+ mkdir 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1
+ all_qc -bam 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_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 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1 -reference ref_genome.fa -region chr20
[W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[mpileup] 1 samples in 1 input files
[W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_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: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.md.bai

0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.md.bai

151524it [00:00, 1514959.71it/s]
313203it [00:00, 1574812.03it/s]
474235it [00:00, 1590989.13it/s]
643373it [00:00, 1630579.60it/s]
806432it [00:00, 1620479.39it/s]
977234it [00:00, 1650096.93it/s]
1150345it [00:00, 1676486.42it/s]
1321908it [00:00, 1688898.95it/s]
1493416it [00:00, 1697047.92it/s]
1514963it [00:00, 1656465.62it/s]
[W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_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: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.md.bai
+ merge_qc -folders 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.md -output 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1_full_basic_stats.tsv
+ head -n1 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1_full_basic_stats.tsv
++ basename Twist_rna_exome_AND_fusion_hg38.bed
+ grep -e Twist_rna_exome_AND_fusion_hg38.bed 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1_full_basic_stats.tsv