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/9a/2a3dac313fd70ee2e50a4cd8a6ec57/.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/73/d9ae15e2e8d53a1e0c67a865046be9/659_cfy-T1-TRNA-1_B23WHTKLT4_1.md.bam Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9a/2a3dac313fd70ee2e50a4cd8a6ec57/.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-platform-sandbox/pipeline-resources/beds/twist/Twist_rna_exome_AND_fusion_hg38.bed Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/73/d9ae15e2e8d53a1e0c67a865046be9/659_cfy-T1-TRNA-1_B23WHTKLT4_1.md.bai Downloading: s3://natera-platform-sandbox/pipeline-resources/Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi ==> STAGING COMPLETE (11 inputs) + mkdir 659_cfy-T1-TRNA-1_B23WHTKLT4_1 + all_qc -bam 659_cfy-T1-TRNA-1_B23WHTKLT4_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_cfy-T1-TRNA-1_B23WHTKLT4_1 -reference ref_genome.fa -region chr20 mkdir -p 659_cfy-T1-TRNA-1_B23WHTKLT4_1/659_cfy-T1-TRNA-1_B23WHTKLT4_1.md/ cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > 659_cfy-T1-TRNA-1_B23WHTKLT4_1/659_cfy-T1-TRNA-1_B23WHTKLT4_1.md/full_bed.bed seqtool depth -bam 659_cfy-T1-TRNA-1_B23WHTKLT4_1.md.bam -bed 659_cfy-T1-TRNA-1_B23WHTKLT4_1/659_cfy-T1-TRNA-1_B23WHTKLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > 659_cfy-T1-TRNA-1_B23WHTKLT4_1/659_cfy-T1-TRNA-1_B23WHTKLT4_1.md/659_cfy-T1-TRNA-1_B23WHTKLT4_1.md.depth.gz saturation_plot -bams 659_cfy-T1-TRNA-1_B23WHTKLT4_1.md.bam -region chr20 -output 659_cfy-T1-TRNA-1_B23WHTKLT4_1/659_cfy-T1-TRNA-1_B23WHTKLT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 659_cfy-T1-TRNA-1_B23WHTKLT4_1.md.bam > 659_cfy-T1-TRNA-1_B23WHTKLT4_1/659_cfy-T1-TRNA-1_B23WHTKLT4_1.md/saturation_qc.tsv fragment_size -bams 659_cfy-T1-TRNA-1_B23WHTKLT4_1.md.bam -region chr20 -output_prefix 659_cfy-T1-TRNA-1_B23WHTKLT4_1/659_cfy-T1-TRNA-1_B23WHTKLT4_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_cfy-T1-TRNA-1_B23WHTKLT4_1.md.bam > 659_cfy-T1-TRNA-1_B23WHTKLT4_1.md.mpileup && contamination -input 659_cfy-T1-TRNA-1_B23WHTKLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > 659_cfy-T1-TRNA-1_B23WHTKLT4_1/659_cfy-T1-TRNA-1_B23WHTKLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TRNA-1_B23WHTKLT4_1.md.bai [mpileup] 1 samples in 1 input files [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TRNA-1_B23WHTKLT4_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_cfy-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TRNA-1_B23WHTKLT4_1.md.bai 0it [00:00, ?it/s] 153573it [00:00, 1535617.97it/s] 315851it [00:00, 1586824.56it/s] 481325it [00:00, 1617791.67it/s] 649570it [00:00, 1643275.91it/s] 815788it [00:00, 1649901.66it/s] 980779it [00:00, 1633408.67it/s] 1147520it [00:00, 1644418.64it/s] 1313835it [00:00, 1650325.78it/s] 1482313it [00:00, 1661038.97it/s] 1651418it [00:01, 1670102.18it/s] 1818555it [00:01, 1670466.93it/s] 1985612it [00:01, 1661070.21it/s] 2151738it [00:01, 1651220.44it/s] 2321072it [00:01, 1663705.29it/s] 2489105it [00:01, 1668665.40it/s] 2655991it [00:01, 1613999.59it/s] 2826290it [00:01, 1640028.58it/s] 2993416it [00:01, 1649216.70it/s] 3158591it [00:01, 1648971.63it/s] 3323665it [00:02, 1597791.70it/s] 3493287it [00:02, 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1681787.03it/s] 8535134it [00:05, 1682165.20it/s] 8706299it [00:05, 1690979.35it/s] 8875401it [00:05, 1675578.38it/s] 9044002it [00:05, 1678518.86it/s] 9212918it [00:05, 1681546.56it/s] 9381497it [00:05, 1682730.50it/s] 9549784it [00:05, 1676466.64it/s] 9717445it [00:05, 1669971.38it/s] 9884455it [00:05, 1668625.45it/s] 10051666it [00:06, 1669645.06it/s] 10218637it [00:06, 1654553.38it/s] 10385948it [00:06, 1660053.99it/s] 10551980it [00:06, 1660087.75it/s] 10721451it [00:06, 1670409.15it/s] 10891037it [00:06, 1678000.43it/s] 11058852it [00:06, 1660940.26it/s] 11226988it [00:06, 1666992.51it/s] 11396874it [00:06, 1676453.54it/s] 11564552it [00:06, 1676397.52it/s] 11732215it [00:07, 1673110.30it/s] 11899543it [00:07, 1668667.16it/s] 12066423it [00:07, 1664718.09it/s] 12236512it [00:07, 1675474.69it/s] 12405897it [00:07, 1680945.43it/s] 12574002it [00:07, 1679452.81it/s] 12742479it [00:07, 1681014.83it/s] 12910651it [00:07, 1681203.71it/s] 13078776it [00:07, 1664327.33it/s] 13245864it [00:07, 1666252.17it/s] 13412945it [00:08, 1667589.92it/s] 13579726it [00:08, 1667303.35it/s] 13747673it [00:08, 1670907.61it/s] 13915012it [00:08, 1671632.21it/s] 14084405it [00:08, 1678290.93it/s] 14253869it [00:08, 1683169.55it/s] 14422192it [00:08, 1682662.58it/s] 14591711it [00:08, 1686354.71it/s] 14760350it [00:08, 1680193.15it/s][W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TRNA-1_B23WHTKLT4_1.md.bai 14929947it [00:08, 1684893.57it/s] 15098443it [00:09, 1674939.57it/s] 15210976it [00:09, 1664628.76it/s] [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TRNA-1_B23WHTKLT4_1.md.bai tabix -s 1 -b 2 -e 2 659_cfy-T1-TRNA-1_B23WHTKLT4_1/659_cfy-T1-TRNA-1_B23WHTKLT4_1.md/659_cfy-T1-TRNA-1_B23WHTKLT4_1.md.depth.gz seqtool depth_hist -nbins 500 659_cfy-T1-TRNA-1_B23WHTKLT4_1/659_cfy-T1-TRNA-1_B23WHTKLT4_1.md/659_cfy-T1-TRNA-1_B23WHTKLT4_1.md.depth.gz > 659_cfy-T1-TRNA-1_B23WHTKLT4_1/659_cfy-T1-TRNA-1_B23WHTKLT4_1.md/659_cfy-T1-TRNA-1_B23WHTKLT4_1.md.depth_hist.tsv cat 659_cfy-T1-TRNA-1_B23WHTKLT4_1/659_cfy-T1-TRNA-1_B23WHTKLT4_1.md/659_cfy-T1-TRNA-1_B23WHTKLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title 659_cfy-T1-TRNA-1_B23WHTKLT4_1.md -output 659_cfy-T1-TRNA-1_B23WHTKLT4_1/659_cfy-T1-TRNA-1_B23WHTKLT4_1.md/659_cfy-T1-TRNA-1_B23WHTKLT4_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_cfy-T1-TRNA-1_B23WHTKLT4_1.md.bam > 659_cfy-T1-TRNA-1_B23WHTKLT4_1/659_cfy-T1-TRNA-1_B23WHTKLT4_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_cfy-T1-TRNA-1_B23WHTKLT4_1.md.bam > 659_cfy-T1-TRNA-1_B23WHTKLT4_1/659_cfy-T1-TRNA-1_B23WHTKLT4_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_cfy-T1-TRNA-1_B23WHTKLT4_1/659_cfy-T1-TRNA-1_B23WHTKLT4_1.md/659_cfy-T1-TRNA-1_B23WHTKLT4_1.md.depth.gz> 659_cfy-T1-TRNA-1_B23WHTKLT4_1/659_cfy-T1-TRNA-1_B23WHTKLT4_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_cfy-T1-TRNA-1_B23WHTKLT4_1.md.bam > 659_cfy-T1-TRNA-1_B23WHTKLT4_1/659_cfy-T1-TRNA-1_B23WHTKLT4_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_cfy-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TRNA-1_B23WHTKLT4_1.md.bai cat 659_cfy-T1-TRNA-1_B23WHTKLT4_1/659_cfy-T1-TRNA-1_B23WHTKLT4_1.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "659_cfy-T1-TRNA-1_B23WHTKLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "659_cfy-T1-TRNA-1_B23WHTKLT4_1/659_cfy-T1-TRNA-1_B23WHTKLT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > 659_cfy-T1-TRNA-1_B23WHTKLT4_1/659_cfy-T1-TRNA-1_B23WHTKLT4_1.md/qc_complete.txt + merge_qc -folders 659_cfy-T1-TRNA-1_B23WHTKLT4_1/659_cfy-T1-TRNA-1_B23WHTKLT4_1.md -output 659_cfy-T1-TRNA-1_B23WHTKLT4_1/659_cfy-T1-TRNA-1_B23WHTKLT4_1_full_basic_stats.tsv + head -n1 659_cfy-T1-TRNA-1_B23WHTKLT4_1/659_cfy-T1-TRNA-1_B23WHTKLT4_1_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed 659_cfy-T1-TRNA-1_B23WHTKLT4_1/659_cfy-T1-TRNA-1_B23WHTKLT4_1_full_basic_stats.tsv