+ mkdir aih-tih-sc-976eb1-R1_B23WHYVLT4_1
+ all_qc -bam aih-tih-sc-976eb1-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-976eb1-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-976eb1-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-976eb1-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-976eb1-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-976eb1-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-976eb1-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-976eb1-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-976eb1-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-976eb1-R1_B23WHYVLT4_1.md.bai
0it [00:00, ?it/s]
138683it [00:00, 1386708.99it/s]
277354it [00:00, 1266469.32it/s]
404689it [00:00, 1232306.86it/s]
528250it [00:00, 1212483.22it/s]
660938it [00:00, 1251886.37it/s]
813628it [00:00, 1342723.08it/s]
964559it [00:00, 1396113.05it/s]
1115042it [00:00, 1430227.19it/s]
1259645it [00:00, 1435089.94it/s]
1403379it [00:01, 1348106.57it/s]
1539351it [00:01, 1292493.23it/s]
1672710it [00:01, 1304172.83it/s]
1803965it [00:01, 1304463.33it/s]
1934996it [00:01, 1270880.17it/s]
2062591it [00:01, 1248319.20it/s]
2187782it [00:01, 1228029.96it/s]
2310831it [00:01, 1225630.70it/s]
2433557it [00:01, 1220157.57it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-976eb1-R1_B23WHYVLT4_1.md.bai
2558857it [00:01, 1229626.09it/s]
2691261it [00:02, 1257424.76it/s]
2826059it [00:02, 1284228.43it/s]
2954600it [00:02, 1249812.21it/s]
3079842it [00:02, 1211142.93it/s]
3166763it [00:02, 1273307.10it/s]
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-976eb1-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-976eb1-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-976eb1-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-976eb1-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-976eb1-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-976eb1-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-976eb1-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-976eb1-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-976eb1-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-976eb1-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-976eb1-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-976eb1-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-976eb1-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-976eb1-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-976eb1-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-976eb1-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-976eb1-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-976eb1-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-976eb1-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-976eb1-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-976eb1-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-976eb1-R1_B23WHYVLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-976eb1-R1_B23WHYVLT4_1.md.bai
+ merge_qc -folders aih-tih-sc-976eb1-R1_B23WHYVLT4_1/aih-tih-sc-976eb1-R1_B23WHYVLT4_1.md -output aih-tih-sc-976eb1-R1_B23WHYVLT4_1/aih-tih-sc-976eb1-R1_B23WHYVLT4_1_full_basic_stats.tsv
+ head -n1 aih-tih-sc-976eb1-R1_B23WHYVLT4_1/aih-tih-sc-976eb1-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-976eb1-R1_B23WHYVLT4_1/aih-tih-sc-976eb1-R1_B23WHYVLT4_1_full_basic_stats.tsv