+ mkdir 1173_NWE_T1_RNA_SLD_01_A23T55JLT4_1 + all_qc -bam 1173_NWE_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_NWE_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_NWE_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_NWE_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_NWE_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_NWE_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_NWE_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_NWE_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_NWE_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_NWE_T1_RNA_SLD_01_A23T55JLT4_1.md.bai 0it [00:00, ?it/s] 114600it [00:00, 1145902.74it/s] 232129it [00:00, 1162449.28it/s] 349305it [00:00, 1166475.02it/s] 467736it [00:00, 1173487.64it/s] 585669it [00:00, 1175569.10it/s] 703895it [00:00, 1177824.92it/s] 821678it [00:00, 1170673.99it/s] 938755it [00:00, 1169165.45it/s] 1055678it [00:00, 1168751.14it/s] 1173098it [00:01, 1170396.15it/s] 1290141it [00:01, 1168949.52it/s] 1407039it [00:01, 1166866.70it/s] 1523728it [00:01, 1163528.03it/s] 1643566it [00:01, 1173989.85it/s] 1761112it [00:01, 1174410.21it/s] 1879790it [00:01, 1178103.74it/s] 1999196it [00:01, 1182875.96it/s] 2118909it [00:01, 1187135.72it/s] 2237626it [00:01, 1178409.60it/s] 2355483it [00:02, 1174761.93it/s] 2473197it [00:02, 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1164811.80it/s] 9417844it [00:08, 1154892.10it/s] 9533367it [00:08, 1141036.09it/s] 9647515it [00:08, 1128218.04it/s] 9760379it [00:08, 1102621.80it/s] 9872278it [00:08, 1107365.34it/s] 9991498it [00:08, 1132249.11it/s] 10110866it [00:08, 1150379.51it/s] 10228395it [00:08, 1157756.74it/s] 10345343it [00:08, 1161230.31it/s] 10461529it [00:08, 1158620.76it/s] 10577619it [00:09, 1159284.69it/s] 10693579it [00:09, 1153023.48it/s] 10808909it [00:09, 1148466.61it/s] 10925356it [00:09, 1153213.76it/s] 11040696it [00:09, 1144889.38it/s] 11159638it [00:09, 1158115.20it/s] 11276715it [00:09, 1161871.36it/s] 11392924it [00:09, 1161798.82it/s] 11512369it [00:09, 1171546.58it/s] 11633745it [00:10, 1184169.76it/s] 11755365it [00:10, 1193747.35it/s] 11875222it [00:10, 1195174.13it/s] 11995311it [00:10, 1196869.09it/s] 12115004it [00:10, 1190787.65it/s] 12234094it [00:10, 1156426.75it/s] 12350809it [00:10, 1159549.36it/s] 12467109it [00:10, 1160547.57it/s] 12585134it [00:10, 1166370.09it/s] 12705412it [00:10, 1177185.04it/s] 12823684it [00:11, 1178719.90it/s] 12941605it [00:11, 1177170.26it/s] 13059356it [00:11, 1173843.02it/s] 13177627it [00:11, 1176472.43it/s] 13295678it [00:11, 1177648.94it/s] 13414055it [00:11, 1179461.08it/s] 13532888it [00:11, 1182100.80it/s] 13651106it [00:11, 1180992.59it/s] 13769211it [00:11, 1178899.34it/s] 13887106it [00:11, 1165298.64it/s] 14003672it [00:12, 1156012.08it/s][W::hts_idx_load3] The index file is older than the data file: 1173_NWE_T1_RNA_SLD_01_A23T55JLT4_1.md.bai 14119307it [00:12, 1130667.65it/s] 14232493it [00:12, 1125232.00it/s] 14345093it [00:12, 1082349.20it/s] 14453661it [00:12, 1059589.30it/s] 14559877it [00:12, 1027057.79it/s] 14662858it [00:12, 1001104.94it/s] 14763426it [00:12, 1002384.79it/s] 14879396it [00:12, 1047684.51it/s] 14996669it [00:12, 1084123.98it/s] 15113709it [00:13, 1109475.20it/s] 15229726it [00:13, 1124453.82it/s] 15345331it [00:13, 1133817.69it/s] 15462718it [00:13, 1145731.50it/s] 15581597it [00:13, 1158566.49it/s] 15700492it [00:13, 1167632.24it/s] 15818524it [00:13, 1171411.31it/s] 15936121it [00:13, 1172757.66it/s] 16054599it [00:13, 1176340.18it/s] 16172753it [00:13, 1177880.61it/s] 16290714it [00:14, 1178381.76it/s] 16342249it [00:14, 1157495.39it/s] [W::hts_idx_load3] The index file is older than the data file: 1173_NWE_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_NWE_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_NWE_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_NWE_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_NWE_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_NWE_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_NWE_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_NWE_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_NWE_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_NWE_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_NWE_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_NWE_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_NWE_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_NWE_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_NWE_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_NWE_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_NWE_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_NWE_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_NWE_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_NWE_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_NWE_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_NWE_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_NWE_T1_RNA_SLD_01_A23T55JLT4_1.md.bai + merge_qc -folders 1173_NWE_T1_RNA_SLD_01_A23T55JLT4_1/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_1.md -output 1173_NWE_T1_RNA_SLD_01_A23T55JLT4_1/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_1_full_basic_stats.tsv + head -n1 1173_NWE_T1_RNA_SLD_01_A23T55JLT4_1/1173_NWE_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_NWE_T1_RNA_SLD_01_A23T55JLT4_1/1173_NWE_T1_RNA_SLD_01_A23T55JLT4_1_full_basic_stats.tsv