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/87/9adc6c468d9078c11bf1f14dad4679/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c2/d1dc963a7109c4d64230e721a97b2e/tih_rna_sample_00111_23H5VFLT4_s30.md.bam 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/87/9adc6c468d9078c11bf1f14dad4679/.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/c2/d1dc963a7109c4d64230e721a97b2e/tih_rna_sample_00111_23H5VFLT4_s30.md.bai Downloading: s3://natera-platform-sandbox/pipeline-resources/Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi ==> STAGING COMPLETE (11 inputs) + mkdir tih_rna_sample_00111_23H5VFLT4_s30 + all_qc -bam tih_rna_sample_00111_23H5VFLT4_s30.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 tih_rna_sample_00111_23H5VFLT4_s30 -reference ref_genome.fa -region chr20 mkdir -p tih_rna_sample_00111_23H5VFLT4_s30/tih_rna_sample_00111_23H5VFLT4_s30.md/ cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > tih_rna_sample_00111_23H5VFLT4_s30/tih_rna_sample_00111_23H5VFLT4_s30.md/full_bed.bed seqtool depth -bam tih_rna_sample_00111_23H5VFLT4_s30.md.bam -bed tih_rna_sample_00111_23H5VFLT4_s30/tih_rna_sample_00111_23H5VFLT4_s30.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > tih_rna_sample_00111_23H5VFLT4_s30/tih_rna_sample_00111_23H5VFLT4_s30.md/tih_rna_sample_00111_23H5VFLT4_s30.md.depth.gz saturation_plot -bams tih_rna_sample_00111_23H5VFLT4_s30.md.bam -region chr20 -output tih_rna_sample_00111_23H5VFLT4_s30/tih_rna_sample_00111_23H5VFLT4_s30.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 tih_rna_sample_00111_23H5VFLT4_s30.md.bam > tih_rna_sample_00111_23H5VFLT4_s30/tih_rna_sample_00111_23H5VFLT4_s30.md/saturation_qc.tsv fragment_size -bams tih_rna_sample_00111_23H5VFLT4_s30.md.bam -region chr20 -output_prefix tih_rna_sample_00111_23H5VFLT4_s30/tih_rna_sample_00111_23H5VFLT4_s30.md/fragsize -threads 1 samtools mpileup -B --min-MQ 60 --min-BQ 30 -f ref_genome.fa -l dbsnp_hg38_contam_sites.bed tih_rna_sample_00111_23H5VFLT4_s30.md.bam > tih_rna_sample_00111_23H5VFLT4_s30.md.mpileup && contamination -input tih_rna_sample_00111_23H5VFLT4_s30.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > tih_rna_sample_00111_23H5VFLT4_s30/tih_rna_sample_00111_23H5VFLT4_s30.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00111_23H5VFLT4_s30.md.bai [mpileup] 1 samples in 1 input files [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00111_23H5VFLT4_s30.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00111_23H5VFLT4_s30.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00111_23H5VFLT4_s30.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00111_23H5VFLT4_s30.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00111_23H5VFLT4_s30.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: tih_rna_sample_00111_23H5VFLT4_s30.md.bai 0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00111_23H5VFLT4_s30.md.bai 136296it [00:00, 1362902.81it/s] 285398it [00:00, 1438231.08it/s] 435561it [00:00, 1467154.80it/s] 582277it [00:00, 1466747.39it/s] 732094it [00:00, 1478056.60it/s] 879900it [00:00, 1473908.11it/s] 1027294it [00:00, 1455256.08it/s] 1172866it [00:00, 1446204.93it/s] 1319553it [00:00, 1452575.84it/s] 1468057it [00:01, 1462504.38it/s] 1614664it [00:01, 1463574.20it/s] 1761043it [00:01, 1456997.23it/s] 1911149it [00:01, 1470249.22it/s] 2060658it [00:01, 1477679.82it/s] 2213133it [00:01, 1491811.93it/s] 2364032it [00:01, 1496955.39it/s] 2513740it [00:01, 1484786.09it/s] 2662249it [00:01, 1456265.88it/s] 2811578it [00:01, 1467167.05it/s] 2958403it [00:02, 1447937.62it/s] 3103308it [00:02, 1444820.74it/s] 3247864it [00:02, 1424130.56it/s] 3391918it [00:02, 1428935.95it/s] 3534886it [00:02, 1405739.32it/s] 3675566it [00:02, 1359842.24it/s] 3811868it [00:02, 1317602.47it/s] 3944001it [00:02, 1265690.87it/s] 4071063it [00:02, 1157143.94it/s] 4206602it [00:03, 1210321.60it/s] 4329465it [00:03, 1180810.46it/s] 4479105it [00:03, 1268370.84it/s] 4632064it [00:03, 1342519.51it/s] 4788360it [00:03, 1406130.76it/s] 4942100it [00:03, 1444433.52it/s] 5096752it [00:03, 1474458.73it/s] 5253599it [00:03, 1502260.76it/s] 5408905it [00:03, 1517331.39it/s] 5561545it [00:03, 1520005.33it/s] 5713842it [00:04, 1514105.31it/s][W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00111_23H5VFLT4_s30.md.bai 5868804it [00:04, 1524673.88it/s] 6023465it [00:04, 1531206.08it/s] 6176697it [00:04, 1520322.41it/s] 6329142it [00:04, 1521531.51it/s] 6481361it [00:04, 1510398.44it/s] 6632461it [00:04, 1506584.18it/s] 6783161it [00:04, 1490014.54it/s] 6932688it [00:04, 1491438.91it/s] 7081875it [00:04, 1487936.88it/s] 7231509it [00:05, 1490409.70it/s] 7381945it [00:05, 1494544.07it/s] 7531859it [00:05, 1495799.31it/s] 7622579it [00:05, 1441343.91it/s] [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00111_23H5VFLT4_s30.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00111_23H5VFLT4_s30.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00111_23H5VFLT4_s30.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00111_23H5VFLT4_s30.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00111_23H5VFLT4_s30.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00111_23H5VFLT4_s30.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00111_23H5VFLT4_s30.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00111_23H5VFLT4_s30.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00111_23H5VFLT4_s30.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00111_23H5VFLT4_s30.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00111_23H5VFLT4_s30.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00111_23H5VFLT4_s30.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00111_23H5VFLT4_s30.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00111_23H5VFLT4_s30.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00111_23H5VFLT4_s30.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00111_23H5VFLT4_s30.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00111_23H5VFLT4_s30.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00111_23H5VFLT4_s30.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00111_23H5VFLT4_s30.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00111_23H5VFLT4_s30.md.bai tabix -s 1 -b 2 -e 2 tih_rna_sample_00111_23H5VFLT4_s30/tih_rna_sample_00111_23H5VFLT4_s30.md/tih_rna_sample_00111_23H5VFLT4_s30.md.depth.gz seqtool depth_hist -nbins 500 tih_rna_sample_00111_23H5VFLT4_s30/tih_rna_sample_00111_23H5VFLT4_s30.md/tih_rna_sample_00111_23H5VFLT4_s30.md.depth.gz > tih_rna_sample_00111_23H5VFLT4_s30/tih_rna_sample_00111_23H5VFLT4_s30.md/tih_rna_sample_00111_23H5VFLT4_s30.md.depth_hist.tsv cat tih_rna_sample_00111_23H5VFLT4_s30/tih_rna_sample_00111_23H5VFLT4_s30.md/tih_rna_sample_00111_23H5VFLT4_s30.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title tih_rna_sample_00111_23H5VFLT4_s30.md -output tih_rna_sample_00111_23H5VFLT4_s30/tih_rna_sample_00111_23H5VFLT4_s30.md/tih_rna_sample_00111_23H5VFLT4_s30.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 tih_rna_sample_00111_23H5VFLT4_s30.md.bam > tih_rna_sample_00111_23H5VFLT4_s30/tih_rna_sample_00111_23H5VFLT4_s30.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 tih_rna_sample_00111_23H5VFLT4_s30.md.bam > tih_rna_sample_00111_23H5VFLT4_s30/tih_rna_sample_00111_23H5VFLT4_s30.md/reads_per_target.Twist_rna_exome_AND_fusion_hg38.bed.tsv seqtool depth_stats -bed Twist_rna_exome_AND_fusion_hg38.bed tih_rna_sample_00111_23H5VFLT4_s30/tih_rna_sample_00111_23H5VFLT4_s30.md/tih_rna_sample_00111_23H5VFLT4_s30.md.depth.gz> tih_rna_sample_00111_23H5VFLT4_s30/tih_rna_sample_00111_23H5VFLT4_s30.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 tih_rna_sample_00111_23H5VFLT4_s30.md.bam > tih_rna_sample_00111_23H5VFLT4_s30/tih_rna_sample_00111_23H5VFLT4_s30.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: tih_rna_sample_00111_23H5VFLT4_s30.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00111_23H5VFLT4_s30.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00111_23H5VFLT4_s30.md.bai cat tih_rna_sample_00111_23H5VFLT4_s30/tih_rna_sample_00111_23H5VFLT4_s30.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "tih_rna_sample_00111_23H5VFLT4_s30.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "tih_rna_sample_00111_23H5VFLT4_s30/tih_rna_sample_00111_23H5VFLT4_s30.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > tih_rna_sample_00111_23H5VFLT4_s30/tih_rna_sample_00111_23H5VFLT4_s30.md/qc_complete.txt + merge_qc -folders tih_rna_sample_00111_23H5VFLT4_s30/tih_rna_sample_00111_23H5VFLT4_s30.md -output tih_rna_sample_00111_23H5VFLT4_s30/tih_rna_sample_00111_23H5VFLT4_s30_full_basic_stats.tsv + head -n1 tih_rna_sample_00111_23H5VFLT4_s30/tih_rna_sample_00111_23H5VFLT4_s30_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed tih_rna_sample_00111_23H5VFLT4_s30/tih_rna_sample_00111_23H5VFLT4_s30_full_basic_stats.tsv