Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/56/a9c38694f3cc61bcd9302919fc45c1/1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.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/44/1bcc0118b468bdecb4e2d2540770b1/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/56/a9c38694f3cc61bcd9302919fc45c1/1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md.bai 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/44/1bcc0118b468bdecb4e2d2540770b1/.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-platform-sandbox/pipeline-resources/Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi ==> STAGING COMPLETE (11 inputs) + mkdir 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2 + all_qc -bam 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.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 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2 -reference ref_genome.fa -region chr20 mkdir -p 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2/1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md/ cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2/1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md/full_bed.bed seqtool depth -bam 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md.bam -bed 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2/1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2/1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md/1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md.depth.gz saturation_plot -bams 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md.bam -region chr20 -output 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2/1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md.bam > 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2/1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md/saturation_qc.tsv fragment_size -bams 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md.bam -region chr20 -output_prefix 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2/1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md/fragsize -threads 1 samtools mpileup -B --min-MQ 60 --min-BQ 30 -f ref_genome.fa -l dbsnp_hg38_contam_sites.bed 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md.bam > 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md.mpileup && contamination -input 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2/1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [mpileup] 1 samples in 1 input files [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.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: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md.bai 0it [00:00, ?it/s] 92537it [00:00, 925289.26it/s] 201258it [00:00, 1020483.81it/s] 309473it [00:00, 1048599.96it/s] 447916it [00:00, 1181144.42it/s] 595045it [00:00, 1285736.24it/s] 752009it [00:00, 1382231.46it/s] 890275it [00:00, 1382328.89it/s] 1028509it [00:00, 1327798.84it/s] 1188457it [00:00, 1410370.41it/s] 1346202it [00:01, 1460884.41it/s] 1501267it [00:01, 1487964.29it/s] 1662754it [00:01, 1525989.00it/s] 1815659it [00:01, 1526818.53it/s] 1968539it [00:01, 1451483.22it/s] 2114575it [00:01, 1412356.55it/s] 2268942it [00:01, 1449918.30it/s] 2433114it [00:01, 1505637.33it/s] 2586069it [00:01, 1512625.76it/s] 2737824it [00:01, 1504838.67it/s] 2893333it [00:02, 1519642.58it/s] 3045561it [00:02, 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1360540.61it/s] 7269898it [00:05, 1302103.31it/s] 7409303it [00:05, 1328077.00it/s] 7559359it [00:05, 1377681.94it/s] 7701056it [00:05, 1389106.06it/s] 7844862it [00:05, 1403469.56it/s] 7997279it [00:05, 1439132.90it/s] 8161446it [00:05, 1499248.16it/s] 8322713it [00:06, 1533006.41it/s] 8483730it [00:06, 1556016.11it/s] 8639509it [00:06, 1487640.52it/s] 8789018it [00:06, 1486794.85it/s] 8949532it [00:06, 1521376.39it/s] 9110204it [00:06, 1546500.57it/s] 9265217it [00:06, 1503598.84it/s] 9416051it [00:06, 1453684.46it/s] 9567859it [00:06, 1472133.41it/s] 9729692it [00:06, 1514597.68it/s] 9881632it [00:07, 1449964.05it/s] 10027446it [00:07, 1421254.22it/s] 10170157it [00:07, 1322153.04it/s] 10303852it [00:07, 1268137.65it/s] 10431821it [00:07, 1254172.27it/s] 10557962it [00:07, 1247000.00it/s] 10683126it [00:07, 1227616.09it/s] 10806177it [00:07, 1220416.31it/s] 10928394it [00:07, 1204223.09it/s] 11048924it [00:08, 1191028.75it/s] 11168086it [00:08, 1185581.69it/s] 11320335it [00:08, 1283763.73it/s] 11458152it [00:08, 1311432.73it/s] 11589565it [00:08, 1211533.27it/s] 11739074it [00:08, 1291089.34it/s] 11893926it [00:08, 1364733.02it/s] 12042673it [00:08, 1400313.82it/s] 12198867it [00:08, 1447658.49it/s] 12347067it [00:08, 1457775.57it/s] 12505295it [00:09, 1494670.20it/s] 12667408it [00:09, 1532273.30it/s] 12830825it [00:09, 1562641.00it/s] 12992521it [00:09, 1578664.99it/s] 13157127it [00:09, 1598799.15it/s] 13324288it [00:09, 1620569.37it/s] 13490291it [00:09, 1632367.64it/s] 13597366it [00:09, 1395550.74it/s] [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md.bai tabix -s 1 -b 2 -e 2 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2/1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md/1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md.depth.gz seqtool depth_hist -nbins 500 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2/1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md/1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md.depth.gz > 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2/1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md/1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md.depth_hist.tsv cat 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2/1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md/1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md -output 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2/1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md/1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.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 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md.bam > 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2/1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.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 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md.bam > 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2/1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md/reads_per_target.Twist_rna_exome_AND_fusion_hg38.bed.tsv seqtool depth_stats -bed Twist_rna_exome_AND_fusion_hg38.bed 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2/1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md/1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md.depth.gz> 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2/1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.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 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md.bam > 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2/1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.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: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md.bai cat 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2/1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2/1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2/1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md/qc_complete.txt + merge_qc -folders 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2/1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.md -output 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2/1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2_full_basic_stats.tsv + head -n1 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2/1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed 1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2/1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2_full_basic_stats.tsv