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/aa/0ac33b591daa7640eeeb05b92e6a69/.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/4c/234ec63194e1731f40a68e31ded1fa/aih-tih-sc-4cd8a8-R1_B23WHYVLT4_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/aa/0ac33b591daa7640eeeb05b92e6a69/.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/4c/234ec63194e1731f40a68e31ded1fa/aih-tih-sc-4cd8a8-R1_B23WHYVLT4_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-4cd8a8-R1_B23WHYVLT4_1 + all_qc -bam aih-tih-sc-4cd8a8-R1_B23WHYVLT4_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-4cd8a8-R1_B23WHYVLT4_1 -reference ref_genome.fa -region chr20 mkdir -p aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1/aih-tih-sc-4cd8a8-R1_B23WHYVLT4_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-4cd8a8-R1_B23WHYVLT4_1/aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.md/full_bed.bed seqtool depth -bam aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.md.bam -bed aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1/aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1/aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.md/aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.md.depth.gz saturation_plot -bams aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.md.bam -region chr20 -output aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1/aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1/aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.md/saturation_qc.tsv fragment_size -bams aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1/aih-tih-sc-4cd8a8-R1_B23WHYVLT4_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-4cd8a8-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.md.mpileup && contamination -input aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1/aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4cd8a8-R1_B23WHYVLT4_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-4cd8a8-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4cd8a8-R1_B23WHYVLT4_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-4cd8a8-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.md.bai 0it [00:00, ?it/s] 142887it [00:00, 1428803.23it/s] 293495it [00:00, 1474231.16it/s] 446616it [00:00, 1500222.88it/s] 606405it [00:00, 1538735.56it/s] 776272it [00:00, 1596385.77it/s] 947669it [00:00, 1636343.90it/s] 1119866it [00:00, 1664317.35it/s] 1291176it [00:00, 1679824.56it/s] 1460406it [00:00, 1683703.63it/s] 1630045it [00:01, 1687598.20it/s] 1801871it [00:01, 1696846.33it/s] 1975227it [00:01, 1707986.19it/s] 2147351it [00:01, 1711979.21it/s] 2318549it [00:01, 1711504.22it/s] 2490676it [00:01, 1714393.54it/s] 2662611it [00:01, 1715863.49it/s] 2834198it [00:01, 1715786.00it/s] 3006199it [00:01, 1717035.91it/s] 3178172it [00:01, 1717825.80it/s] 3349955it [00:02, 1702448.03it/s] 3522998it [00:02, 1710772.69it/s] 3698558it [00:02, 1724145.87it/s] 3871533it [00:02, 1725792.03it/s] 4044131it [00:02, 1708748.15it/s] 4218069it [00:02, 1717834.56it/s] 4393086it [00:02, 1727459.01it/s] 4569002it [00:02, 1736909.50it/s] 4745056it [00:02, 1743959.91it/s] 4920894it [00:02, 1748256.40it/s] 5095828it [00:03, 1748559.03it/s] 5271153it [00:03, 1749791.60it/s] 5446141it [00:03, 1748547.67it/s] 5621002it [00:03, 1738810.42it/s] 5794899it [00:03, 1734743.49it/s] 5968385it [00:03, 1729348.26it/s] 6143444it [00:03, 1735664.39it/s] 6317021it [00:03, 1730997.93it/s] 6490662it [00:03, 1732592.26it/s] 6663928it [00:03, 1722726.42it/s] 6836215it [00:04, 1710613.89it/s] 7008321it [00:04, 1713667.90it/s] 7181013it [00:04, 1717595.87it/s] 7354903it [00:04, 1723937.16it/s] 7531240it [00:04, 1735708.00it/s] 7707088it [00:04, 1742436.19it/s] 7882379it [00:04, 1745548.76it/s] 8058477it [00:04, 1750152.02it/s] 8233976it [00:04, 1751581.45it/s] 8297353it [00:04, 1710104.03it/s] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.md.bai tabix -s 1 -b 2 -e 2 aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1/aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.md/aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.md.depth.gz seqtool depth_hist -nbins 500 aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1/aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.md/aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.md.depth.gz > aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1/aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.md/aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.md.depth_hist.tsv cat aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1/aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.md/aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.md -output aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1/aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.md/aih-tih-sc-4cd8a8-R1_B23WHYVLT4_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-4cd8a8-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1/aih-tih-sc-4cd8a8-R1_B23WHYVLT4_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-4cd8a8-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1/aih-tih-sc-4cd8a8-R1_B23WHYVLT4_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-4cd8a8-R1_B23WHYVLT4_1/aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.md/aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.md.depth.gz> aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1/aih-tih-sc-4cd8a8-R1_B23WHYVLT4_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-4cd8a8-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1/aih-tih-sc-4cd8a8-R1_B23WHYVLT4_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-4cd8a8-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.md.bai cat aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1/aih-tih-sc-4cd8a8-R1_B23WHYVLT4_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-4cd8a8-R1_B23WHYVLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1/aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1/aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.md/qc_complete.txt + merge_qc -folders aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1/aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1.md -output aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1/aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1_full_basic_stats.tsv + head -n1 aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1/aih-tih-sc-4cd8a8-R1_B23WHYVLT4_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-4cd8a8-R1_B23WHYVLT4_1/aih-tih-sc-4cd8a8-R1_B23WHYVLT4_1_full_basic_stats.tsv