+ mkdir aih-tih-sc-505123-R1_B23WHYVLT4_1
+ all_qc -bam aih-tih-sc-505123-R1_B23WHYVLT4_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 aih-tih-sc-505123-R1_B23WHYVLT4_1 -reference ref_genome.fa -region chr20
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.md.bai
[mpileup] 1 samples in 1 input files
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_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: aih-tih-sc-505123-R1_B23WHYVLT4_1.md.bai

0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.md.bai

133296it [00:00, 1332859.58it/s]
274500it [00:00, 1379141.64it/s]
420270it [00:00, 1414985.80it/s]
561769it [00:00, 1412125.23it/s]
702983it [00:00, 1410918.42it/s]
844076it [00:00, 1337645.71it/s]
978504it [00:00, 1202853.50it/s]
1101269it [00:00, 1134966.01it/s]
1216733it [00:00, 1117429.99it/s]
1329710it [00:01, 1110093.59it/s]
1441518it [00:01, 1065936.41it/s]
1574449it [00:01, 1139644.37it/s]
1721009it [00:01, 1232700.53it/s]
1865143it [00:01, 1293075.02it/s]
1995632it [00:01, 1267991.73it/s]
2123313it [00:01, 1140047.85it/s]
2240125it [00:01, 1069792.05it/s]
2349505it [00:02, 1012216.23it/s]
2452564it [00:02, 982422.52it/s] 
2551963it [00:02, 955930.84it/s]
2648255it [00:02, 945825.48it/s]
2743248it [00:02, 935395.64it/s]
2859963it [00:02, 1000239.40it/s]
2978484it [00:02, 1053054.34it/s]
3100543it [00:02, 1101584.22it/s]
3236497it [00:02, 1177080.56it/s]
3370860it [00:02, 1226121.71it/s]
3509558it [00:03, 1273679.39it/s]
3655452it [00:03, 1328751.45it/s]
3788680it [00:03, 1289608.06it/s]
3921458it [00:03, 1300739.92it/s]
4080164it [00:03, 1385064.88it/s]
4238113it [00:03, 1442626.68it/s]
4382738it [00:03, 1351557.83it/s]
4519270it [00:03, 1197521.97it/s]
4646816it [00:03, 1218094.04it/s]
4786103it [00:04, 1265909.66it/s]
4915207it [00:04, 1220938.05it/s]
5039215it [00:04, 1220579.54it/s]
5179320it [00:04, 1271650.47it/s]
5320787it [00:04, 1312848.64it/s]
5463838it [00:04, 1347001.81it/s]
5602419it [00:04, 1358391.08it/s]
5741887it [00:04, 1369053.34it/s]
5879225it [00:04, 1366517.08it/s]
6016179it [00:04, 1366384.69it/s]
6153601it [00:05, 1368686.79it/s]
6290619it [00:05, 1366437.61it/s]
6427368it [00:05, 1363269.08it/s]
6563769it [00:05, 1352498.19it/s]
6639198it [00:05, 1231497.50it/s]
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_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: aih-tih-sc-505123-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.md.bai
+ merge_qc -folders aih-tih-sc-505123-R1_B23WHYVLT4_1/aih-tih-sc-505123-R1_B23WHYVLT4_1.md -output aih-tih-sc-505123-R1_B23WHYVLT4_1/aih-tih-sc-505123-R1_B23WHYVLT4_1_full_basic_stats.tsv
+ head -n1 aih-tih-sc-505123-R1_B23WHYVLT4_1/aih-tih-sc-505123-R1_B23WHYVLT4_1_full_basic_stats.tsv
++ basename Twist_rna_exome_AND_fusion_hg38.bed
+ grep -e Twist_rna_exome_AND_fusion_hg38.bed aih-tih-sc-505123-R1_B23WHYVLT4_1/aih-tih-sc-505123-R1_B23WHYVLT4_1_full_basic_stats.tsv