Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa Downloading: s3://natera-platform-sandbox/pipeline-resources/Homo_sapiens_assembly38.dbsnp138.vcf.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e9/75312982a8f51ef36533081e5806f8/.command.sh Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.dict Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c0/a6cf6e461a5618bdcc9b6f0f4ee877/aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md.bai Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/gatk4/dbsnp_hg38_contam_sites.bed Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e9/75312982a8f51ef36533081e5806f8/.command.run Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa.fai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c0/a6cf6e461a5618bdcc9b6f0f4ee877/aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md.bam Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/twist/Twist_rna_exome_AND_fusion_hg38.bed Downloading: s3://natera-platform-sandbox/pipeline-resources/Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi ==> STAGING COMPLETE (11 inputs) + mkdir aih-tih-sc-2ca847-R1_A23WJ53LT4_1 + all_qc -bam aih-tih-sc-2ca847-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-2ca847-R1_A23WJ53LT4_1 -reference ref_genome.fa -region chr20 mkdir -p aih-tih-sc-2ca847-R1_A23WJ53LT4_1/aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md/ cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > aih-tih-sc-2ca847-R1_A23WJ53LT4_1/aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md/full_bed.bed seqtool depth -bam aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md.bam -bed aih-tih-sc-2ca847-R1_A23WJ53LT4_1/aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-2ca847-R1_A23WJ53LT4_1/aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md/aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md.depth.gz saturation_plot -bams aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md.bam -region chr20 -output aih-tih-sc-2ca847-R1_A23WJ53LT4_1/aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-2ca847-R1_A23WJ53LT4_1/aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md/saturation_qc.tsv fragment_size -bams aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-2ca847-R1_A23WJ53LT4_1/aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md/fragsize -threads 1 samtools mpileup -B --min-MQ 60 --min-BQ 30 -f ref_genome.fa -l dbsnp_hg38_contam_sites.bed aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md.mpileup && contamination -input aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-2ca847-R1_A23WJ53LT4_1/aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2ca847-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-2ca847-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2ca847-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-2ca847-R1_A23WJ53LT4_1.md.bai 0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md.bai 126449it [00:00, 1264352.54it/s] 252885it [00:00, 1251609.21it/s] 378055it [00:00, 1251512.77it/s] 505909it [00:00, 1262114.84it/s] 669782it [00:00, 1397485.75it/s] 838683it [00:00, 1496411.41it/s] 1008451it [00:00, 1562108.58it/s] 1176394it [00:00, 1599398.73it/s] 1346352it [00:00, 1630666.09it/s] 1509437it [00:01, 1608164.71it/s] 1680493it [00:01, 1639058.32it/s] 1852772it [00:01, 1664312.76it/s] 2019281it [00:01, 1649670.99it/s] 2191334it [00:01, 1670708.05it/s] 2362764it [00:01, 1683722.70it/s] 2534423it [00:01, 1693505.88it/s] 2704354it [00:01, 1695068.93it/s] 2876649it [00:01, 1703392.82it/s] 3047505it [00:01, 1704809.72it/s] 3218004it [00:02, 1634647.21it/s] 3382089it [00:02, 1606391.19it/s] 3543200it [00:02, 1596816.11it/s] 3703194it [00:02, 1558032.51it/s] 3859329it [00:02, 1556331.43it/s] 4022339it [00:02, 1577798.56it/s] 4180339it [00:02, 1406719.07it/s] 4335247it [00:02, 1444776.56it/s] 4504251it [00:02, 1513435.94it/s] 4671937it [00:02, 1560107.60it/s] 4829883it [00:03, 1528789.71it/s] 4986713it [00:03, 1540128.19it/s] 5146863it [00:03, 1557895.83it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md.bai 5303435it [00:03, 1477775.61it/s] 5452516it [00:03, 1337333.37it/s] 5598627it [00:03, 1370493.62it/s] 5771540it [00:03, 1469880.65it/s] 5944204it [00:03, 1542685.41it/s] 6113604it [00:03, 1586295.40it/s] 6273972it [00:04, 1580127.04it/s] 6433195it [00:04, 1579988.44it/s] 6595724it [00:04, 1593296.65it/s] 6771361it [00:04, 1641542.86it/s] 6948135it [00:04, 1679020.85it/s] 7122858it [00:04, 1699321.34it/s] 7296879it [00:04, 1711502.80it/s] 7469914it [00:04, 1717107.34it/s] 7644228it [00:04, 1724854.29it/s] 7819955it [00:04, 1734530.36it/s] 7995142it [00:05, 1739688.27it/s] 8169881it [00:05, 1741963.79it/s] 8344114it [00:05, 1727902.98it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md.bai 8516956it [00:05, 1665679.22it/s] 8688207it [00:05, 1679278.05it/s] 8865215it [00:05, 1705917.31it/s] 9038538it [00:05, 1713956.24it/s] 9216450it [00:05, 1733271.04it/s] 9389966it [00:05, 1725545.98it/s] 9565413it [00:05, 1734113.08it/s] 9741819it [00:06, 1743006.79it/s] 9916197it [00:06, 1730860.93it/s] 9934368it [00:06, 1606762.77it/s] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md.bai tabix -s 1 -b 2 -e 2 aih-tih-sc-2ca847-R1_A23WJ53LT4_1/aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md/aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md.depth.gz seqtool depth_hist -nbins 500 aih-tih-sc-2ca847-R1_A23WJ53LT4_1/aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md/aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md.depth.gz > aih-tih-sc-2ca847-R1_A23WJ53LT4_1/aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md/aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md.depth_hist.tsv cat aih-tih-sc-2ca847-R1_A23WJ53LT4_1/aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md/aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md -output aih-tih-sc-2ca847-R1_A23WJ53LT4_1/aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md/aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md.depth.png [W::hts_idx_load3] The index file is older than the data file: Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi seqtool read_qc -bed Twist_rna_exome_AND_fusion_hg38.bed -n_threads 1 -bam_threads 2 aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-2ca847-R1_A23WJ53LT4_1/aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md/read_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv seqtool reads_per_target -bed Twist_rna_exome_AND_fusion_hg38.bed -threads 1 -bam_threads 2 aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-2ca847-R1_A23WJ53LT4_1/aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md/reads_per_target.Twist_rna_exome_AND_fusion_hg38.bed.tsv seqtool depth_stats -bed Twist_rna_exome_AND_fusion_hg38.bed aih-tih-sc-2ca847-R1_A23WJ53LT4_1/aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md/aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md.depth.gz> aih-tih-sc-2ca847-R1_A23WJ53LT4_1/aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md/depth_stats.Twist_rna_exome_AND_fusion_hg38.bed.tsv seqtool gc_bias -reference ref_genome.fa -bed Twist_rna_exome_AND_fusion_hg38.bed -bin_size 0.05 -threads 1 -bam_threads 2 aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md.bam > aih-tih-sc-2ca847-R1_A23WJ53LT4_1/aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md.bai cat aih-tih-sc-2ca847-R1_A23WJ53LT4_1/aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "aih-tih-sc-2ca847-R1_A23WJ53LT4_1/aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > aih-tih-sc-2ca847-R1_A23WJ53LT4_1/aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md/qc_complete.txt + merge_qc -folders aih-tih-sc-2ca847-R1_A23WJ53LT4_1/aih-tih-sc-2ca847-R1_A23WJ53LT4_1.md -output aih-tih-sc-2ca847-R1_A23WJ53LT4_1/aih-tih-sc-2ca847-R1_A23WJ53LT4_1_full_basic_stats.tsv + head -n1 aih-tih-sc-2ca847-R1_A23WJ53LT4_1/aih-tih-sc-2ca847-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-2ca847-R1_A23WJ53LT4_1/aih-tih-sc-2ca847-R1_A23WJ53LT4_1_full_basic_stats.tsv