+ mkdir tih_rna_sample_00570_B23MVV7LT4_1 + all_qc -bam tih_rna_sample_00570_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_00570_B23MVV7LT4_1 -reference ref_genome.fa -region chr20 [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_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_00570_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_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_00570_B23MVV7LT4_1.md.bai 0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_1.md.bai 140517it [00:00, 1405060.79it/s] 298968it [00:00, 1510574.25it/s] 460962it [00:00, 1560476.34it/s] 629263it [00:00, 1608821.49it/s] 792037it [00:00, 1615616.19it/s] 960162it [00:00, 1637903.66it/s] 1131315it [00:00, 1661936.00it/s] 1299966it [00:00, 1669726.46it/s] 1469000it [00:00, 1676147.07it/s] 1639243it [00:01, 1684234.08it/s] 1808851it [00:01, 1687728.14it/s] 1980010it [00:01, 1694964.96it/s] 2149507it [00:01, 1663776.07it/s] 2316610it [00:01, 1665915.50it/s] 2487533it [00:01, 1678828.42it/s] 2657125it [00:01, 1683914.19it/s] 2830033it [00:01, 1697410.86it/s] 3005627it [00:01, 1714921.24it/s] 3177596it [00:01, 1716321.39it/s] 3349255it [00:02, 1701488.55it/s] 3522750it [00:02, 1711373.34it/s] 3698370it [00:02, 1724599.18it/s] 3870864it [00:02, 1720020.20it/s] 4042891it [00:02, 1704059.19it/s] 4215589it [00:02, 1710828.11it/s] 4386710it [00:02, 1709158.58it/s] 4557652it [00:02, 1697180.61it/s] 4727510it [00:02, 1697556.32it/s] 4897288it [00:02, 1691740.44it/s] 5066479it [00:03, 1652434.65it/s] 5233983it [00:03, 1658956.46it/s] 5405829it [00:03, 1676504.27it/s] 5577640it [00:03, 1688816.08it/s] 5749960it [00:03, 1698965.12it/s] 5924289it [00:03, 1712147.42it/s] 6095567it [00:03, 1708147.14it/s] 6266427it [00:03, 1705964.74it/s] 6437055it [00:03, 1700124.47it/s] 6607092it [00:03, 1699686.66it/s] 6779891it [00:04, 1708100.35it/s] 6950716it [00:04, 1691067.48it/s] 7122606it [00:04, 1699313.13it/s] 7292577it [00:04, 1699138.46it/s] 7464879it [00:04, 1706240.66it/s] 7635526it [00:04, 1705815.94it/s] 7806683it [00:04, 1707510.43it/s] 7980396it [00:04, 1716349.70it/s] 8153160it [00:04, 1719708.60it/s] 8327571it [00:04, 1726902.28it/s] 8500839it [00:05, 1728611.49it/s] 8675501it [00:05, 1733972.36it/s] 8850594it [00:05, 1738932.83it/s] 9024490it [00:05, 1736025.56it/s] 9198096it [00:05, 1689491.81it/s] 9370496it [00:05, 1699612.80it/s] 9545491it [00:05, 1714350.61it/s] 9717364it [00:05, 1715626.38it/s] 9890570it [00:05, 1720499.40it/s] 10062707it [00:05, 1716602.01it/s] 10234589it [00:06, 1717233.94it/s] 10407473it [00:06, 1720675.50it/s] 10579572it [00:06, 1717362.71it/s] 10752612it [00:06, 1721233.80it/s] 10924753it [00:06, 1718299.79it/s] 11098414it [00:06, 1723683.44it/s] 11117330it [00:06, 1696118.10it/s] [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_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_00570_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_1.md.bai + merge_qc -folders tih_rna_sample_00570_B23MVV7LT4_1/tih_rna_sample_00570_B23MVV7LT4_1.md -output tih_rna_sample_00570_B23MVV7LT4_1/tih_rna_sample_00570_B23MVV7LT4_1_full_basic_stats.tsv + head -n1 tih_rna_sample_00570_B23MVV7LT4_1/tih_rna_sample_00570_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_00570_B23MVV7LT4_1/tih_rna_sample_00570_B23MVV7LT4_1_full_basic_stats.tsv