+ mkdir 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_1 + all_qc -bam 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_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 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_1 -reference ref_genome.fa -region chr20 [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [mpileup] 1 samples in 1 input files [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_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: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_1.md.bai 0it [00:00, ?it/s] 127346it [00:00, 1273339.78it/s] 270403it [00:00, 1365765.94it/s] 406980it [00:00, 1215493.79it/s] 530269it [00:00, 1119796.72it/s] 643880it [00:00, 1099270.08it/s] 802813it [00:00, 1252073.24it/s] 954714it [00:00, 1334303.00it/s] 1107224it [00:00, 1392429.28it/s] 1260733it [00:00, 1435744.41it/s] 1416910it [00:01, 1473753.78it/s] 1577106it [00:01, 1512420.27it/s] 1739361it [00:01, 1545567.83it/s] 1895564it [00:01, 1550445.23it/s] 2059760it [00:01, 1577910.19it/s] 2217804it [00:01, 1564012.84it/s] 2382134it [00:01, 1587636.78it/s] 2550964it [00:01, 1617683.41it/s] 2723696it [00:01, 1650441.44it/s] 2888847it [00:01, 1629351.73it/s] 3051913it [00:02, 1593680.62it/s] 3211512it [00:02, 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1553917.35it/s] 7737779it [00:05, 1519404.38it/s] 7891088it [00:05, 1523316.52it/s] 8053671it [00:05, 1553172.25it/s] 8222549it [00:05, 1593015.98it/s] 8388115it [00:05, 1611411.74it/s] 8551167it [00:05, 1616958.62it/s] 8717619it [00:05, 1631035.02it/s] 8887491it [00:06, 1651132.45it/s] 9053682it [00:06, 1654321.81it/s] 9219175it [00:06, 1652339.79it/s] 9384452it [00:06, 1611451.98it/s] 9545842it [00:06, 1417106.36it/s] 9691799it [00:06, 1348102.18it/s] 9829824it [00:06, 1308230.71it/s] 9962800it [00:06, 1285961.82it/s] 10092781it [00:06, 1257712.91it/s] 10219435it [00:07, 1253745.39it/s] 10345398it [00:07, 1238655.16it/s] 10469629it [00:07, 1234499.73it/s] 10593316it [00:07, 1234165.20it/s] 10716897it [00:07, 1233515.85it/s] 10840362it [00:07, 1233692.00it/s] 10966710it [00:07, 1242462.41it/s] 11091026it [00:07, 1229674.49it/s] 11214298it [00:07, 1230545.46it/s] 11337400it [00:07, 1222164.36it/s] 11459655it [00:08, 1220708.38it/s] 11581752it [00:08, 1209985.64it/s] 11702964it [00:08, 1210590.73it/s] 11824045it [00:08, 1200945.37it/s] 11949195it [00:08, 1215882.91it/s] 12072555it [00:08, 1221121.62it/s] 12194730it [00:08, 1221278.10it/s] 12316909it [00:08, 1221401.80it/s] 12439238it [00:08, 1221938.19it/s] 12561442it [00:08, 1218720.86it/s] 12683544it [00:09, 1219381.71it/s] 12807284it [00:09, 1224745.20it/s] 12930600it [00:09, 1227116.85it/s] 13053316it [00:09, 1222780.03it/s] 13178053it [00:09, 1230107.21it/s] 13301071it [00:09, 1226574.99it/s] 13423735it [00:09, 1221718.39it/s] 13546366it [00:09, 1223054.90it/s] 13668738it [00:09, 1223225.26it/s] 13681643it [00:09, 1382662.71it/s] [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_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: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_1.md.bai + merge_qc -folders 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_1/1173_D6K_T1_RNA_SLD_01_A23T55JLT4_1.md -output 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_1/1173_D6K_T1_RNA_SLD_01_A23T55JLT4_1_full_basic_stats.tsv + head -n1 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_1/1173_D6K_T1_RNA_SLD_01_A23T55JLT4_1_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_1/1173_D6K_T1_RNA_SLD_01_A23T55JLT4_1_full_basic_stats.tsv