Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/89/6108b41fd9cb3ad2b68da6f6b336a7/aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md.bam 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/a6/510e4ec17c522cfb034354e0ebdbab/.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/a6/510e4ec17c522cfb034354e0ebdbab/.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/89/6108b41fd9cb3ad2b68da6f6b336a7/aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md.bai 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-31d31f-R1_A23YTGFLT4_1 + all_qc -bam aih-tih-sc-31d31f-R1_A23YTGFLT4_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-31d31f-R1_A23YTGFLT4_1 -reference ref_genome.fa -region chr20 mkdir -p aih-tih-sc-31d31f-R1_A23YTGFLT4_1/aih-tih-sc-31d31f-R1_A23YTGFLT4_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-31d31f-R1_A23YTGFLT4_1/aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md/full_bed.bed seqtool depth -bam aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md.bam -bed aih-tih-sc-31d31f-R1_A23YTGFLT4_1/aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-31d31f-R1_A23YTGFLT4_1/aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md/aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md.depth.gz saturation_plot -bams aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md.bam -region chr20 -output aih-tih-sc-31d31f-R1_A23YTGFLT4_1/aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-31d31f-R1_A23YTGFLT4_1/aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md/saturation_qc.tsv fragment_size -bams aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-31d31f-R1_A23YTGFLT4_1/aih-tih-sc-31d31f-R1_A23YTGFLT4_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-31d31f-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md.mpileup && contamination -input aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-31d31f-R1_A23YTGFLT4_1/aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-31d31f-R1_A23YTGFLT4_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-31d31f-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-31d31f-R1_A23YTGFLT4_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-31d31f-R1_A23YTGFLT4_1.md.bai 0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md.bai 159988it [00:00, 1599786.17it/s] 336356it [00:00, 1696150.11it/s] 513915it [00:00, 1732389.88it/s] 694214it [00:00, 1760107.84it/s] 873897it [00:00, 1773124.15it/s] 1053151it [00:00, 1779696.41it/s] 1231450it [00:00, 1780743.08it/s] 1409525it [00:00, 1780131.10it/s] 1588083it [00:00, 1781809.32it/s] 1766264it [00:01, 1774671.64it/s] 1944786it [00:01, 1777867.76it/s] 2127103it [00:01, 1791598.12it/s] 2310164it [00:01, 1803373.70it/s] 2490508it [00:01, 1798530.53it/s] 2671160it [00:01, 1800905.96it/s] 2851256it [00:01, 1791318.13it/s] 3030587it [00:01, 1791891.59it/s] 3210654it [00:01, 1794495.02it/s] 3392000it [00:01, 1800149.14it/s] 3572022it [00:02, 1776334.11it/s] 3749728it [00:02, 1773795.64it/s] 3930823it [00:02, 1784832.16it/s] 4109947it [00:02, 1786725.05it/s] 4289431it [00:02, 1789127.40it/s] 4468367it [00:02, 1787892.94it/s] 4647845it [00:02, 1789925.09it/s] 4826850it [00:02, 1783471.15it/s] 5005775it [00:02, 1785175.89it/s] 5185835it [00:02, 1789770.97it/s] 5366578it [00:03, 1795036.27it/s] 5546089it [00:03, 1792405.99it/s] 5725335it [00:03, 1771714.84it/s] 5902561it [00:03, 1762269.91it/s] 6081221it [00:03, 1769458.17it/s] 6258203it [00:03, 1769179.54it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md.bai 6435147it [00:03, 1764329.64it/s] 6611606it [00:03, 1764380.20it/s] 6788057it [00:03, 1755208.88it/s] 6966293it [00:03, 1763265.88it/s] 7142729it [00:04, 1763503.98it/s] 7320288it [00:04, 1767097.22it/s] 7500551it [00:04, 1777711.90it/s] 7680239it [00:04, 1783433.31it/s] 7858590it [00:04, 1780743.08it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md.bai 8040114it [00:04, 1790870.22it/s] 8219965it [00:04, 1793139.02it/s] 8399284it [00:04, 1788629.11it/s] 8578789it [00:04, 1790524.35it/s] 8759416it [00:04, 1795218.62it/s] 8938942it [00:05, 1790609.83it/s] 9120875it [00:05, 1799176.57it/s] 9300799it [00:05, 1798615.68it/s] 9482124it [00:05, 1802972.71it/s] 9625444it [00:05, 1781493.74it/s] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md.bai tabix -s 1 -b 2 -e 2 aih-tih-sc-31d31f-R1_A23YTGFLT4_1/aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md/aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md.depth.gz seqtool depth_hist -nbins 500 aih-tih-sc-31d31f-R1_A23YTGFLT4_1/aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md/aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md.depth.gz > aih-tih-sc-31d31f-R1_A23YTGFLT4_1/aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md/aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md.depth_hist.tsv cat aih-tih-sc-31d31f-R1_A23YTGFLT4_1/aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md/aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md -output aih-tih-sc-31d31f-R1_A23YTGFLT4_1/aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md/aih-tih-sc-31d31f-R1_A23YTGFLT4_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-31d31f-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-31d31f-R1_A23YTGFLT4_1/aih-tih-sc-31d31f-R1_A23YTGFLT4_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-31d31f-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-31d31f-R1_A23YTGFLT4_1/aih-tih-sc-31d31f-R1_A23YTGFLT4_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-31d31f-R1_A23YTGFLT4_1/aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md/aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md.depth.gz> aih-tih-sc-31d31f-R1_A23YTGFLT4_1/aih-tih-sc-31d31f-R1_A23YTGFLT4_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-31d31f-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-31d31f-R1_A23YTGFLT4_1/aih-tih-sc-31d31f-R1_A23YTGFLT4_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-31d31f-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md.bai cat aih-tih-sc-31d31f-R1_A23YTGFLT4_1/aih-tih-sc-31d31f-R1_A23YTGFLT4_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-31d31f-R1_A23YTGFLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "aih-tih-sc-31d31f-R1_A23YTGFLT4_1/aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > aih-tih-sc-31d31f-R1_A23YTGFLT4_1/aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md/qc_complete.txt + merge_qc -folders aih-tih-sc-31d31f-R1_A23YTGFLT4_1/aih-tih-sc-31d31f-R1_A23YTGFLT4_1.md -output aih-tih-sc-31d31f-R1_A23YTGFLT4_1/aih-tih-sc-31d31f-R1_A23YTGFLT4_1_full_basic_stats.tsv + head -n1 aih-tih-sc-31d31f-R1_A23YTGFLT4_1/aih-tih-sc-31d31f-R1_A23YTGFLT4_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-31d31f-R1_A23YTGFLT4_1/aih-tih-sc-31d31f-R1_A23YTGFLT4_1_full_basic_stats.tsv