+ mkdir A673_FFPE_RNA_0001_B23LG7FLT4_3 + all_qc -bam A673_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 A673_FFPE_RNA_0001_B23LG7FLT4_3 -reference ref_genome.fa -region chr20 [W::hts_idx_load3] The index file is older than the data file: A673_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: A673_FFPE_RNA_0001_B23LG7FLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_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: A673_FFPE_RNA_0001_B23LG7FLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_3.md.bai 0it [00:00, ?it/s] 149422it [00:00, 1494089.62it/s] 312548it [00:00, 1574639.15it/s] 479555it [00:00, 1618182.74it/s] 648416it [00:00, 1645961.04it/s] 819012it [00:00, 1667572.39it/s] 989211it [00:00, 1679248.65it/s] 1159064it [00:00, 1685517.01it/s] 1327616it [00:00, 1684162.25it/s] 1496355it [00:00, 1685147.36it/s] 1666846it [00:01, 1691222.85it/s] 1836122it [00:01, 1691667.74it/s] 2005290it [00:01, 1673075.84it/s] 2176167it [00:01, 1683781.66it/s] 2348597it [00:01, 1695931.57it/s] 2519543it [00:01, 1699895.67it/s] 2689559it [00:01, 1696358.86it/s] 2859214it [00:01, 1687357.81it/s] 3028735it [00:01, 1689686.51it/s] 3197720it [00:01, 1689416.68it/s] 3366673it [00:02, 1677205.24it/s] 3534418it [00:02, 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1700893.71it/s] 8538312it [00:05, 1704915.62it/s] 8710370it [00:05, 1709590.11it/s] 8881344it [00:05, 1702880.30it/s] 9053405it [00:05, 1708161.72it/s] 9224235it [00:05, 1700952.13it/s] 9394345it [00:05, 1699359.75it/s] 9564291it [00:05, 1694427.19it/s] 9735157it [00:05, 1698610.69it/s] 9906189it [00:05, 1702016.30it/s] 10076436it [00:06, 1702133.14it/s] 10246654it [00:06, 1699886.34it/s] 10416647it [00:06, 1694012.81it/s] 10586870it [00:06, 1696451.91it/s] 10756521it [00:06, 1695754.92it/s] 10928412it [00:06, 1702665.88it/s] 11099522it [00:06, 1705024.62it/s] 11270028it [00:06, 1704564.43it/s] 11442758it [00:06, 1711359.16it/s] 11617645it [00:06, 1722586.42it/s] 11789906it [00:07, 1712452.53it/s] 11961167it [00:07, 1708801.12it/s] 12132220it [00:07, 1709300.82it/s] 12303833it [00:07, 1711323.85it/s] 12474972it [00:07, 1705281.49it/s] 12645508it [00:07, 1704969.01it/s] 12818168it [00:07, 1711419.78it/s] 12989316it [00:07, 1706629.24it/s] 13159986it [00:07, 1701700.81it/s] 13330162it [00:07, 1691027.39it/s] 13501090it [00:08, 1696442.04it/s] 13670749it [00:08, 1677774.20it/s] 13841770it [00:08, 1687375.09it/s] 14011442it [00:08, 1690035.40it/s] 14182979it [00:08, 1697573.71it/s] 14352764it [00:08, 1696134.26it/s] 14522397it [00:08, 1685680.82it/s] 14690990it [00:08, 1677827.66it/s] 14700009it [00:08, 1673187.08it/s] [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_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: A673_FFPE_RNA_0001_B23LG7FLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_3.md.bai [W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_3.md.bai + merge_qc -folders A673_FFPE_RNA_0001_B23LG7FLT4_3/A673_FFPE_RNA_0001_B23LG7FLT4_3.md -output A673_FFPE_RNA_0001_B23LG7FLT4_3/A673_FFPE_RNA_0001_B23LG7FLT4_3_full_basic_stats.tsv + head -n1 A673_FFPE_RNA_0001_B23LG7FLT4_3/A673_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 A673_FFPE_RNA_0001_B23LG7FLT4_3/A673_FFPE_RNA_0001_B23LG7FLT4_3_full_basic_stats.tsv