+ mkdir tih_rna_sample_00592_B23MVV7LT4_1 + all_qc -bam tih_rna_sample_00592_B23MVV7LT4_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 tih_rna_sample_00592_B23MVV7LT4_1 -reference ref_genome.fa -region chr20 [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai [mpileup] 1 samples in 1 input files [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_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: tih_rna_sample_00592_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai 0it [00:00, ?it/s] 135599it [00:00, 1355564.68it/s] 280235it [00:00, 1408809.54it/s] 430039it [00:00, 1449524.10it/s] 576905it [00:00, 1457058.04it/s] 723358it [00:00, 1459731.47it/s] 872374it [00:00, 1470056.87it/s] 1019380it [00:00, 1457447.01it/s] 1167469it [00:00, 1464819.07it/s] 1313971it [00:00, 1438247.62it/s] 1457902it [00:01, 1213769.52it/s] 1585009it [00:01, 1202087.80it/s] 1709105it [00:01, 1181475.54it/s] 1829865it [00:01, 1160587.80it/s] 1947668it [00:01, 1151983.60it/s] 2072793it [00:01, 1179887.89it/s] 2191797it [00:01, 1177324.19it/s] 2315331it [00:01, 1194102.78it/s] 2436336it [00:01, 1198744.80it/s] 2556610it [00:02, 1191682.66it/s] 2687580it [00:02, 1226438.29it/s] 2810481it [00:02, 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6385646it [00:05, 1095783.30it/s] 6495467it [00:05, 1096032.00it/s] 6615321it [00:05, 1126231.87it/s] 6737072it [00:05, 1153263.69it/s] 6852552it [00:05, 1127654.01it/s] 6965534it [00:05, 1117967.85it/s] 7078059it [00:06, 1120084.88it/s] 7190178it [00:06, 1111059.28it/s] 7301366it [00:06, 1069690.06it/s] 7411069it [00:06, 1077563.49it/s] 7521370it [00:06, 1084973.29it/s] 7635983it [00:06, 1102950.84it/s] 7751121it [00:06, 1117259.99it/s] 7862992it [00:06, 1106088.14it/s] 7973719it [00:06, 1103600.05it/s] 8084823it [00:06, 1105680.72it/s] 8199486it [00:07, 1117840.64it/s] 8311321it [00:07, 1099536.48it/s] 8421369it [00:07, 1081077.84it/s] 8529587it [00:07, 1066205.46it/s] 8646597it [00:07, 1096524.80it/s] 8756395it [00:07, 1095329.35it/s] 8866028it [00:07, 1070264.03it/s] 8973222it [00:07, 995102.12it/s] 9104135it [00:07, 1082855.62it/s] 9239773it [00:08, 1160848.96it/s] 9369501it [00:08, 1200245.36it/s] 9490818it [00:08, 1203943.60it/s] 9622040it [00:08, 1235839.40it/s] 9747801it [00:08, 1242155.66it/s] 9877927it [00:08, 1259714.39it/s] 10004213it [00:08, 1259113.12it/s] 10130344it [00:08, 1229899.54it/s] 10186320it [00:08, 1158468.86it/s] [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_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: tih_rna_sample_00592_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00592_B23MVV7LT4_1.md.bai + merge_qc -folders tih_rna_sample_00592_B23MVV7LT4_1/tih_rna_sample_00592_B23MVV7LT4_1.md -output tih_rna_sample_00592_B23MVV7LT4_1/tih_rna_sample_00592_B23MVV7LT4_1_full_basic_stats.tsv + head -n1 tih_rna_sample_00592_B23MVV7LT4_1/tih_rna_sample_00592_B23MVV7LT4_1_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed tih_rna_sample_00592_B23MVV7LT4_1/tih_rna_sample_00592_B23MVV7LT4_1_full_basic_stats.tsv