+ mkdir GM24385_0001_RNA_0001_23H5VFLT4_s24 + all_qc -bam GM24385_0001_RNA_0001_23H5VFLT4_s24.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 GM24385_0001_RNA_0001_23H5VFLT4_s24 -reference ref_genome.fa -region chr20 [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai [mpileup] 1 samples in 1 input files [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.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: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai 0it [00:00, ?it/s] 143913it [00:00, 1439025.01it/s][W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai 287816it [00:00, 1385346.19it/s] 426488it [00:00, 1346315.60it/s] 585827it [00:00, 1440881.30it/s] 746420it [00:00, 1499202.88it/s] 908045it [00:00, 1538418.67it/s] 1072399it [00:00, 1572422.62it/s] 1237651it [00:00, 1597712.19it/s] 1403244it [00:00, 1615406.14it/s] 1568301it [00:01, 1626177.80it/s] 1732933it [00:01, 1632263.00it/s] 1900572it [00:01, 1645618.01it/s] 2067850it [00:01, 1653780.61it/s] 2233260it [00:01, 1643638.63it/s] 2397660it [00:01, 1615595.85it/s] 2559340it [00:01, 1558654.64it/s] 2725058it [00:01, 1587166.79it/s] 2884191it [00:01, 1553694.40it/s] 3039937it [00:01, 1500592.46it/s] 3202570it [00:02, 1536510.01it/s] 3367491it [00:02, 1568664.53it/s] 3524845it [00:02, 1510304.00it/s] 3676575it [00:02, 1509982.40it/s] 3828080it [00:02, 1511407.52it/s] 3987398it [00:02, 1535314.31it/s] 4148629it [00:02, 1557890.82it/s] 4307323it [00:02, 1566300.62it/s] 4464134it [00:02, 1539401.25it/s] 4620905it [00:02, 1547690.07it/s] 4781775it [00:03, 1565655.18it/s] 4939023it [00:03, 1567643.70it/s] 5095886it [00:03, 1519327.10it/s] 5248188it [00:03, 1464841.45it/s] 5395239it [00:03, 1377820.60it/s] 5555093it [00:03, 1439129.04it/s] 5719135it [00:03, 1496295.07it/s] 5879949it [00:03, 1528552.27it/s] 6045313it [00:03, 1565043.26it/s] 6202612it [00:04, 1527364.34it/s] 6356054it [00:04, 1449047.88it/s] 6502120it [00:04, 1438158.41it/s] 6657581it [00:04, 1471367.16it/s] 6823921it [00:04, 1526948.49it/s] 6992921it [00:04, 1574627.76it/s] 7156747it [00:04, 1593335.77it/s] 7319901it [00:04, 1604601.36it/s] 7480695it [00:04, 1593590.26it/s] 7640298it [00:04, 1447112.08it/s] 7787674it [00:05, 1360276.49it/s] 7926225it [00:05, 1300055.81it/s] 8058124it [00:05, 1243640.17it/s] 8183875it [00:05, 1212611.80it/s] 8305981it [00:05, 1206783.14it/s] 8447335it [00:05, 1264204.48it/s] 8603427it [00:05, 1348484.14it/s] 8767066it [00:05, 1431572.80it/s] 8928557it [00:05, 1485069.01it/s] 9088486it [00:06, 1518656.31it/s] 9242658it [00:06, 1525445.40it/s] 9404018it [00:06, 1551605.88it/s] 9564437it [00:06, 1567232.30it/s] 9724940it [00:06, 1578474.65it/s] 9882980it [00:06, 1520166.84it/s] 10044218it [00:06, 1546992.44it/s] 10207500it [00:06, 1572179.01it/s] 10374105it [00:06, 1599894.66it/s] 10542278it [00:06, 1624083.82it/s] 10705566it [00:07, 1626663.94it/s][W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai 10872383it [00:07, 1638962.92it/s] 11036407it [00:07, 1634083.30it/s] 11199907it [00:07, 1628344.85it/s] 11338844it [00:07, 1518564.53it/s] [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.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: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.md.bai + merge_qc -folders GM24385_0001_RNA_0001_23H5VFLT4_s24/GM24385_0001_RNA_0001_23H5VFLT4_s24.md -output GM24385_0001_RNA_0001_23H5VFLT4_s24/GM24385_0001_RNA_0001_23H5VFLT4_s24_full_basic_stats.tsv + head -n1 GM24385_0001_RNA_0001_23H5VFLT4_s24/GM24385_0001_RNA_0001_23H5VFLT4_s24_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed GM24385_0001_RNA_0001_23H5VFLT4_s24/GM24385_0001_RNA_0001_23H5VFLT4_s24_full_basic_stats.tsv