+ mkdir tih_rna_sample_00089_23H5VFLT4_s39 + all_qc -bam tih_rna_sample_00089_23H5VFLT4_s39.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_00089_23H5VFLT4_s39 -reference ref_genome.fa -region chr20 [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.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_00089_23H5VFLT4_s39.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.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_00089_23H5VFLT4_s39.md.bai 0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.md.bai 99400it [00:00, 993704.80it/s] 214967it [00:00, 1088907.85it/s] 331376it [00:00, 1123068.53it/s] 446663it [00:00, 1134790.86it/s] 577673it [00:00, 1197927.45it/s] 702126it [00:00, 1209391.13it/s] 839982it [00:00, 1264516.66it/s] 970158it [00:00, 1276304.63it/s] 1107860it [00:00, 1307716.75it/s] 1238641it [00:01, 1276506.77it/s] 1366454it [00:01, 1273895.94it/s] 1493954it [00:01, 1165935.14it/s] 1612285it [00:01, 1110946.98it/s] 1724859it [00:01, 1097733.63it/s] 1835598it [00:01, 1073846.71it/s] 1943624it [00:01, 1064448.85it/s] 2084619it [00:01, 1162470.70it/s] 2226722it [00:01, 1237070.39it/s] 2357502it [00:01, 1257510.17it/s] 2491629it [00:02, 1282130.98it/s] 2631496it [00:02, 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1315411.63it/s] 6888834it [00:05, 1296137.16it/s] 7018920it [00:05, 1210861.37it/s] 7141277it [00:05, 1019590.17it/s] 7260836it [00:05, 1063652.21it/s] 7406418it [00:05, 1166971.26it/s] 7542445it [00:05, 1219788.92it/s] 7675739it [00:06, 1251542.46it/s] 7805775it [00:06, 1265497.81it/s] 7953437it [00:06, 1326672.00it/s] 8095898it [00:06, 1355348.02it/s] 8240506it [00:06, 1382098.45it/s] 8383578it [00:06, 1396484.27it/s] 8524267it [00:06, 1399545.71it/s] 8664679it [00:06, 1374568.14it/s] 8802549it [00:06, 1370277.76it/s] 8946061it [00:06, 1389410.57it/s] 9085231it [00:07, 1380407.38it/s] 9235013it [00:07, 1415168.50it/s] 9392422it [00:07, 1462400.36it/s] 9547203it [00:07, 1487830.62it/s] 9704019it [00:07, 1511792.77it/s] 9862095it [00:07, 1532295.63it/s] 10016328it [00:07, 1535263.72it/s] 10169906it [00:07, 1516988.41it/s] 10321688it [00:07, 1474356.08it/s] 10469411it [00:07, 1462060.65it/s] 10615812it [00:08, 1457329.76it/s] 10765699it [00:08, 1469390.58it/s] 10912753it [00:08, 1313017.94it/s] 11055983it [00:08, 1345674.80it/s] 11203022it [00:08, 1380734.84it/s] 11348039it [00:08, 1400608.63it/s] 11492481it [00:08, 1413302.67it/s] 11636035it [00:08, 1419690.45it/s] 11781243it [00:08, 1429149.71it/s] 11933871it [00:09, 1457924.03it/s] 12085990it [00:09, 1476656.71it/s] 12233961it [00:09, 1470212.32it/s] 12381200it [00:09, 1398681.50it/s] 12530880it [00:09, 1426884.16it/s] 12685492it [00:09, 1461552.89it/s] 12834171it [00:09, 1468906.85it/s] 12981495it [00:09, 1434625.54it/s] 13125401it [00:09, 1374174.11it/s] 13263549it [00:09, 1338925.83it/s] 13338540it [00:10, 1329972.88it/s] [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.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_00089_23H5VFLT4_s39.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00089_23H5VFLT4_s39.md.bai + merge_qc -folders tih_rna_sample_00089_23H5VFLT4_s39/tih_rna_sample_00089_23H5VFLT4_s39.md -output tih_rna_sample_00089_23H5VFLT4_s39/tih_rna_sample_00089_23H5VFLT4_s39_full_basic_stats.tsv + head -n1 tih_rna_sample_00089_23H5VFLT4_s39/tih_rna_sample_00089_23H5VFLT4_s39_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed tih_rna_sample_00089_23H5VFLT4_s39/tih_rna_sample_00089_23H5VFLT4_s39_full_basic_stats.tsv