+ mkdir tih_rna_sample_00594_B23MVV7LT4_1 + all_qc -bam tih_rna_sample_00594_B23MVV7LT4_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 tih_rna_sample_00594_B23MVV7LT4_1 -reference ref_genome.fa -region chr20 [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00594_B23MVV7LT4_1.md.bai [mpileup] 1 samples in 1 input files [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00594_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00594_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00594_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00594_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00594_B23MVV7LT4_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: tih_rna_sample_00594_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00594_B23MVV7LT4_1.md.bai 0it [00:00, ?it/s] 152601it [00:00, 1525920.50it/s] 309599it [00:00, 1551788.04it/s] 479968it [00:00, 1621114.74it/s] 651818it [00:00, 1659526.43it/s] 822105it [00:00, 1675036.98it/s] 992912it [00:00, 1686237.94it/s] 1163276it [00:00, 1691900.91it/s] 1335442it [00:00, 1701321.89it/s] 1505679it [00:00, 1701518.15it/s] 1677967it [00:01, 1708091.52it/s] 1850446it [00:01, 1713182.25it/s] 2021765it [00:01, 1700636.58it/s] 2197142it [00:01, 1716625.37it/s] 2370029it [00:01, 1720225.80it/s] 2542392it [00:01, 1721195.51it/s] 2715452it [00:01, 1724004.33it/s] 2887960it [00:01, 1724309.35it/s] 3060398it [00:01, 1723342.99it/s] 3232737it [00:01, 1721311.15it/s] 3404872it [00:02, 1700218.16it/s] 3574952it [00:02, 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[00:07, 1720114.71it/s] 13705477it [00:08, 1719383.01it/s] 13877421it [00:08, 1690797.17it/s] 14048601it [00:08, 1696997.42it/s] 14220191it [00:08, 1702596.90it/s] 14390688it [00:08, 1703250.02it/s] 14561205it [00:08, 1703807.97it/s] 14732226it [00:08, 1705709.23it/s] 14905333it [00:08, 1713284.07it/s] 15078335it [00:08, 1718267.55it/s] 15252154it [00:08, 1724214.34it/s] 15426723it [00:09, 1730514.89it/s] 15599782it [00:09, 1714548.05it/s] 15771777it [00:09, 1716142.05it/s] 15943419it [00:09, 1707886.30it/s] 16114233it [00:09, 1706520.97it/s] 16284902it [00:09, 1698729.90it/s] 16454791it [00:09, 1686032.76it/s] 16623694it [00:09, 1686905.37it/s] 16794433it [00:09, 1692986.99it/s] 16963756it [00:09, 1693041.94it/s] 17133073it [00:10, 1676717.91it/s] 17304833it [00:10, 1688852.93it/s] 17476656it [00:10, 1697591.21it/s] 17646915it [00:10, 1699061.51it/s] 17816845it [00:10, 1689851.53it/s] 17987972it [00:10, 1696218.04it/s] 18157616it [00:10, 1694092.54it/s] 18331248it [00:10, 1706694.92it/s] 18504660it [00:10, 1714883.30it/s] 18676713it [00:10, 1716556.16it/s] 18849226it [00:11, 1719061.47it/s][W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00594_B23MVV7LT4_1.md.bai 19023388it [00:11, 1725803.20it/s] 19195974it [00:11, 1724734.65it/s] 19368452it [00:11, 1717583.30it/s] 19540220it [00:11, 1700878.99it/s] 19714089it [00:11, 1712101.26it/s] 19887168it [00:11, 1717653.34it/s] 20059827it [00:11, 1720307.79it/s] 20231880it [00:11, 1693458.24it/s] 20402387it [00:11, 1696878.12it/s] 20465254it [00:12, 1703488.24it/s] [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00594_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00594_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00594_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00594_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00594_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00594_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00594_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00594_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00594_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00594_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00594_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00594_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00594_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00594_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00594_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00594_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00594_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00594_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00594_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00594_B23MVV7LT4_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: tih_rna_sample_00594_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00594_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00594_B23MVV7LT4_1.md.bai + merge_qc -folders tih_rna_sample_00594_B23MVV7LT4_1/tih_rna_sample_00594_B23MVV7LT4_1.md -output tih_rna_sample_00594_B23MVV7LT4_1/tih_rna_sample_00594_B23MVV7LT4_1_full_basic_stats.tsv + head -n1 tih_rna_sample_00594_B23MVV7LT4_1/tih_rna_sample_00594_B23MVV7LT4_1_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed tih_rna_sample_00594_B23MVV7LT4_1/tih_rna_sample_00594_B23MVV7LT4_1_full_basic_stats.tsv