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/c7/4d659f12101793bc2604d6a9155441/.command.sh Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.dict 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/00/d6f1958fbb2e8686869dfe78c33df4/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bam Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c7/4d659f12101793bc2604d6a9155441/.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-platform-sandbox/pipeline-resources/beds/twist/Twist_rna_exome_AND_fusion_hg38.bed Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/00/d6f1958fbb2e8686869dfe78c33df4/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai Downloading: s3://natera-platform-sandbox/pipeline-resources/Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi ==> STAGING COMPLETE (11 inputs) + mkdir 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1 + all_qc -bam 1173_F0Y_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_F0Y_T1_RNA_SLD_01_A23T55JLT4_1 -reference ref_genome.fa -region chr20 mkdir -p 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md/ cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md/full_bed.bed seqtool depth -bam 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bam -bed 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.depth.gz saturation_plot -bams 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bam -region chr20 -output 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bam > 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md/saturation_qc.tsv fragment_size -bams 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bam -region chr20 -output_prefix 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md/fragsize -threads 1 samtools mpileup -B --min-MQ 60 --min-BQ 30 -f ref_genome.fa -l dbsnp_hg38_contam_sites.bed 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bam > 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.mpileup && contamination -input 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_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_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_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_F0Y_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_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai 154645it [00:00, 1546374.05it/s] 322047it [00:00, 1621418.36it/s] 492863it [00:00, 1660993.63it/s] 666662it [00:00, 1691365.29it/s] 841090it [00:00, 1710424.75it/s] 1015485it [00:00, 1721798.51it/s] 1189436it [00:00, 1727566.30it/s] 1362907it [00:00, 1729818.66it/s] 1537403it [00:00, 1734529.19it/s] 1712196it [00:01, 1738647.50it/s] 1886061it [00:01, 1725616.86it/s] 2058645it [00:01, 1725419.73it/s] 2238121it [00:01, 1746325.30it/s] 2415772it [00:01, 1755396.27it/s] 2591327it [00:01, 1747501.83it/s] 2766095it [00:01, 1741872.27it/s] 2940818it [00:01, 1743450.27it/s] 3116888it [00:01, 1748570.80it/s] 3291755it [00:01, 1745882.91it/s] 3466351it [00:02, 1725680.59it/s] 3641379it [00:02, 1732951.67it/s] 3814719it [00:02, 1719544.67it/s] 3986719it [00:02, 1717200.38it/s] 4158470it [00:02, 1691297.96it/s] 4327931it [00:02, 1692237.70it/s] 4501581it [00:02, 1705328.94it/s] 4673701it [00:02, 1710016.97it/s] 4846901it [00:02, 1716472.22it/s] 5022720it [00:02, 1728805.72it/s] 5199264it [00:03, 1739731.30it/s] 5377937it [00:03, 1753765.18it/s] 5553334it [00:03, 1750357.86it/s] 5728385it [00:03, 1747799.88it/s] 5903176it [00:03, 1737041.17it/s] 6076901it [00:03, 1730128.62it/s] 6252971it [00:03, 1739206.32it/s] 6427072it [00:03, 1739714.24it/s] 6601057it [00:03, 1737787.26it/s] 6774987it [00:03, 1738212.83it/s] 6948815it [00:04, 1722373.19it/s] 7122644it [00:04, 1727085.94it/s] 7297240it [00:04, 1732690.87it/s] 7470660it [00:04, 1733012.68it/s] 7645037it [00:04, 1736210.19it/s] 7821404it [00:04, 1744409.83it/s] 7997003it [00:04, 1747857.04it/s] 8171797it [00:04, 1745178.88it/s] 8347601it [00:04, 1748899.75it/s] 8522837it [00:04, 1749916.98it/s] 8698456it [00:05, 1751778.88it/s] 8874817it [00:05, 1755303.84it/s] 9050962it [00:05, 1757123.47it/s] 9227162it [00:05, 1758566.32it/s] 9403020it [00:05, 1739765.45it/s] 9578799it [00:05, 1745113.22it/s][W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai 9754820it [00:05, 1749598.41it/s] 9929808it [00:05, 1744048.60it/s] 10104235it [00:05, 1712754.05it/s] 10279027it [00:05, 1723114.17it/s] 10456245it [00:06, 1737647.01it/s] 10632168it [00:06, 1744031.30it/s] 10807823it [00:06, 1747615.99it/s] 10983774it [00:06, 1751151.76it/s] 11159656it [00:06, 1753427.53it/s] 11335025it [00:06, 1746411.81it/s] 11509923it [00:06, 1747162.10it/s] 11684656it [00:06, 1737640.15it/s] 11859475it [00:06, 1740768.33it/s] 12034747it [00:06, 1744318.32it/s] 12211740it [00:07, 1751962.41it/s] 12390798it [00:07, 1763508.07it/s] 12567198it [00:07, 1763517.39it/s] 12743557it [00:07, 1755592.03it/s] 12923196it [00:07, 1767665.77it/s] 13101564it [00:07, 1772434.42it/s] 13278819it [00:07, 1771131.87it/s] 13455940it [00:07, 1767850.42it/s] 13632732it [00:07, 1756631.18it/s][W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai 13808413it [00:07, 1750137.05it/s] 13983728it [00:08, 1751018.92it/s] 14159656it [00:08, 1753465.55it/s] 14335057it [00:08, 1753612.57it/s] 14511247it [00:08, 1756074.45it/s] 14686860it [00:08, 1746795.72it/s] 14861553it [00:08, 1744034.67it/s] 15039149it [00:08, 1753552.85it/s] 15217006it [00:08, 1761015.62it/s] 15394929it [00:08, 1766451.74it/s] 15571583it [00:08, 1764641.35it/s] 15750312it [00:09, 1771406.27it/s] 15927458it [00:09, 1767670.12it/s] 16104231it [00:09, 1760256.64it/s] 16280266it [00:09, 1760234.89it/s] 16288669it [00:09, 1740887.15it/s] [W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai tabix -s 1 -b 2 -e 2 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.depth.gz seqtool depth_hist -nbins 500 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.depth.gz > 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.depth_hist.tsv cat 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md -output 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_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 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bam > 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_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 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bam > 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md/reads_per_target.Twist_rna_exome_AND_fusion_hg38.bed.tsv seqtool depth_stats -bed Twist_rna_exome_AND_fusion_hg38.bed 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.depth.gz> 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_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 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bam > 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_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: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md.bai cat 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md/qc_complete.txt + merge_qc -folders 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.md -output 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1_full_basic_stats.tsv + head -n1 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1/1173_F0Y_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_F0Y_T1_RNA_SLD_01_A23T55JLT4_1/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1_full_basic_stats.tsv