+ mkdir A673_FFPE_RNA_0001_B23LG7FLT4_1 + all_qc -bam A673_FFPE_RNA_0001_B23LG7FLT4_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 A673_FFPE_RNA_0001_B23LG7FLT4_1 -reference ref_genome.fa -region chr20 [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [mpileup] 1 samples in 1 input files [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_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: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai 0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai 157903it [00:00, 1578952.45it/s] 323728it [00:00, 1625570.68it/s] 491333it [00:00, 1648602.91it/s] 662282it [00:00, 1672442.30it/s] 833810it [00:00, 1687854.29it/s] 1004571it [00:00, 1694557.58it/s] 1174952it [00:00, 1697569.55it/s] 1344709it [00:00, 1695989.50it/s] 1514309it [00:00, 1690743.17it/s] 1685474it [00:01, 1697167.53it/s] 1856301it [00:01, 1700541.21it/s] 2026359it [00:01, 1697786.37it/s] 2196636it [00:01, 1699281.28it/s] 2367922it [00:01, 1703363.92it/s] 2538261it [00:01, 1699329.06it/s] 2708903it [00:01, 1701282.28it/s] 2879035it [00:01, 1695781.67it/s] 3048748it [00:01, 1696062.40it/s] 3219591it [00:01, 1699756.04it/s] 3389571it [00:02, 1683805.47it/s] 3558146it [00:02, 1684251.13it/s] 3726943it [00:02, 1685278.79it/s] 3897102it [00:02, 1690136.76it/s] 4070648it [00:02, 1703687.28it/s] 4241031it [00:02, 1702122.71it/s] 4411253it [00:02, 1697691.12it/s] 4581710it [00:02, 1699731.75it/s] 4752640it [00:02, 1702443.21it/s] 4922890it [00:02, 1691649.17it/s] 5092073it [00:03, 1683692.06it/s] 5264295it [00:03, 1695091.51it/s] 5435294it [00:03, 1699520.58it/s] 5606418it [00:03, 1703006.08it/s] 5778724it [00:03, 1708921.02it/s] 5949627it [00:03, 1708767.48it/s] 6122606it [00:03, 1715049.14it/s] 6294117it [00:03, 1702698.73it/s] 6464411it [00:03, 1700002.61it/s] 6634428it [00:03, 1689539.50it/s] 6803820it [00:04, 1690776.52it/s] 6972914it [00:04, 1683188.99it/s] 7141647it [00:04, 1684306.95it/s] 7310089it [00:04, 1683144.53it/s] 7478411it [00:04, 1680324.59it/s] 7647983it [00:04, 1684909.65it/s] 7816902it [00:04, 1686175.00it/s] 7986778it [00:04, 1689859.10it/s] 8158235it [00:04, 1697252.66it/s] 8327964it [00:04, 1695242.63it/s] 8499410it [00:05, 1700981.29it/s] 8669511it [00:05, 1697348.55it/s] 8840431it [00:05, 1700883.11it/s] 9010523it [00:05, 1700525.47it/s] 9180578it [00:05, 1697701.51it/s] 9350351it [00:05, 1696978.91it/s] 9520051it [00:05, 1690500.28it/s] 9691303it [00:05, 1697041.07it/s] 9861014it [00:05, 1696207.99it/s] 10030649it [00:05, 1696236.45it/s] 10200276it [00:06, 1693916.00it/s] 10369754it [00:06, 1694157.00it/s] 10539172it [00:06, 1680314.09it/s] 10709151it [00:06, 1686104.68it/s] 10881527it [00:06, 1697334.85it/s] 11051281it [00:06, 1696912.80it/s] 11223014it [00:06, 1703008.34it/s] 11394350it [00:06, 1706096.62it/s] 11568115it [00:06, 1715535.34it/s] 11739676it [00:06, 1713260.13it/s] 11911661it [00:07, 1715134.06it/s] 12083179it [00:07, 1711245.80it/s] 12254309it [00:07, 1709850.89it/s] 12425298it [00:07, 1703426.23it/s] 12597124it [00:07, 1707844.73it/s] 12767915it [00:07, 1702809.43it/s] 12938203it [00:07, 1700759.43it/s] 13108284it [00:07, 1698959.09it/s] 13278337it [00:07, 1699417.14it/s] 13448281it [00:07, 1697816.81it/s] 13619216it [00:08, 1701257.08it/s] 13789344it [00:08, 1694540.17it/s] 13958805it [00:08, 1681588.90it/s] 14126987it [00:08, 1676235.29it/s] 14294626it [00:08, 1674955.43it/s] 14462132it [00:08, 1674887.07it/s] 14550647it [00:08, 1694072.71it/s] [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_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: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.md.bai + merge_qc -folders A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1.md -output A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1_full_basic_stats.tsv + head -n1 A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed A673_FFPE_RNA_0001_B23LG7FLT4_1/A673_FFPE_RNA_0001_B23LG7FLT4_1_full_basic_stats.tsv