Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/56/00f6f55e17af48e3608f4727041294/659_bTo-T1-TRNA-1_B23MHV2LT4_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/74/7b503fcf1df6734acafd7aead69c73/.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/74/7b503fcf1df6734acafd7aead69c73/.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/56/00f6f55e17af48e3608f4727041294/659_bTo-T1-TRNA-1_B23MHV2LT4_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 659_bTo-T1-TRNA-1_B23MHV2LT4_1 + all_qc -bam 659_bTo-T1-TRNA-1_B23MHV2LT4_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 659_bTo-T1-TRNA-1_B23MHV2LT4_1 -reference ref_genome.fa -region chr20 mkdir -p 659_bTo-T1-TRNA-1_B23MHV2LT4_1/659_bTo-T1-TRNA-1_B23MHV2LT4_1.md/ cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > 659_bTo-T1-TRNA-1_B23MHV2LT4_1/659_bTo-T1-TRNA-1_B23MHV2LT4_1.md/full_bed.bed saturation_plot -bams 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bam -region chr20 -output 659_bTo-T1-TRNA-1_B23MHV2LT4_1/659_bTo-T1-TRNA-1_B23MHV2LT4_1.md/saturation_plot.png -threads 1 seqtool depth -bam 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bam -bed 659_bTo-T1-TRNA-1_B23MHV2LT4_1/659_bTo-T1-TRNA-1_B23MHV2LT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > 659_bTo-T1-TRNA-1_B23MHV2LT4_1/659_bTo-T1-TRNA-1_B23MHV2LT4_1.md/659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bTo-T1-TRNA-1_B23MHV2LT4_1/659_bTo-T1-TRNA-1_B23MHV2LT4_1.md/saturation_qc.tsv fragment_size -bams 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bam -region chr20 -output_prefix 659_bTo-T1-TRNA-1_B23MHV2LT4_1/659_bTo-T1-TRNA-1_B23MHV2LT4_1.md/fragsize -threads 1 samtools mpileup -B --min-MQ 60 --min-BQ 30 -f ref_genome.fa -l dbsnp_hg38_contam_sites.bed 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.mpileup && contamination -input 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > 659_bTo-T1-TRNA-1_B23MHV2LT4_1/659_bTo-T1-TRNA-1_B23MHV2LT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai [mpileup] 1 samples in 1 input files [W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_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: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai 0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai 91768it [00:00, 917588.99it/s] 197778it [00:00, 1001362.77it/s] 297915it [00:00, 978592.32it/s] 409102it [00:00, 1030445.28it/s] 514245it [00:00, 1037840.70it/s] 622911it [00:00, 1054306.91it/s] 753886it [00:00, 1137449.69it/s] 889607it [00:00, 1207183.90it/s] 1012038it [00:00, 1212497.99it/s] 1133337it [00:01, 1210223.28it/s] 1254394it [00:01, 1198704.24it/s] 1386348it [00:01, 1235126.31it/s] 1509923it [00:01, 1194961.26it/s] 1629724it [00:01, 1194302.77it/s] 1762173it [00:01, 1232733.19it/s] 1897918it [00:01, 1269713.74it/s] 2025100it [00:01, 1262416.86it/s] 2166854it [00:01, 1308467.83it/s] 2305291it [00:01, 1330917.37it/s] 2442826it [00:02, 1344160.70it/s] 2579710it [00:02, 1351517.39it/s] 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[W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai tabix -s 1 -b 2 -e 2 659_bTo-T1-TRNA-1_B23MHV2LT4_1/659_bTo-T1-TRNA-1_B23MHV2LT4_1.md/659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz seqtool depth_hist -nbins 500 659_bTo-T1-TRNA-1_B23MHV2LT4_1/659_bTo-T1-TRNA-1_B23MHV2LT4_1.md/659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz > 659_bTo-T1-TRNA-1_B23MHV2LT4_1/659_bTo-T1-TRNA-1_B23MHV2LT4_1.md/659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.depth_hist.tsv cat 659_bTo-T1-TRNA-1_B23MHV2LT4_1/659_bTo-T1-TRNA-1_B23MHV2LT4_1.md/659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md -output 659_bTo-T1-TRNA-1_B23MHV2LT4_1/659_bTo-T1-TRNA-1_B23MHV2LT4_1.md/659_bTo-T1-TRNA-1_B23MHV2LT4_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 2 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bTo-T1-TRNA-1_B23MHV2LT4_1/659_bTo-T1-TRNA-1_B23MHV2LT4_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 2 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bTo-T1-TRNA-1_B23MHV2LT4_1/659_bTo-T1-TRNA-1_B23MHV2LT4_1.md/reads_per_target.Twist_rna_exome_AND_fusion_hg38.bed.tsv seqtool depth_stats -bed Twist_rna_exome_AND_fusion_hg38.bed 659_bTo-T1-TRNA-1_B23MHV2LT4_1/659_bTo-T1-TRNA-1_B23MHV2LT4_1.md/659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz> 659_bTo-T1-TRNA-1_B23MHV2LT4_1/659_bTo-T1-TRNA-1_B23MHV2LT4_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 2 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bTo-T1-TRNA-1_B23MHV2LT4_1/659_bTo-T1-TRNA-1_B23MHV2LT4_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: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.md.bai cat 659_bTo-T1-TRNA-1_B23MHV2LT4_1/659_bTo-T1-TRNA-1_B23MHV2LT4_1.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "659_bTo-T1-TRNA-1_B23MHV2LT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "659_bTo-T1-TRNA-1_B23MHV2LT4_1/659_bTo-T1-TRNA-1_B23MHV2LT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > 659_bTo-T1-TRNA-1_B23MHV2LT4_1/659_bTo-T1-TRNA-1_B23MHV2LT4_1.md/qc_complete.txt + merge_qc -folders 659_bTo-T1-TRNA-1_B23MHV2LT4_1/659_bTo-T1-TRNA-1_B23MHV2LT4_1.md -output 659_bTo-T1-TRNA-1_B23MHV2LT4_1/659_bTo-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv + head -n1 659_bTo-T1-TRNA-1_B23MHV2LT4_1/659_bTo-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed 659_bTo-T1-TRNA-1_B23MHV2LT4_1/659_bTo-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv