+ mkdir BT-20_FFPE_RNA_0001_B23LG7FLT4_1
+ all_qc -bam BT-20_FFPE_RNA_0001_B23LG7FLT4_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 BT-20_FFPE_RNA_0001_B23LG7FLT4_1 -reference ref_genome.fa -region chr20
[W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[mpileup] 1 samples in 1 input files
[W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_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: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
93111it [00:00, 930837.91it/s]
186195it [00:00, 920256.52it/s]
278229it [00:00, 889869.78it/s]
367319it [00:00, 883736.84it/s]
465064it [00:00, 916786.19it/s]
558594it [00:00, 922958.10it/s]
650966it [00:00, 920016.91it/s]
750392it [00:00, 943428.41it/s]
845403it [00:00, 945324.36it/s]
941317it [00:01, 949552.93it/s]
1036301it [00:01, 947719.20it/s]
1136346it [00:01, 963688.39it/s]
1233513it [00:01, 966083.99it/s]
1332646it [00:01, 973677.85it/s]
1430025it [00:01, 910422.36it/s]
1521898it [00:01, 793026.01it/s]
1604232it [00:01, 729008.45it/s]
1679799it [00:01, 690435.96it/s]
1750707it [00:02, 665435.02it/s]
1818432it [00:02, 647127.40it/s]
1883852it [00:02, 633936.33it/s]
1947646it [00:02, 624061.21it/s]
2010266it [00:02, 616163.56it/s]
2071986it [00:02, 610908.86it/s]
2133122it [00:02, 606872.69it/s]
2193823it [00:02, 604895.37it/s]
2254315it [00:02, 601490.45it/s]
2314458it [00:03, 599588.53it/s]
2374409it [00:03, 598378.92it/s]
2434637it [00:03, 599514.67it/s]
2494585it [00:03, 599406.72it/s][W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
2554862it [00:03, 600393.18it/s]
2614901it [00:03, 599925.37it/s]
2674893it [00:03, 598257.53it/s]
2734719it [00:03, 583607.73it/s]
2833773it [00:03, 703114.76it/s]
2933236it [00:03, 789261.54it/s][W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
3032059it [00:04, 848316.14it/s]
3130425it [00:04, 888603.69it/s][W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
3230216it [00:04, 921206.16it/s]
3328736it [00:04, 940316.27it/s]
3422905it [00:04, 930541.09it/s]
3516077it [00:04, 924157.03it/s]
3608776it [00:04, 924975.71it/s]
3701336it [00:04, 916334.15it/s]
3793025it [00:04, 904242.55it/s]
3883865it [00:04, 905447.77it/s]
3989241it [00:05, 949227.32it/s]
4095419it [00:05, 982667.24it/s]
4196600it [00:05, 991331.37it/s]
4296026it [00:05, 992189.34it/s]
4374251it [00:05, 807935.67it/s]
[W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_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: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
+ merge_qc -folders BT-20_FFPE_RNA_0001_B23LG7FLT4_1/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md -output BT-20_FFPE_RNA_0001_B23LG7FLT4_1/BT-20_FFPE_RNA_0001_B23LG7FLT4_1_full_basic_stats.tsv
+ head -n1 BT-20_FFPE_RNA_0001_B23LG7FLT4_1/BT-20_FFPE_RNA_0001_B23LG7FLT4_1_full_basic_stats.tsv
++ basename Twist_rna_exome_AND_fusion_hg38.bed
+ grep -e Twist_rna_exome_AND_fusion_hg38.bed BT-20_FFPE_RNA_0001_B23LG7FLT4_1/BT-20_FFPE_RNA_0001_B23LG7FLT4_1_full_basic_stats.tsv