+ mkdir BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1 + all_qc -bam BVT_FFPE_TRNA_bst_02_A23WKFTLT4_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 BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1 -reference ref_genome.fa -region chr20 [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.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_bst_02_A23WKFTLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_02_A23WKFTLT4_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: BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.md.bai 0it [00:00, ?it/s] 143880it [00:00, 1438743.06it/s] 298009it [00:00, 1499033.11it/s] 457082it [00:00, 1540878.51it/s] 616528it [00:00, 1562007.02it/s] 774472it [00:00, 1568272.29it/s] 932049it [00:00, 1570707.38it/s] 1089677it [00:00, 1572509.96it/s] 1247187it [00:00, 1573318.22it/s] 1404519it [00:00, 1572613.66it/s] 1561781it [00:01, 1564978.14it/s] 1719304it [00:01, 1568087.76it/s] 1876120it [00:01, 1565660.10it/s] 2032691it [00:01, 1559663.91it/s] 2188665it [00:01, 1558193.97it/s] 2344489it [00:01, 1542502.30it/s] 2501624it [00:01, 1551086.40it/s] 2657545it [00:01, 1553496.20it/s] 2817441it [00:01, 1566947.88it/s] 2975205it [00:01, 1570130.61it/s] 3132236it [00:02, 1560596.42it/s] 3288319it [00:02, 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1560407.55it/s] 8033265it [00:05, 1575334.76it/s] 8194191it [00:05, 1585333.90it/s] 8353339it [00:05, 1587148.62it/s] 8512085it [00:05, 1583716.98it/s] 8670479it [00:05, 1582985.66it/s] 8828793it [00:05, 1577834.86it/s] 8986590it [00:05, 1571300.45it/s] 9143733it [00:05, 1565134.20it/s] 9300258it [00:05, 1562172.37it/s] 9458361it [00:06, 1567722.23it/s] 9615142it [00:06, 1559443.73it/s] 9771609it [00:06, 1560892.71it/s] 9930460it [00:06, 1569118.26it/s] 10087383it [00:06, 1566222.55it/s] 10246248it [00:06, 1572874.90it/s] 10404230it [00:06, 1574935.48it/s] 10562821it [00:06, 1578200.85it/s] 10722290it [00:06, 1583120.17it/s] 10885150it [00:06, 1596591.24it/s] 11044813it [00:07, 1590978.97it/s] 11203918it [00:07, 1586725.68it/s] 11362597it [00:07, 1584754.89it/s] 11521486it [00:07, 1585961.96it/s] 11680855it [00:07, 1588254.47it/s] 11839684it [00:07, 1583306.41it/s] 11998020it [00:07, 1578592.55it/s] 12155885it [00:07, 1570143.62it/s] 12312910it [00:07, 1564736.33it/s] 12469392it [00:07, 1564161.95it/s] 12626722it [00:08, 1566814.41it/s] 12783409it [00:08, 1559757.47it/s] 12939393it [00:08, 1547385.06it/s] 13094153it [00:08, 1546146.04it/s] 13250091it [00:08, 1550066.55it/s] 13405111it [00:08, 1546405.22it/s] 13560104it [00:08, 1547437.68it/s] 13714855it [00:08, 1531554.01it/s] 13869712it [00:08, 1536584.11it/s] 13927110it [00:08, 1565811.20it/s] [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_02_A23WKFTLT4_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: BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.md.bai + merge_qc -folders BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.md -output BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1_full_basic_stats.tsv + head -n1 BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1_full_basic_stats.tsv