Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/17/a780b1e2c2af60fec124b18ddaf373/GM24385_0001_RNA_0001_23H5VFLT4_s16.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/7c/2117c0af0270a1e54ec3e536dfdf46/.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/7c/2117c0af0270a1e54ec3e536dfdf46/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/17/a780b1e2c2af60fec124b18ddaf373/GM24385_0001_RNA_0001_23H5VFLT4_s16.md.bai Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa.fai 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 GM24385_0001_RNA_0001_23H5VFLT4_s16 + all_qc -bam GM24385_0001_RNA_0001_23H5VFLT4_s16.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 GM24385_0001_RNA_0001_23H5VFLT4_s16 -reference ref_genome.fa -region chr20 mkdir -p GM24385_0001_RNA_0001_23H5VFLT4_s16/GM24385_0001_RNA_0001_23H5VFLT4_s16.md/ cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > GM24385_0001_RNA_0001_23H5VFLT4_s16/GM24385_0001_RNA_0001_23H5VFLT4_s16.md/full_bed.bed seqtool depth -bam GM24385_0001_RNA_0001_23H5VFLT4_s16.md.bam -bed GM24385_0001_RNA_0001_23H5VFLT4_s16/GM24385_0001_RNA_0001_23H5VFLT4_s16.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > GM24385_0001_RNA_0001_23H5VFLT4_s16/GM24385_0001_RNA_0001_23H5VFLT4_s16.md/GM24385_0001_RNA_0001_23H5VFLT4_s16.md.depth.gz saturation_plot -bams GM24385_0001_RNA_0001_23H5VFLT4_s16.md.bam -region chr20 -output GM24385_0001_RNA_0001_23H5VFLT4_s16/GM24385_0001_RNA_0001_23H5VFLT4_s16.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 GM24385_0001_RNA_0001_23H5VFLT4_s16.md.bam > GM24385_0001_RNA_0001_23H5VFLT4_s16/GM24385_0001_RNA_0001_23H5VFLT4_s16.md/saturation_qc.tsv fragment_size -bams GM24385_0001_RNA_0001_23H5VFLT4_s16.md.bam -region chr20 -output_prefix GM24385_0001_RNA_0001_23H5VFLT4_s16/GM24385_0001_RNA_0001_23H5VFLT4_s16.md/fragsize -threads 1 samtools mpileup -B --min-MQ 60 --min-BQ 30 -f ref_genome.fa -l dbsnp_hg38_contam_sites.bed GM24385_0001_RNA_0001_23H5VFLT4_s16.md.bam > GM24385_0001_RNA_0001_23H5VFLT4_s16.md.mpileup && contamination -input GM24385_0001_RNA_0001_23H5VFLT4_s16.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > GM24385_0001_RNA_0001_23H5VFLT4_s16/GM24385_0001_RNA_0001_23H5VFLT4_s16.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s16.md.bai [mpileup] 1 samples in 1 input files [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s16.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s16.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s16.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s16.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s16.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: GM24385_0001_RNA_0001_23H5VFLT4_s16.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s16.md.bai 0it [00:00, ?it/s] 145806it [00:00, 1457991.87it/s] 293721it [00:00, 1470405.42it/s] 449912it [00:00, 1512163.36it/s] 611671it [00:00, 1553763.77it/s] 772889it [00:00, 1574806.12it/s] 935706it [00:00, 1592929.29it/s] 1098194it [00:00, 1603298.74it/s] 1262361it [00:00, 1615495.82it/s] 1426425it [00:00, 1623339.49it/s] 1590631it [00:01, 1628994.48it/s] 1753531it [00:01, 1628374.08it/s] 1917529it [00:01, 1631885.13it/s] 2080738it [00:01, 1631929.98it/s] 2243932it [00:01, 1625038.32it/s] 2411319it [00:01, 1639593.13it/s] 2577271it [00:01, 1645560.72it/s] 2741835it [00:01, 1642886.07it/s] 2906130it [00:01, 1642214.28it/s] 3071897it [00:01, 1646829.32it/s] 3236584it [00:02, 1616306.01it/s] 3400981it [00:02, 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1604130.99it/s] 8315440it [00:05, 1618982.41it/s] 8479706it [00:05, 1625964.35it/s] 8644974it [00:05, 1633616.36it/s] 8811228it [00:05, 1642227.91it/s] 8977742it [00:05, 1649031.67it/s] 9143642it [00:05, 1651992.36it/s] 9309524it [00:05, 1653959.39it/s] 9478870it [00:05, 1665771.64it/s] 9645934it [00:05, 1667212.18it/s] 9813555it [00:06, 1669715.67it/s] 9984054it [00:06, 1680273.42it/s] 10154972it [00:06, 1688923.15it/s] 10326843it [00:06, 1697813.46it/s] 10496770it [00:06, 1698215.60it/s] 10666594it [00:06, 1689906.40it/s] 10835596it [00:06, 1667222.51it/s] 11002388it [00:06, 1663819.81it/s] 11168816it [00:06, 1660514.96it/s] 11334910it [00:06, 1660621.85it/s] 11503250it [00:07, 1667392.99it/s] 11670009it [00:07, 1663432.11it/s] 11837051it [00:07, 1665501.55it/s] 12003612it [00:07, 1664115.48it/s] 12170504it [00:07, 1665535.38it/s] 12337364it [00:07, 1666334.45it/s] 12504370it [00:07, 1667431.91it/s] 12671117it [00:07, 1662601.66it/s] 12838191it [00:07, 1665016.73it/s] 13006004it [00:07, 1668923.31it/s] 13177030it [00:08, 1681289.86it/s] 13345164it [00:08, 1672704.28it/s] 13513147it [00:08, 1674814.28it/s][W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s16.md.bai 13680638it [00:08, 1662306.43it/s] 13846894it [00:08, 1633094.49it/s] 14010317it [00:08, 1559626.30it/s] 14161939it [00:08, 1627227.26it/s] [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s16.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s16.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s16.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s16.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s16.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s16.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s16.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s16.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s16.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s16.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s16.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s16.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s16.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s16.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s16.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s16.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s16.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s16.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s16.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s16.md.bai tabix -s 1 -b 2 -e 2 GM24385_0001_RNA_0001_23H5VFLT4_s16/GM24385_0001_RNA_0001_23H5VFLT4_s16.md/GM24385_0001_RNA_0001_23H5VFLT4_s16.md.depth.gz seqtool depth_hist -nbins 500 GM24385_0001_RNA_0001_23H5VFLT4_s16/GM24385_0001_RNA_0001_23H5VFLT4_s16.md/GM24385_0001_RNA_0001_23H5VFLT4_s16.md.depth.gz > GM24385_0001_RNA_0001_23H5VFLT4_s16/GM24385_0001_RNA_0001_23H5VFLT4_s16.md/GM24385_0001_RNA_0001_23H5VFLT4_s16.md.depth_hist.tsv cat GM24385_0001_RNA_0001_23H5VFLT4_s16/GM24385_0001_RNA_0001_23H5VFLT4_s16.md/GM24385_0001_RNA_0001_23H5VFLT4_s16.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title GM24385_0001_RNA_0001_23H5VFLT4_s16.md -output GM24385_0001_RNA_0001_23H5VFLT4_s16/GM24385_0001_RNA_0001_23H5VFLT4_s16.md/GM24385_0001_RNA_0001_23H5VFLT4_s16.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 GM24385_0001_RNA_0001_23H5VFLT4_s16.md.bam > GM24385_0001_RNA_0001_23H5VFLT4_s16/GM24385_0001_RNA_0001_23H5VFLT4_s16.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 GM24385_0001_RNA_0001_23H5VFLT4_s16.md.bam > GM24385_0001_RNA_0001_23H5VFLT4_s16/GM24385_0001_RNA_0001_23H5VFLT4_s16.md/reads_per_target.Twist_rna_exome_AND_fusion_hg38.bed.tsv seqtool depth_stats -bed Twist_rna_exome_AND_fusion_hg38.bed GM24385_0001_RNA_0001_23H5VFLT4_s16/GM24385_0001_RNA_0001_23H5VFLT4_s16.md/GM24385_0001_RNA_0001_23H5VFLT4_s16.md.depth.gz> GM24385_0001_RNA_0001_23H5VFLT4_s16/GM24385_0001_RNA_0001_23H5VFLT4_s16.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 GM24385_0001_RNA_0001_23H5VFLT4_s16.md.bam > GM24385_0001_RNA_0001_23H5VFLT4_s16/GM24385_0001_RNA_0001_23H5VFLT4_s16.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: GM24385_0001_RNA_0001_23H5VFLT4_s16.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s16.md.bai [W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s16.md.bai cat GM24385_0001_RNA_0001_23H5VFLT4_s16/GM24385_0001_RNA_0001_23H5VFLT4_s16.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "GM24385_0001_RNA_0001_23H5VFLT4_s16.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "GM24385_0001_RNA_0001_23H5VFLT4_s16/GM24385_0001_RNA_0001_23H5VFLT4_s16.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > GM24385_0001_RNA_0001_23H5VFLT4_s16/GM24385_0001_RNA_0001_23H5VFLT4_s16.md/qc_complete.txt + merge_qc -folders GM24385_0001_RNA_0001_23H5VFLT4_s16/GM24385_0001_RNA_0001_23H5VFLT4_s16.md -output GM24385_0001_RNA_0001_23H5VFLT4_s16/GM24385_0001_RNA_0001_23H5VFLT4_s16_full_basic_stats.tsv + head -n1 GM24385_0001_RNA_0001_23H5VFLT4_s16/GM24385_0001_RNA_0001_23H5VFLT4_s16_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed GM24385_0001_RNA_0001_23H5VFLT4_s16/GM24385_0001_RNA_0001_23H5VFLT4_s16_full_basic_stats.tsv