+ mkdir 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_2 + all_qc -bam 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_2.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 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_2 -reference ref_genome.fa -region chr20 [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [mpileup] 1 samples in 1 input files [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_2.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: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_2.md.bai 0it [00:00, ?it/s] 150912it [00:00, 1508855.23it/s] 315462it [00:00, 1589187.25it/s] 482118it [00:00, 1624434.75it/s] 652770it [00:00, 1656814.74it/s] 823104it [00:00, 1673570.25it/s] 994431it [00:00, 1687046.31it/s] 1166723it [00:00, 1698734.65it/s] 1338115it [00:00, 1703548.58it/s] 1508470it [00:00, 1698878.58it/s] 1680662it [00:01, 1705953.71it/s] 1854068it [00:01, 1714518.38it/s] 2025524it [00:01, 1700313.53it/s] 2197443it [00:01, 1705973.43it/s] 2373981it [00:01, 1723811.76it/s] 2547340it [00:01, 1726728.10it/s] 2720031it [00:01, 1721355.02it/s] 2893911it [00:01, 1726559.30it/s] 3066580it [00:01, 1717563.93it/s] 3238906it [00:01, 1719243.73it/s] 3410844it [00:02, 1701057.99it/s] 3584716it [00:02, 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1726584.71it/s] 18520888it [00:10, 1725413.57it/s] 18693432it [00:10, 1723136.13it/s] 18865748it [00:11, 1721866.47it/s] 19037936it [00:11, 1719099.54it/s] 19209848it [00:11, 1714300.00it/s] 19381940it [00:11, 1716265.84it/s] 19554322it [00:11, 1718455.71it/s] 19727788it [00:11, 1723188.12it/s] 19900110it [00:11, 1721217.46it/s] 20072234it [00:11, 1715900.03it/s] 20243852it [00:11, 1715969.55it/s] 20418589it [00:11, 1725279.21it/s] 20591242it [00:12, 1725635.82it/s] 20767373it [00:12, 1736308.41it/s] 20941008it [00:12, 1731051.33it/s] 21115117it [00:12, 1734039.16it/s] 21288526it [00:12, 1726241.80it/s] 21461161it [00:12, 1724313.83it/s] 21635541it [00:12, 1730119.87it/s] 21808560it [00:12, 1724507.73it/s] 21981019it [00:12, 1720265.29it/s] 22151608it [00:13, 1703753.09it/s] [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_2.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: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_2.md.bai + merge_qc -folders 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_2/1173_CRL_T1_RNA_SLD_01_A23T55JLT4_2.md -output 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_2/1173_CRL_T1_RNA_SLD_01_A23T55JLT4_2_full_basic_stats.tsv + head -n1 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_2/1173_CRL_T1_RNA_SLD_01_A23T55JLT4_2_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_2/1173_CRL_T1_RNA_SLD_01_A23T55JLT4_2_full_basic_stats.tsv