+ mkdir 786-O_FFPE_RNA_0001_B23LG7FLT4_3 + all_qc -bam 786-O_FFPE_RNA_0001_B23LG7FLT4_3.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 786-O_FFPE_RNA_0001_B23LG7FLT4_3 -reference ref_genome.fa -region chr20 [W::hts_idx_load3] The index file is older than the data file: 786-O_FFPE_RNA_0001_B23LG7FLT4_3.md.bai [mpileup] 1 samples in 1 input files [W::hts_idx_load3] The index file is older than the data file: 786-O_FFPE_RNA_0001_B23LG7FLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: 786-O_FFPE_RNA_0001_B23LG7FLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: 786-O_FFPE_RNA_0001_B23LG7FLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: 786-O_FFPE_RNA_0001_B23LG7FLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: 786-O_FFPE_RNA_0001_B23LG7FLT4_3.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: 786-O_FFPE_RNA_0001_B23LG7FLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: 786-O_FFPE_RNA_0001_B23LG7FLT4_3.md.bai 0it [00:00, ?it/s] 160885it [00:00, 1608794.00it/s] 329110it [00:00, 1651973.60it/s] 502024it [00:00, 1687187.48it/s] 673504it [00:00, 1698071.45it/s] 844897it [00:00, 1703773.07it/s] 1016191it [00:00, 1706875.11it/s] 1186879it [00:00, 1705533.27it/s] 1357433it [00:00, 1703085.10it/s] 1530029it [00:00, 1710211.61it/s] 1701052it [00:01, 1701336.41it/s] 1871197it [00:01, 1695963.23it/s] 2044267it [00:01, 1706456.55it/s] 2215734it [00:01, 1708921.40it/s] 2387498it [00:01, 1711532.66it/s] 2558659it [00:01, 1706996.10it/s] 2731044it [00:01, 1711910.56it/s] 2902242it [00:01, 1709837.96it/s] 3074904it [00:01, 1714854.37it/s] 3246394it [00:01, 1713655.78it/s] 3417763it [00:02, 1694577.82it/s] 3588488it [00:02, 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1716975.23it/s] 8724497it [00:05, 1716810.09it/s] 8897432it [00:05, 1720554.99it/s] 9070496it [00:05, 1723564.06it/s] 9242854it [00:05, 1711173.63it/s] 9413993it [00:05, 1711004.94it/s] 9585108it [00:05, 1709814.56it/s] 9756100it [00:05, 1709419.98it/s] 9928541it [00:05, 1713783.34it/s] 10100878it [00:05, 1716635.31it/s] 10275109it [00:06, 1724308.01it/s] 10449687it [00:06, 1730723.60it/s] 10622763it [00:06, 1722298.00it/s] 10795005it [00:06, 1718006.54it/s] 10970037it [00:06, 1727502.96it/s] 11143679it [00:06, 1729993.68it/s] 11317135it [00:06, 1731197.84it/s] 11493267it [00:06, 1740202.44it/s] 11667293it [00:06, 1732959.05it/s] 11840599it [00:06, 1723382.78it/s] 12012954it [00:07, 1718503.25it/s] 12184816it [00:07, 1715811.20it/s] 12358614it [00:07, 1722399.85it/s] 12531198it [00:07, 1723411.05it/s] 12704120it [00:07, 1725130.86it/s] 12876639it [00:07, 1722972.10it/s] 13048940it [00:07, 1719862.79it/s] 13221159it [00:07, 1720543.49it/s] 13393216it [00:07, 1717418.46it/s] 13564961it [00:07, 1710965.85it/s] 13736064it [00:08, 1706785.49it/s] 13906747it [00:08, 1702049.13it/s] 14076956it [00:08, 1676454.22it/s] 14245839it [00:08, 1680045.57it/s] 14413903it [00:08, 1677674.63it/s] 14585289it [00:08, 1688427.93it/s] 14754903it [00:08, 1690713.16it/s] 14925943it [00:08, 1696580.25it/s] 15096224it [00:08, 1698427.43it/s] 15266645it [00:08, 1699965.08it/s] 15438879it [00:09, 1706553.61it/s] 15610047it [00:09, 1708073.28it/s] 15781078it [00:09, 1708640.47it/s] 15781895it [00:09, 1708116.07it/s] [W::hts_idx_load3] The index file is older than the data file: 786-O_FFPE_RNA_0001_B23LG7FLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: 786-O_FFPE_RNA_0001_B23LG7FLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: 786-O_FFPE_RNA_0001_B23LG7FLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: 786-O_FFPE_RNA_0001_B23LG7FLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: 786-O_FFPE_RNA_0001_B23LG7FLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: 786-O_FFPE_RNA_0001_B23LG7FLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: 786-O_FFPE_RNA_0001_B23LG7FLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: 786-O_FFPE_RNA_0001_B23LG7FLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: 786-O_FFPE_RNA_0001_B23LG7FLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: 786-O_FFPE_RNA_0001_B23LG7FLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: 786-O_FFPE_RNA_0001_B23LG7FLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: 786-O_FFPE_RNA_0001_B23LG7FLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: 786-O_FFPE_RNA_0001_B23LG7FLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: 786-O_FFPE_RNA_0001_B23LG7FLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: 786-O_FFPE_RNA_0001_B23LG7FLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: 786-O_FFPE_RNA_0001_B23LG7FLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: 786-O_FFPE_RNA_0001_B23LG7FLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: 786-O_FFPE_RNA_0001_B23LG7FLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: 786-O_FFPE_RNA_0001_B23LG7FLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: 786-O_FFPE_RNA_0001_B23LG7FLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: 786-O_FFPE_RNA_0001_B23LG7FLT4_3.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: 786-O_FFPE_RNA_0001_B23LG7FLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: 786-O_FFPE_RNA_0001_B23LG7FLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: 786-O_FFPE_RNA_0001_B23LG7FLT4_3.md.bai + merge_qc -folders 786-O_FFPE_RNA_0001_B23LG7FLT4_3/786-O_FFPE_RNA_0001_B23LG7FLT4_3.md -output 786-O_FFPE_RNA_0001_B23LG7FLT4_3/786-O_FFPE_RNA_0001_B23LG7FLT4_3_full_basic_stats.tsv + head -n1 786-O_FFPE_RNA_0001_B23LG7FLT4_3/786-O_FFPE_RNA_0001_B23LG7FLT4_3_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed 786-O_FFPE_RNA_0001_B23LG7FLT4_3/786-O_FFPE_RNA_0001_B23LG7FLT4_3_full_basic_stats.tsv