+ mkdir FFPE_HD789_01_RNA_13_B23MVV7LT4_1
+ all_qc -bam FFPE_HD789_01_RNA_13_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 FFPE_HD789_01_RNA_13_B23MVV7LT4_1 -reference ref_genome.fa -region chr20
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
[mpileup] 1 samples in 1 input files
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_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: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
90817it [00:00, 908092.92it/s]
225656it [00:00, 1148048.92it/s]
363869it [00:00, 1253719.76it/s]
508170it [00:00, 1328004.67it/s]
658928it [00:00, 1392087.33it/s]
798162it [00:00, 1366198.18it/s]
964142it [00:00, 1460775.68it/s]
1119233it [00:00, 1489157.90it/s]
1278189it [00:00, 1520294.94it/s]
1433222it [00:01, 1529489.25it/s]
1586270it [00:01, 1514547.26it/s]
1737822it [00:01, 1511178.08it/s]
1889006it [00:01, 1489635.61it/s]
2047480it [00:01, 1517869.99it/s]
2199381it [00:01, 1483762.05it/s]
2353425it [00:01, 1500281.17it/s]
2513208it [00:01, 1529088.20it/s]
2672683it [00:01, 1548550.76it/s]
2827689it [00:01, 1388158.88it/s]
2969657it [00:02, 1373740.71it/s]
3109176it [00:02, 1361528.69it/s]
3251721it [00:02, 1379561.72it/s]
3397146it [00:02, 1400989.50it/s]
3538128it [00:02, 1401319.78it/s]
3688494it [00:02, 1431225.95it/s]
3847473it [00:02, 1478022.63it/s]
3995699it [00:02, 1476505.97it/s]
4152154it [00:02, 1502488.69it/s]
4302633it [00:02, 1464977.79it/s]
4449481it [00:03, 1373746.48it/s]
4588121it [00:03, 1281489.31it/s]
4718042it [00:03, 1232465.80it/s]
4861319it [00:03, 1286863.30it/s]
4991474it [00:03, 1280781.97it/s]
5120549it [00:03, 1259052.50it/s]
5256893it [00:03, 1288724.40it/s]
5394508it [00:03, 1313963.33it/s]
5526704it [00:03, 1316209.66it/s]
5686609it [00:04, 1399481.15it/s]
5856271it [00:04, 1487445.34it/s]
6024502it [00:04, 1545349.19it/s]
6193592it [00:04, 1588709.59it/s]
6363013it [00:04, 1620187.83it/s]
6525233it [00:04, 1610520.89it/s]
6693508it [00:04, 1632016.88it/s]
6863721it [00:04, 1652918.71it/s]
7032217it [00:04, 1662469.08it/s]
7201548it [00:04, 1671669.34it/s]
7368766it [00:05, 1669720.70it/s]
7535774it [00:05, 1629432.04it/s]
7698951it [00:05, 1609149.14it/s]
7860559it [00:05, 1611151.61it/s]
8021810it [00:05, 1606663.49it/s]
8182568it [00:05, 1602729.72it/s]
8349254it [00:05, 1621728.47it/s]
8516228it [00:05, 1635993.43it/s]
8685093it [00:05, 1651546.58it/s]
8853836it [00:05, 1662245.55it/s]
9021368it [00:06, 1666126.78it/s]
9191977it [00:06, 1678059.67it/s]
9359805it [00:06, 1672483.93it/s]
9527072it [00:06, 1667774.76it/s]
9695814it [00:06, 1673611.23it/s]
9863188it [00:06, 1673000.04it/s]
10031104it [00:06, 1674809.42it/s]
10198592it [00:06, 1660018.00it/s]
10364626it [00:06, 1638656.64it/s]
10534440it [00:06, 1656214.15it/s]
10704377it [00:07, 1669000.86it/s]
10872102it [00:07, 1671424.21it/s]
11039292it [00:07, 1671275.29it/s]
11208428it [00:07, 1677244.83it/s]
11379326it [00:07, 1686705.62it/s]
11548795it [00:07, 1689063.36it/s]
11717716it [00:07, 1688367.24it/s]
11886563it [00:07, 1658770.45it/s]
12052561it [00:07, 1652830.44it/s]
12221887it [00:07, 1664780.05it/s]
12388437it [00:08, 1548272.19it/s]
12553017it [00:08, 1575753.75it/s]
12719873it [00:08, 1602417.24it/s]
12881133it [00:08, 1594491.97it/s]
13045001it [00:08, 1607389.71it/s]
13212536it [00:08, 1627389.42it/s]
13378793it [00:08, 1637784.69it/s]
13542866it [00:08, 1623190.68it/s]
13705411it [00:08, 1606467.39it/s]
13866237it [00:09, 1499471.57it/s]
14030074it [00:09, 1538561.38it/s]
14193288it [00:09, 1565357.29it/s]
14357244it [00:09, 1586926.95it/s]
14524853it [00:09, 1613079.83it/s]
14687653it [00:09, 1617461.20it/s]
14849820it [00:09, 1615979.85it/s]
15018438it [00:09, 1636821.11it/s]
15185717it [00:09, 1647514.62it/s]
15301882it [00:09, 1541552.37it/s]
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_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: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
+ merge_qc -folders FFPE_HD789_01_RNA_13_B23MVV7LT4_1/FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md -output FFPE_HD789_01_RNA_13_B23MVV7LT4_1/FFPE_HD789_01_RNA_13_B23MVV7LT4_1_full_basic_stats.tsv
+ head -n1 FFPE_HD789_01_RNA_13_B23MVV7LT4_1/FFPE_HD789_01_RNA_13_B23MVV7LT4_1_full_basic_stats.tsv
++ basename Twist_rna_exome_AND_fusion_hg38.bed
+ grep -e Twist_rna_exome_AND_fusion_hg38.bed FFPE_HD789_01_RNA_13_B23MVV7LT4_1/FFPE_HD789_01_RNA_13_B23MVV7LT4_1_full_basic_stats.tsv