+ mkdir 659_bTo-T1-TRNA-1_B23MHV2LT4_1
+ all_qc -bam 659_bTo-T1-TRNA-1_B23MHV2LT4_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 659_bTo-T1-TRNA-1_B23MHV2LT4_1 -reference ref_genome.fa -region chr20
[W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai
[mpileup] 1 samples in 1 input files
[W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_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: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai
0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai
153425it [00:00, 1534174.65it/s]
321655it [00:00, 1621176.76it/s]
490908it [00:00, 1653728.30it/s]
662324it [00:00, 1677561.98it/s]
833030it [00:00, 1688179.06it/s]
1002856it [00:00, 1691586.46it/s]
1175905it [00:00, 1704283.85it/s]
1347239it [00:00, 1707146.60it/s]
1521125it [00:00, 1717044.29it/s]
1692830it [00:01, 1716706.67it/s]
1865209it [00:01, 1718857.14it/s]
2037162it [00:01, 1719043.61it/s]
2209579it [00:01, 1720575.81it/s]
2382121it [00:01, 1721917.87it/s]
2554313it [00:01, 1715206.57it/s]
2729724it [00:01, 1726868.21it/s]
2902795it [00:01, 1728003.11it/s]
3075601it [00:01, 1722607.93it/s]
3249122it [00:01, 1726362.92it/s]
3421765it [00:02, 1719614.82it/s]
3595196it [00:02, 1723987.71it/s]
3767603it [00:02, 1716512.66it/s]
3939697it [00:02, 1717818.96it/s]
4111541it [00:02, 1717816.56it/s]
4284794it [00:02, 1722193.09it/s]
4457019it [00:02, 1719230.16it/s]
4628947it [00:02, 1718642.24it/s]
4801883it [00:02, 1721738.71it/s]
4974060it [00:02, 1711225.14it/s]
5145198it [00:03, 1709610.29it/s]
5318340it [00:03, 1716104.29it/s]
5490190it [00:03, 1716798.02it/s]
5663503it [00:03, 1721666.62it/s]
5837466it [00:03, 1727028.18it/s]
6010174it [00:03, 1723377.30it/s]
6182517it [00:03, 1719220.78it/s]
6355245it [00:03, 1721611.51it/s]
6527963it [00:03, 1723116.40it/s]
6700278it [00:03, 1717579.70it/s]
6872042it [00:04, 1708848.77it/s]
7043895it [00:04, 1711715.61it/s]
7215077it [00:04, 1708642.73it/s]
7390265it [00:04, 1721478.92it/s]
7563496it [00:04, 1724689.53it/s]
7737325it [00:04, 1728612.31it/s]
7910193it [00:04, 1727449.98it/s]
8082943it [00:04, 1726824.19it/s]
8255629it [00:04, 1725863.99it/s]
8428218it [00:04, 1723334.00it/s]
8600554it [00:05, 1723050.76it/s]
8772861it [00:05, 1716845.35it/s]
8946067it [00:05, 1721376.76it/s]
9118210it [00:05, 1721267.92it/s]
9290341it [00:05, 1715668.42it/s]
9462820it [00:05, 1718376.07it/s]
9636075it [00:05, 1722598.47it/s]
9811095it [00:05, 1730847.58it/s]
9986561it [00:05, 1737964.35it/s]
10160485it [00:05, 1738328.57it/s]
10334321it [00:06, 1738052.74it/s]
10508129it [00:06, 1737660.19it/s]
10681897it [00:06, 1737137.61it/s]
10855612it [00:06, 1731906.23it/s]
11028807it [00:06, 1718439.76it/s]
11201545it [00:06, 1721082.16it/s]
11373672it [00:06, 1715168.98it/s]
11545666it [00:06, 1716477.49it/s]
11717325it [00:06, 1715232.55it/s]
11889545it [00:06, 1717133.61it/s]
12061265it [00:07, 1715361.06it/s]
12232806it [00:07, 1710945.03it/s]
12403905it [00:07, 1707527.09it/s]
12576657it [00:07, 1713481.33it/s]
12748010it [00:07, 1711593.04it/s]
12920838it [00:07, 1716561.64it/s]
13092498it [00:07, 1711881.93it/s]
13264368it [00:07, 1713899.22it/s]
13435968it [00:07, 1714510.15it/s]
13548611it [00:07, 1716763.54it/s]
[W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_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: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai
+ merge_qc -folders 659_bTo-T1-TRNA-1_B23MHV2LT4_1/659_bTo-T1-TRNA-1_B23MHV2LT4_1.md -output 659_bTo-T1-TRNA-1_B23MHV2LT4_1/659_bTo-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv
+ head -n1 659_bTo-T1-TRNA-1_B23MHV2LT4_1/659_bTo-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv
++ basename Twist_rna_exome_AND_fusion_hg38.bed
+ grep -e Twist_rna_exome_AND_fusion_hg38.bed 659_bTo-T1-TRNA-1_B23MHV2LT4_1/659_bTo-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv