+ mkdir 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2 + all_qc -bam 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.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_DSO_T1_RNA_SLD_01_A23T55JLT4_2 -reference ref_genome.fa -region chr20 [W::hts_idx_load3] The index file is older than the data file: 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [mpileup] 1 samples in 1 input files [W::hts_idx_load3] The index file is older than the data file: 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.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_DSO_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.md.bai 0it [00:00, ?it/s] 131647it [00:00, 1316292.37it/s] 279118it [00:00, 1409391.81it/s] 436156it [00:00, 1482838.77it/s] 597507it [00:00, 1534373.16it/s] 754092it [00:00, 1535470.96it/s] 910333it [00:00, 1544544.09it/s] 1065585it [00:00, 1547100.97it/s] 1227867it [00:00, 1570966.53it/s] 1390388it [00:00, 1587851.53it/s] 1549335it [00:01, 1588307.91it/s] 1711832it [00:01, 1599353.63it/s] 1873332it [00:01, 1604063.37it/s] 2033742it [00:01, 1581077.21it/s] 2191925it [00:01, 1532463.37it/s] 2351355it [00:01, 1550518.38it/s] 2512666it [00:01, 1568827.37it/s] 2678990it [00:01, 1596756.98it/s] 2846509it [00:01, 1619898.90it/s] 3011695it [00:01, 1629387.68it/s] 3174759it [00:02, 1580168.77it/s] 3333168it [00:02, 1508253.99it/s] 3484825it [00:02, 1494742.43it/s] 3635347it [00:02, 1497700.04it/s] 3785513it [00:02, 1492539.25it/s] 3935034it [00:02, 1481184.33it/s] 4094680it [00:02, 1514938.58it/s] 4246379it [00:02, 1430917.39it/s] 4397779it [00:02, 1454495.03it/s] 4544062it [00:02, 1405728.85it/s] 4702781it [00:03, 1457399.77it/s] 4868198it [00:03, 1514238.77it/s] 5028431it [00:03, 1539960.36it/s] 5183049it [00:03, 1496762.71it/s] 5348367it [00:03, 1542094.77it/s] 5503182it [00:03, 1537096.19it/s] 5661393it [00:03, 1550290.56it/s] 5820850it [00:03, 1563356.79it/s] 5984669it [00:03, 1585543.72it/s] 6143414it [00:03, 1581063.58it/s] 6301654it [00:04, 1562845.21it/s] 6458069it [00:04, 1529760.17it/s] 6611255it [00:04, 1487099.64it/s] 6760286it [00:04, 1479554.65it/s] 6908448it [00:04, 1472013.61it/s] 7059986it [00:04, 1484663.25it/s] 7210717it [00:04, 1491292.65it/s] 7363976it [00:04, 1503491.93it/s] 7514410it [00:04, 1463828.34it/s] 7671608it [00:05, 1495433.69it/s] 7821414it [00:05, 1495237.31it/s] 7971122it [00:05, 1483919.01it/s] 8119649it [00:05, 1464629.30it/s] 8266238it [00:05, 1458409.48it/s] 8412162it [00:05, 1426526.95it/s] 8557594it [00:05, 1434598.05it/s] 8702641it [00:05, 1439161.32it/s] 8850973it [00:05, 1452190.09it/s] 9002329it [00:05, 1470375.01it/s] 9150086it [00:06, 1472477.51it/s] 9313908it [00:06, 1521925.21it/s] 9472984it [00:06, 1542471.69it/s] 9637281it [00:06, 1572511.08it/s] 9799394it [00:06, 1587037.67it/s] 9958131it [00:06, 1547415.45it/s] 10113110it [00:06, 1484020.80it/s] 10262142it [00:06, 1447382.52it/s] 10407391it [00:06, 1444176.79it/s] 10552153it [00:06, 1415231.93it/s] 10693954it [00:07, 1399158.50it/s] 10834046it [00:07, 1393134.03it/s] 10978898it [00:07, 1409223.86it/s] 11127623it [00:07, 1432012.37it/s] 11275494it [00:07, 1445770.36it/s] 11432345it [00:07, 1482175.31it/s] 11591998it [00:07, 1516088.15it/s] 11743713it [00:07, 1510410.34it/s] 11898098it [00:07, 1520335.63it/s] 12052929it [00:07, 1528585.19it/s] 12205833it [00:08, 1441177.66it/s] 12350993it [00:08, 1361237.54it/s] 12488530it [00:08, 1303633.65it/s] 12620092it [00:08, 1273136.64it/s] 12748186it [00:08, 1262447.18it/s] 12874919it [00:08, 1246614.95it/s] 12999875it [00:08, 1227662.48it/s] 13122868it [00:08, 1228274.86it/s] 13245823it [00:08, 1218174.46it/s] 13385378it [00:09, 1269743.79it/s] 13522913it [00:09, 1300706.92it/s] 13666552it [00:09, 1340764.72it/s] 13800842it [00:09, 1306278.70it/s] 13931786it [00:09, 1255752.10it/s] 14057900it [00:09, 1239372.33it/s] 14182195it [00:09, 1216356.60it/s] 14304089it [00:09, 1209789.53it/s] 14425230it [00:09, 1202269.76it/s] 14546584it [00:10, 1205532.91it/s] 14686855it [00:10, 1263437.65it/s][W::hts_idx_load3] The index file is older than the data file: 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.md.bai 14830415it [00:10, 1314308.27it/s] 14967865it [00:10, 1332063.80it/s] 15101229it [00:10, 1286664.38it/s] 15230316it [00:10, 1249560.57it/s] 15372108it [00:10, 1297928.62it/s] 15514997it [00:10, 1336026.21it/s] 15659884it [00:10, 1369147.33it/s] 15808734it [00:10, 1404396.41it/s] 15952061it [00:11, 1412807.37it/s][W::hts_idx_load3] The index file is older than the data file: 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.md.bai 16100796it [00:11, 1434981.05it/s] 16247302it [00:11, 1443930.86it/s] 16394876it [00:11, 1453257.10it/s] 16540300it [00:11, 1434134.68it/s] 16683836it [00:11, 1433231.52it/s] 16829558it [00:11, 1440213.10it/s] 16894083it [00:11, 1444837.24it/s] [W::hts_idx_load3] The index file is older than the data file: 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.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_DSO_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.md.bai + merge_qc -folders 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2/1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.md -output 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2/1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2_full_basic_stats.tsv + head -n1 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2/1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed 1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2/1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2_full_basic_stats.tsv