+ mkdir 659_b7Z-T1-TRNA-1_B23MHV2LT4_1
+ all_qc -bam 659_b7Z-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_b7Z-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_b7Z-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_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_b7Z-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_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai
0it [00:00, ?it/s]
154721it [00:00, 1547122.95it/s][W::hts_idx_load3] The index file is older than the data file: 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai
321792it [00:00, 1619788.64it/s]
490325it [00:00, 1649637.21it/s]
659309it [00:00, 1665480.56it/s]
828366it [00:00, 1674503.75it/s]
998396it [00:00, 1683250.18it/s]
1166809it [00:00, 1683362.51it/s]
1338779it [00:00, 1694906.92it/s]
1508488it [00:00, 1695563.30it/s]
1678045it [00:01, 1694340.03it/s]
1847480it [00:01, 1692941.02it/s]
2016775it [00:01, 1690363.50it/s]
2186471it [00:01, 1692340.54it/s]
2357682it [00:01, 1698285.57it/s]
2533857it [00:01, 1717378.87it/s]
2705598it [00:01, 1717050.07it/s]
2877305it [00:01, 1708782.21it/s]
3048194it [00:01, 1707090.94it/s]
3218922it [00:01, 1707129.75it/s]
3389640it [00:02, 1685346.02it/s]
3558237it [00:02, 1639664.66it/s]
3722477it [00:02, 1590353.07it/s]
3881919it [00:02, 1581403.95it/s]
4045922it [00:02, 1598270.69it/s]
4205989it [00:02, 1585429.42it/s]
4364696it [00:02, 1577235.17it/s]
4522527it [00:02, 1570718.34it/s]
4679668it [00:02, 1529192.06it/s]
4839442it [00:02, 1549114.30it/s]
4994577it [00:03, 1514858.63it/s]
5146324it [00:03, 1490667.87it/s]
5314873it [00:03, 1547153.47it/s]
5483515it [00:03, 1587929.70it/s]
5656109it [00:03, 1628527.69it/s]
5823500it [00:03, 1641914.89it/s]
5991577it [00:03, 1653458.04it/s]
6159343it [00:03, 1660658.08it/s]
6328565it [00:03, 1670070.69it/s]
6496810it [00:03, 1673755.23it/s]
6664249it [00:04, 1669051.51it/s]
6832514it [00:04, 1673098.35it/s]
7000264it [00:04, 1674393.41it/s]
7169034it [00:04, 1678356.26it/s]
7337994it [00:04, 1681702.96it/s]
7508582it [00:04, 1688931.04it/s]
7678490it [00:04, 1691955.01it/s]
7848034it [00:04, 1692927.92it/s]
8018260it [00:04, 1695706.49it/s]
8189024it [00:04, 1699213.26it/s]
8358948it [00:05, 1697062.78it/s]
8529802it [00:05, 1700483.45it/s]
8699853it [00:05, 1699781.18it/s]
8869833it [00:05, 1685476.89it/s]
9039138it [00:05, 1687715.42it/s]
9209458it [00:05, 1692322.10it/s]
9382095it [00:05, 1702487.35it/s]
9552359it [00:05, 1701327.87it/s]
9725636it [00:05, 1710725.63it/s]
9897062it [00:05, 1711767.77it/s]
10068246it [00:06, 1709011.84it/s]
10239153it [00:06, 1703759.24it/s]
10409536it [00:06, 1695571.03it/s]
10581913it [00:06, 1703967.64it/s]
10754557it [00:06, 1710665.34it/s]
10925636it [00:06, 1705210.87it/s]
11096168it [00:06, 1700719.82it/s]
11266249it [00:06, 1699726.11it/s]
11436228it [00:06, 1698864.44it/s]
11607037it [00:06, 1701597.51it/s]
11778048it [00:07, 1704129.27it/s]
11951143it [00:07, 1712128.43it/s]
12122360it [00:07, 1706926.42it/s]
12293058it [00:07, 1703051.32it/s]
12443725it [00:07, 1668057.35it/s]
[W::hts_idx_load3] The index file is older than the data file: 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_b7Z-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_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md.bai
+ merge_qc -folders 659_b7Z-T1-TRNA-1_B23MHV2LT4_1/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.md -output 659_b7Z-T1-TRNA-1_B23MHV2LT4_1/659_b7Z-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv
+ head -n1 659_b7Z-T1-TRNA-1_B23MHV2LT4_1/659_b7Z-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_b7Z-T1-TRNA-1_B23MHV2LT4_1/659_b7Z-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv