+ mkdir aih-tih-sc-284856-R1_A23WJ53LT4_1
+ all_qc -bam aih-tih-sc-284856-R1_A23WJ53LT4_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-284856-R1_A23WJ53LT4_1 -reference ref_genome.fa -region chr20
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-R1_A23WJ53LT4_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-284856-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-R1_A23WJ53LT4_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-284856-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bai

0it [00:00, ?it/s]
123436it [00:00, 1233990.48it/s]
257514it [00:00, 1296766.28it/s]
394498it [00:00, 1330106.53it/s]
529790it [00:00, 1339092.83it/s]
665842it [00:00, 1346796.56it/s]
801638it [00:00, 1350452.30it/s]
937933it [00:00, 1354340.73it/s]
1073457it [00:00, 1354599.62it/s]
1208917it [00:00, 1346563.04it/s]
1344496it [00:01, 1349378.27it/s]
1480579it [00:01, 1352852.56it/s]
1615871it [00:01, 1342247.79it/s]
1751236it [00:01, 1345652.37it/s]
1887462it [00:01, 1350624.42it/s]
2023248it [00:01, 1352779.04it/s]
2159496it [00:01, 1355594.42it/s]
2295064it [00:01, 1349576.05it/s]
2430033it [00:01, 1349463.25it/s]
2565648it [00:01, 1351397.21it/s]
2700794it [00:02, 1342400.80it/s]
2837771it [00:02, 1350480.89it/s]
2975105it [00:02, 1357295.02it/s]
3111537it [00:02, 1359379.50it/s]
3247486it [00:02, 1283229.92it/s]
3376685it [00:02, 1227768.22it/s]
3512527it [00:02, 1264552.44it/s]
3648560it [00:02, 1291863.80it/s]
3785506it [00:02, 1314409.82it/s]
3919400it [00:02, 1321529.56it/s]
4054281it [00:03, 1329570.44it/s]
4188290it [00:03, 1332673.67it/s]
4324760it [00:03, 1342193.59it/s]
4461488it [00:03, 1349661.41it/s]
4596575it [00:03, 1321461.46it/s]
4728929it [00:03, 1274064.65it/s]
4857157it [00:03, 1276384.52it/s]
4985117it [00:03, 1276526.62it/s]
5112996it [00:03, 1269899.62it/s]
5246993it [00:03, 1290530.24it/s]
5250617it [00:03, 1322629.94it/s]
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-R1_A23WJ53LT4_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-284856-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bai
+ merge_qc -folders aih-tih-sc-284856-R1_A23WJ53LT4_1/aih-tih-sc-284856-R1_A23WJ53LT4_1.md -output aih-tih-sc-284856-R1_A23WJ53LT4_1/aih-tih-sc-284856-R1_A23WJ53LT4_1_full_basic_stats.tsv
+ head -n1 aih-tih-sc-284856-R1_A23WJ53LT4_1/aih-tih-sc-284856-R1_A23WJ53LT4_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-284856-R1_A23WJ53LT4_1/aih-tih-sc-284856-R1_A23WJ53LT4_1_full_basic_stats.tsv