009it [00:03, 1732977.39it/s] 6367109it [00:03, 1744200.85it/s] 6547008it [00:03, 1760446.74it/s] 6723118it [00:03, 1736836.32it/s] 6896904it [00:03, 1729557.26it/s] 7074455it [00:04, 1743073.39it/s] 7253476it [00:04, 1757054.46it/s] 7430206it [00:04, 1759996.11it/s] 7610995it [00:04, 1774268.42it/s] 7788459it [00:04, 1631421.03it/s] 7953858it [00:04, 1511157.99it/s][W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_utn_04_A23WKFTLT4_3.md.bai 8107890it [00:04, 1497852.95it/s] 8282366it [00:04, 1566039.06it/s] 8455889it [00:04, 1613889.48it/s] 8630867it [00:05, 1652987.79it/s] 8808935it [00:05, 1690172.61it/s] 8988311it [00:05, 1720592.64it/s] 9162575it [00:05, 1727033.84it/s] 9343617it [00:05, 1751773.72it/s] 9525276it [00:05, 1771052.65it/s] 9707913it [00:05, 1787541.67it/s] 9889160it [00:05, 1794968.95it/s] 10072278it [00:05, 1805779.01it/s] 10255177it [00:05, 1812706.17it/s] 10436666it [00:06, 1813336.42it/s] 10618057it [00:06, 1796803.22it/s] 10797811it [00:06, 1782886.03it/s] 10976167it [00:06, 1779639.15it/s] 11156751it [00:06, 1787406.21it/s] 11337227it [00:06, 1792442.15it/s] 11516501it [00:06, 1643305.44it/s] 11683237it [00:06, 1592147.83it/s] 11844243it [00:06, 1525944.51it/s] 11998335it [00:06, 1487490.77it/s] 12148083it [00:07, 1460819.58it/s] 12294785it [00:07, 1431934.97it/s] 12472753it [00:07, 1529663.95it/s] 12651198it [00:07, 1602641.21it/s] 12830033it [00:07, 1656545.73it/s][W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_utn_04_A23WKFTLT4_3.md.bai 12936467it [00:07, 1708410.36it/s] [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_utn_04_A23WKFTLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_utn_04_A23WKFTLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_utn_04_A23WKFTLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_utn_04_A23WKFTLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_utn_04_A23WKFTLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_utn_04_A23WKFTLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_utn_04_A23WKFTLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_utn_04_A23WKFTLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_utn_04_A23WKFTLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_utn_04_A23WKFTLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_utn_04_A23WKFTLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_utn_04_A23WKFTLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_utn_04_A23WKFTLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_utn_04_A23WKFTLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_utn_04_A23WKFTLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_utn_04_A23WKFTLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_utn_04_A23WKFTLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_utn_04_A23WKFTLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_utn_04_A23WKFTLT4_3.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: BVT_FFPE_TRNA_utn_04_A23WKFTLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_utn_04_A23WKFTLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_utn_04_A23WKFTLT4_3.md.bai + merge_qc -folders BVT_FFPE_TRNA_utn_04_A23WKFTLT4_3/BVT_FFPE_TRNA_utn_04_A23WKFTLT4_3.md -output BVT_FFPE_TRNA_utn_04_A23WKFTLT4_3/BVT_FFPE_TRNA_utn_04_A23WKFTLT4_3_full_basic_stats.tsv + head -n1 BVT_FFPE_TRNA_utn_04_A23WKFTLT4_3/BVT_FFPE_TRNA_utn_04_A23WKFTLT4_3_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed BVT_FFPE_TRNA_utn_04_A23WKFTLT4_3/BVT_FFPE_TRNA_utn_04_A23WKFTLT4_3_full_basic_stats.tsv