+ mkdir tih_rna_sample_00150_B23WHTKLT4_1 + all_qc -bam tih_rna_sample_00150_B23WHTKLT4_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_00150_B23WHTKLT4_1 -reference ref_genome.fa -region chr20 [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00150_B23WHTKLT4_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_00150_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00150_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00150_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00150_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00150_B23WHTKLT4_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_00150_B23WHTKLT4_1.md.bai 0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00150_B23WHTKLT4_1.md.bai 138668it [00:00, 1386231.84it/s] 277292it [00:00, 1345610.20it/s] 411935it [00:00, 1247062.44it/s] 566822it [00:00, 1359574.02it/s] 727598it [00:00, 1445724.45it/s] 895654it [00:00, 1523614.43it/s] 1063255it [00:00, 1572594.64it/s] 1233118it [00:00, 1612245.18it/s] 1394842it [00:00, 1604317.76it/s] 1559030it [00:01, 1615784.77it/s] 1726170it [00:01, 1632574.67it/s] 1894917it [00:01, 1649172.31it/s] 2061816it [00:01, 1655056.65it/s] 2230852it [00:01, 1665680.21it/s] 2397491it [00:01, 1663848.10it/s] 2563925it [00:01, 1651046.83it/s] 2730566it [00:01, 1655509.25it/s] 2896159it [00:01, 1650664.58it/s] 3061256it [00:01, 1640893.81it/s] 3227436it [00:02, 1647100.85it/s] 3399751it [00:02, 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1663557.89it/s] 8421686it [00:05, 1677038.25it/s] 8589450it [00:05, 1675025.21it/s] 8756994it [00:05, 1668078.12it/s] 8924348it [00:05, 1669660.57it/s] 9094423it [00:05, 1678921.54it/s] 9263090it [00:05, 1681065.10it/s] 9431212it [00:05, 1649298.62it/s] 9596281it [00:05, 1645038.33it/s] 9762580it [00:05, 1650253.04it/s] 9927678it [00:06, 1640142.98it/s] 10091749it [00:06, 1611923.76it/s] 10257722it [00:06, 1625954.75it/s] 10424855it [00:06, 1639362.37it/s] 10595916it [00:06, 1660508.32it/s] 10764185it [00:06, 1667097.98it/s] 10934965it [00:06, 1679224.51it/s] 11102940it [00:06, 1622600.65it/s] 11268901it [00:06, 1633389.95it/s] 11433736it [00:06, 1637772.34it/s] 11598490it [00:07, 1640640.56it/s] 11762728it [00:07, 1637962.35it/s] 11926645it [00:07, 1615447.24it/s] 12088329it [00:07, 1501847.59it/s] 12253249it [00:07, 1543342.49it/s] 12412161it [00:07, 1556458.77it/s] 12575586it [00:07, 1578996.93it/s] 12734274it [00:07, 1569340.15it/s] 12891756it [00:07, 1542417.43it/s][W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00150_B23WHTKLT4_1.md.bai 13054508it [00:08, 1567233.53it/s] 13211610it [00:08, 1558198.59it/s] 13367692it [00:08, 1450206.98it/s] 13519683it [00:08, 1445709.96it/s] 13675093it [00:08, 1476401.73it/s] 13837852it [00:08, 1519944.51it/s] 13997679it [00:08, 1542766.34it/s] 14053897it [00:08, 1613700.88it/s] [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00150_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00150_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00150_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00150_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00150_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00150_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00150_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00150_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00150_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00150_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00150_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00150_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00150_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00150_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00150_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00150_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00150_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00150_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00150_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00150_B23WHTKLT4_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_00150_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00150_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00150_B23WHTKLT4_1.md.bai + merge_qc -folders tih_rna_sample_00150_B23WHTKLT4_1/tih_rna_sample_00150_B23WHTKLT4_1.md -output tih_rna_sample_00150_B23WHTKLT4_1/tih_rna_sample_00150_B23WHTKLT4_1_full_basic_stats.tsv + head -n1 tih_rna_sample_00150_B23WHTKLT4_1/tih_rna_sample_00150_B23WHTKLT4_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_00150_B23WHTKLT4_1/tih_rna_sample_00150_B23WHTKLT4_1_full_basic_stats.tsv