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/d0/3bcd4937af3d51c2e3edc8e39ab4ea/.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/d6/c014c26322bff8a249c37b432d7f0a/aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.md.bam 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/d0/3bcd4937af3d51c2e3edc8e39ab4ea/.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/d6/c014c26322bff8a249c37b432d7f0a/aih-tih-sc-ecc0bc-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-ecc0bc-R1_A23YTGFLT4_1 + all_qc -bam aih-tih-sc-ecc0bc-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-ecc0bc-R1_A23YTGFLT4_1 -reference ref_genome.fa -region chr20 mkdir -p aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1/aih-tih-sc-ecc0bc-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-ecc0bc-R1_A23YTGFLT4_1/aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.md/full_bed.bed saturation_plot -bams aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.md.bam -region chr20 -output aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1/aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.md/saturation_plot.png -threads 1 seqtool depth -bam aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.md.bam -bed aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1/aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1/aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.md/aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.md.depth.gz seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1/aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.md/saturation_qc.tsv fragment_size -bams aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1/aih-tih-sc-ecc0bc-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-ecc0bc-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.md.mpileup && contamination -input aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1/aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ecc0bc-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-ecc0bc-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ecc0bc-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-ecc0bc-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.md.bai 0it [00:00, ?it/s] 74687it [00:00, 746274.66it/s] 153913it [00:00, 773205.84it/s] 235410it [00:00, 792204.44it/s] 316306it [00:00, 798797.24it/s] 396985it [00:00, 801520.17it/s] 479036it [00:00, 807854.39it/s] 559822it [00:00, 806265.04it/s] 641398it [00:00, 809268.11it/s] 722326it [00:00, 806772.64it/s] 804056it [00:01, 809810.90it/s] 885040it [00:01, 807619.02it/s] 966556it [00:01, 809890.29it/s] 1049661it [00:01, 816269.97it/s] 1132807it [00:01, 820737.35it/s] 1215933it [00:01, 823888.86it/s] 1299939it [00:01, 828540.74it/s] 1383446it [00:01, 830308.84it/s] 1466679it [00:01, 830883.85it/s] 1550005it [00:01, 831579.51it/s] 1633502it [00:02, 832579.44it/s] 1716761it [00:02, 831871.63it/s] 1799949it 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928297.85it/s] 4504535it [00:05, 954117.49it/s] 4600478it [00:05, 955690.46it/s] 4696056it [00:05, 941392.94it/s] 4790249it [00:05, 938075.23it/s] 4884093it [00:05, 932469.55it/s] 4977368it [00:05, 923867.45it/s] 5073430it [00:05, 934547.00it/s] 5169657it [00:06, 942538.92it/s] 5263944it [00:06, 932020.84it/s] 5357189it [00:06, 913696.97it/s] 5448648it [00:06, 900908.49it/s] 5538815it [00:06, 889981.13it/s] 5627870it [00:06, 883488.04it/s] 5716252it [00:06, 881252.80it/s] 5804397it [00:06, 878133.51it/s] 5892221it [00:06, 877073.68it/s] 5979934it [00:06, 876192.21it/s] 6068290it [00:07, 878367.60it/s] 6156131it [00:07, 863882.26it/s] 6243638it [00:07, 867170.75it/s] 6332614it [00:07, 873856.74it/s] 6420451it [00:07, 875183.41it/s] 6508425it [00:07, 876312.98it/s] 6596075it [00:07, 875281.14it/s] 6683616it [00:07, 875155.27it/s] 6771141it [00:07, 873197.64it/s] 6858468it [00:07, 872362.73it/s] 6945709it [00:08, 870092.89it/s] 7033624it [00:08, 872784.99it/s] 7120925it [00:08, 872837.61it/s] 7210881it [00:08, 880695.18it/s] 7300406it [00:08, 884813.86it/s] 7389287it [00:08, 885782.39it/s] 7479901it [00:08, 891840.14it/s] 7569087it [00:08, 888857.41it/s] 7658654it [00:08, 890874.57it/s] 7747745it [00:08, 890768.44it/s] 7836824it [00:09, 889863.83it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.md.bai 7925812it [00:09, 879425.79it/s] 8013782it [00:09, 871388.08it/s] 8100950it [00:09, 859079.26it/s] 8186903it [00:09, 839126.62it/s] 8270916it [00:09, 829724.87it/s] 8353957it [00:09, 802006.80it/s] 8434339it [00:09, 787511.89it/s] 8513218it [00:09, 778946.35it/s] 8591540it [00:10, 779963.52it/s] 8670648it [00:10, 783186.51it/s] 8749015it [00:10, 776371.57it/s] 8826843it [00:10, 776918.12it/s] 8908894it [00:10, 789793.60it/s] 8990740it [00:10, 798292.25it/s] 9070604it [00:10, 798117.18it/s] 9150458it [00:10, 798048.25it/s] 9230871it [00:10, 799848.99it/s] 9314095it [00:10, 809522.69it/s] 9397111it [00:11, 815684.97it/s] 9478689it [00:11, 809031.51it/s] 9559611it [00:11, 807309.82it/s] 9642371it [00:11, 813157.52it/s] 9723699it [00:11, 810301.53it/s] 9804739it [00:11, 796363.18it/s] 9884429it [00:11, 785091.44it/s] 9963035it [00:11, 785282.03it/s] 10043214it [00:11, 790144.23it/s] 10127579it [00:11, 805866.32it/s] 10208207it [00:12, 799143.09it/s] 10288692it [00:12, 800480.57it/s] 10368768it [00:12, 792254.21it/s] 10448026it [00:12, 780581.35it/s] 10463950it [00:12, 846474.82it/s] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.md.bai tabix -s 1 -b 2 -e 2 aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1/aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.md/aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.md.depth.gz seqtool depth_hist -nbins 500 aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1/aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.md/aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.md.depth.gz > aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1/aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.md/aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.md.depth_hist.tsv cat aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1/aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.md/aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.md -output aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1/aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.md/aih-tih-sc-ecc0bc-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-ecc0bc-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1/aih-tih-sc-ecc0bc-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-ecc0bc-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1/aih-tih-sc-ecc0bc-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-ecc0bc-R1_A23YTGFLT4_1/aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.md/aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.md.depth.gz> aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1/aih-tih-sc-ecc0bc-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-ecc0bc-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1/aih-tih-sc-ecc0bc-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-ecc0bc-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.md.bai cat aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1/aih-tih-sc-ecc0bc-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-ecc0bc-R1_A23YTGFLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1/aih-tih-sc-ecc0bc-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-ecc0bc-R1_A23YTGFLT4_1/aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.md/qc_complete.txt + merge_qc -folders aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1/aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1.md -output aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1/aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1_full_basic_stats.tsv + head -n1 aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1/aih-tih-sc-ecc0bc-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-ecc0bc-R1_A23YTGFLT4_1/aih-tih-sc-ecc0bc-R1_A23YTGFLT4_1_full_basic_stats.tsv