+ mkdir A673_FFPE_RNA_0001_B23LG7FLT4_2
+ all_qc -bam A673_FFPE_RNA_0001_B23LG7FLT4_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 A673_FFPE_RNA_0001_B23LG7FLT4_2 -reference ref_genome.fa -region chr20
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[mpileup] 1 samples in 1 input files
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_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: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
139250it [00:00, 1392328.71it/s]
290540it [00:00, 1463051.20it/s]
448985it [00:00, 1518443.14it/s]
606961it [00:00, 1542620.06it/s]
770314it [00:00, 1575374.33it/s]
927852it [00:00, 1567457.40it/s]
1091129it [00:00, 1588708.65it/s]
1250013it [00:00, 1587954.83it/s]
1413629it [00:00, 1602966.83it/s]
1573935it [00:01, 1592539.22it/s]
1737633it [00:01, 1606037.16it/s]
1901143it [00:01, 1614816.96it/s]
2064586it [00:01, 1620704.41it/s]
2226671it [00:01, 1607380.25it/s]
2389107it [00:01, 1612431.55it/s]
2550377it [00:01, 1602340.70it/s]
2710640it [00:01, 1542698.18it/s]
2865367it [00:01, 1479325.18it/s]
3014018it [00:01, 1432695.10it/s]
3175691it [00:02, 1484636.50it/s]
3335067it [00:02, 1515894.72it/s]
3496369it [00:02, 1544141.48it/s]
3657214it [00:02, 1562972.08it/s]
3813943it [00:02, 1547724.98it/s]
3969033it [00:02, 1542934.47it/s]
4128592it [00:02, 1558462.30it/s]
4284615it [00:02, 1525653.79it/s]
4437428it [00:02, 1471258.22it/s]
4597699it [00:02, 1509024.86it/s]
4749109it [00:03, 1358079.50it/s]
4887884it [00:03, 1298209.42it/s]
5019946it [00:03, 1270117.76it/s]
5175746it [00:03, 1348650.44it/s]
5337047it [00:03, 1422769.26it/s]
5499295it [00:03, 1479855.57it/s]
5661965it [00:03, 1522332.03it/s]
5825508it [00:03, 1555414.46it/s]
5984830it [00:03, 1566361.40it/s]
6142131it [00:04, 1538788.29it/s]
6300713it [00:04, 1552562.51it/s]
6461179it [00:04, 1567923.12it/s]
6618287it [00:04, 1521823.80it/s]
6783437it [00:04, 1559571.99it/s]
6945886it [00:04, 1578623.90it/s]
7109873it [00:04, 1596703.07it/s]
7274356it [00:04, 1610962.81it/s]
7437661it [00:04, 1617511.72it/s]
7599990it [00:04, 1619152.96it/s]
7762464it [00:05, 1620792.46it/s]
7924617it [00:05, 1593941.24it/s]
8090886it [00:05, 1614253.20it/s]
8254866it [00:05, 1621818.60it/s]
8417147it [00:05, 1559532.02it/s]
8582761it [00:05, 1587556.63it/s]
8746107it [00:05, 1600988.07it/s]
8911432it [00:05, 1616242.24it/s]
9073336it [00:05, 1596063.67it/s]
9235426it [00:05, 1603239.50it/s]
9395926it [00:06, 1583761.13it/s]
9559682it [00:06, 1599459.94it/s]
9723262it [00:06, 1610193.51it/s]
9884390it [00:06, 1608241.90it/s]
10048308it [00:06, 1617429.05it/s]
10212265it [00:06, 1623825.34it/s]
10376582it [00:06, 1629570.34it/s]
10539915it [00:06, 1630651.68it/s]
10704839it [00:06, 1636180.24it/s]
10868475it [00:06, 1621125.28it/s]
11033320it [00:07, 1629225.84it/s]
11199345it [00:07, 1638449.24it/s]
11366297it [00:07, 1647700.56it/s]
11531092it [00:07, 1594924.87it/s]
11694319it [00:07, 1605789.99it/s]
11860066it [00:07, 1620920.79it/s]
12024310it [00:07, 1627262.65it/s]
12187204it [00:07, 1591391.00it/s]
12351355it [00:07, 1605989.41it/s]
12513447it [00:08, 1610361.73it/s]
12680279it [00:08, 1627530.63it/s]
12844806it [00:08, 1632757.96it/s]
13011604it [00:08, 1643232.18it/s]
13176639it [00:08, 1645327.12it/s]
13341224it [00:08, 1645039.28it/s]
13506637it [00:08, 1647727.27it/s]
13672865it [00:08, 1652056.55it/s]
13838641it [00:08, 1653730.85it/s]
14004028it [00:08, 1628333.12it/s]
14166957it [00:09, 1616947.56it/s]
14330104it [00:09, 1621097.21it/s]
14495227it [00:09, 1630014.16it/s]
14564283it [00:09, 1573014.02it/s]
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_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: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.md.bai
+ merge_qc -folders A673_FFPE_RNA_0001_B23LG7FLT4_2/A673_FFPE_RNA_0001_B23LG7FLT4_2.md -output A673_FFPE_RNA_0001_B23LG7FLT4_2/A673_FFPE_RNA_0001_B23LG7FLT4_2_full_basic_stats.tsv
+ head -n1 A673_FFPE_RNA_0001_B23LG7FLT4_2/A673_FFPE_RNA_0001_B23LG7FLT4_2_full_basic_stats.tsv
++ basename Twist_rna_exome_AND_fusion_hg38.bed
+ grep -e Twist_rna_exome_AND_fusion_hg38.bed A673_FFPE_RNA_0001_B23LG7FLT4_2/A673_FFPE_RNA_0001_B23LG7FLT4_2_full_basic_stats.tsv