+ 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 0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_3.md.bai 99527it [00:00, 995192.65it/s] 207591it [00:00, 1045418.12it/s] 312479it [00:00, 1046969.65it/s] 417578it [00:00, 1048454.54it/s] 522424it [00:00, 1022354.49it/s] 624770it [00:00, 983296.95it/s] 723390it [00:00, 974552.88it/s] 822046it [00:00, 978199.37it/s] 920001it [00:00, 972004.00it/s] 1017290it [00:01, 965525.09it/s] 1113901it [00:01, 965405.20it/s] 1219953it [00:01, 993928.67it/s] 1326663it [00:01, 1015864.39it/s] 1434637it [00:01, 1034991.71it/s] 1541161it [00:01, 1044047.04it/s] 1649870it [00:01, 1056935.06it/s] 1755600it [00:01, 1013441.22it/s] 1857343it [00:01, 1002998.52it/s] 1957918it [00:01, 994907.37it/s] 2057654it [00:02, 995470.16it/s] 2171115it [00:02, 1036409.42it/s] 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[00:11, 1074275.61it/s] 11811416it [00:11, 1074661.72it/s] 11918936it [00:11, 1074799.76it/s] 12027814it [00:11, 1078959.39it/s] 12135719it [00:11, 1078464.35it/s] 12244415it [00:11, 1080863.02it/s] 12352507it [00:11, 1076997.79it/s] 12460213it [00:11, 1072130.35it/s] 12567434it [00:11, 1044152.41it/s] 12673354it [00:11, 1048472.85it/s] 12782456it [00:12, 1061018.03it/s] 12888660it [00:12, 1059806.59it/s] 12996741it [00:12, 1066033.43it/s] 13104956it [00:12, 1070817.39it/s] 13212079it [00:12, 1064721.23it/s] 13318586it [00:12, 1061012.01it/s] 13424712it [00:12, 1052227.12it/s] 13529963it [00:12, 1031926.07it/s] 13633243it [00:12, 1028573.02it/s] 13741842it [00:12, 1045480.26it/s] 13849716it [00:13, 1055316.19it/s] 13955309it [00:13, 1022971.67it/s] 14057842it [00:13, 979378.12it/s] 14156753it [00:13, 982066.09it/s] 14261981it [00:13, 1002365.27it/s] 14368122it [00:13, 1019551.56it/s] 14473675it [00:13, 1030135.88it/s] 14578986it [00:13, 1036922.95it/s] 14684392it [00:13, 1042002.01it/s] 14700009it [00:13, 1059854.28it/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