Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e6/46dbcc4a070de16ae5cff5eceac3fe/659_bIB-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/4c/23384aa407c291d99c81eae7f6561f/.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/4c/23384aa407c291d99c81eae7f6561f/.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/e6/46dbcc4a070de16ae5cff5eceac3fe/659_bIB-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_bIB-T1-TRNA-1_B23MHV2LT4_1 + all_qc -bam 659_bIB-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_bIB-T1-TRNA-1_B23MHV2LT4_1 -reference ref_genome.fa -region chr20 mkdir -p 659_bIB-T1-TRNA-1_B23MHV2LT4_1/659_bIB-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_bIB-T1-TRNA-1_B23MHV2LT4_1/659_bIB-T1-TRNA-1_B23MHV2LT4_1.md/full_bed.bed seqtool depth -bam 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bam -bed 659_bIB-T1-TRNA-1_B23MHV2LT4_1/659_bIB-T1-TRNA-1_B23MHV2LT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > 659_bIB-T1-TRNA-1_B23MHV2LT4_1/659_bIB-T1-TRNA-1_B23MHV2LT4_1.md/659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz saturation_plot -bams 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bam -region chr20 -output 659_bIB-T1-TRNA-1_B23MHV2LT4_1/659_bIB-T1-TRNA-1_B23MHV2LT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bIB-T1-TRNA-1_B23MHV2LT4_1/659_bIB-T1-TRNA-1_B23MHV2LT4_1.md/saturation_qc.tsv fragment_size -bams 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bam -region chr20 -output_prefix 659_bIB-T1-TRNA-1_B23MHV2LT4_1/659_bIB-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_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.mpileup && contamination -input 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > 659_bIB-T1-TRNA-1_B23MHV2LT4_1/659_bIB-T1-TRNA-1_B23MHV2LT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: 659_bIB-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_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bIB-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_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai 0it [00:00, ?it/s] 156047it [00:00, 1560397.08it/s] 319802it [00:00, 1605742.90it/s] 491739it [00:00, 1657601.68it/s] 664478it [00:00, 1685120.02it/s] 836498it [00:00, 1697747.00it/s] 1009027it [00:00, 1707088.42it/s] 1180776it [00:00, 1710293.43it/s] 1353112it [00:00, 1714435.10it/s] 1525529it [00:00, 1717412.11it/s] 1698777it [00:01, 1722045.02it/s] 1871698it [00:01, 1724091.06it/s] 2045602it [00:01, 1728490.81it/s] 2218452it [00:01, 1722911.29it/s] 2390748it [00:01, 1722433.94it/s] 2562995it [00:01, 1717934.88it/s] 2735426it [00:01, 1719823.69it/s] 2907412it [00:01, 1718641.30it/s] 3079279it [00:01, 1717990.79it/s] 3254872it [00:01, 1729344.62it/s] 3427810it [00:02, 1700787.63it/s] 3598275it [00:02, 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1705070.78it/s] [W::hts_idx_load3] The index file is older than the data file: 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai tabix -s 1 -b 2 -e 2 659_bIB-T1-TRNA-1_B23MHV2LT4_1/659_bIB-T1-TRNA-1_B23MHV2LT4_1.md/659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz seqtool depth_hist -nbins 500 659_bIB-T1-TRNA-1_B23MHV2LT4_1/659_bIB-T1-TRNA-1_B23MHV2LT4_1.md/659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz > 659_bIB-T1-TRNA-1_B23MHV2LT4_1/659_bIB-T1-TRNA-1_B23MHV2LT4_1.md/659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.depth_hist.tsv cat 659_bIB-T1-TRNA-1_B23MHV2LT4_1/659_bIB-T1-TRNA-1_B23MHV2LT4_1.md/659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md -output 659_bIB-T1-TRNA-1_B23MHV2LT4_1/659_bIB-T1-TRNA-1_B23MHV2LT4_1.md/659_bIB-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_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bIB-T1-TRNA-1_B23MHV2LT4_1/659_bIB-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_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bIB-T1-TRNA-1_B23MHV2LT4_1/659_bIB-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_bIB-T1-TRNA-1_B23MHV2LT4_1/659_bIB-T1-TRNA-1_B23MHV2LT4_1.md/659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz> 659_bIB-T1-TRNA-1_B23MHV2LT4_1/659_bIB-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_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bIB-T1-TRNA-1_B23MHV2LT4_1/659_bIB-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_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bIB-T1-TRNA-1_B23MHV2LT4_1.md.bai cat 659_bIB-T1-TRNA-1_B23MHV2LT4_1/659_bIB-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_bIB-T1-TRNA-1_B23MHV2LT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "659_bIB-T1-TRNA-1_B23MHV2LT4_1/659_bIB-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_bIB-T1-TRNA-1_B23MHV2LT4_1/659_bIB-T1-TRNA-1_B23MHV2LT4_1.md/qc_complete.txt + merge_qc -folders 659_bIB-T1-TRNA-1_B23MHV2LT4_1/659_bIB-T1-TRNA-1_B23MHV2LT4_1.md -output 659_bIB-T1-TRNA-1_B23MHV2LT4_1/659_bIB-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv + head -n1 659_bIB-T1-TRNA-1_B23MHV2LT4_1/659_bIB-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_bIB-T1-TRNA-1_B23MHV2LT4_1/659_bIB-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv