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/d2/a6e7d4d46f989d53ca3393131d076c/.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/3d/123bc858f773c1022182b283dbfe54/tih_rna_sample_00582_B23MVV7LT4_1.md.bam Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d2/a6e7d4d46f989d53ca3393131d076c/.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/3d/123bc858f773c1022182b283dbfe54/tih_rna_sample_00582_B23MVV7LT4_1.md.bai Downloading: s3://natera-platform-sandbox/pipeline-resources/Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi ==> STAGING COMPLETE (11 inputs) + mkdir tih_rna_sample_00582_B23MVV7LT4_1 + all_qc -bam tih_rna_sample_00582_B23MVV7LT4_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 tih_rna_sample_00582_B23MVV7LT4_1 -reference ref_genome.fa -region chr20 mkdir -p tih_rna_sample_00582_B23MVV7LT4_1/tih_rna_sample_00582_B23MVV7LT4_1.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_00582_B23MVV7LT4_1/tih_rna_sample_00582_B23MVV7LT4_1.md/full_bed.bed seqtool depth -bam tih_rna_sample_00582_B23MVV7LT4_1.md.bam -bed tih_rna_sample_00582_B23MVV7LT4_1/tih_rna_sample_00582_B23MVV7LT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > tih_rna_sample_00582_B23MVV7LT4_1/tih_rna_sample_00582_B23MVV7LT4_1.md/tih_rna_sample_00582_B23MVV7LT4_1.md.depth.gz saturation_plot -bams tih_rna_sample_00582_B23MVV7LT4_1.md.bam -region chr20 -output tih_rna_sample_00582_B23MVV7LT4_1/tih_rna_sample_00582_B23MVV7LT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 tih_rna_sample_00582_B23MVV7LT4_1.md.bam > tih_rna_sample_00582_B23MVV7LT4_1/tih_rna_sample_00582_B23MVV7LT4_1.md/saturation_qc.tsv fragment_size -bams tih_rna_sample_00582_B23MVV7LT4_1.md.bam -region chr20 -output_prefix tih_rna_sample_00582_B23MVV7LT4_1/tih_rna_sample_00582_B23MVV7LT4_1.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_00582_B23MVV7LT4_1.md.bam > tih_rna_sample_00582_B23MVV7LT4_1.md.mpileup && contamination -input tih_rna_sample_00582_B23MVV7LT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > tih_rna_sample_00582_B23MVV7LT4_1/tih_rna_sample_00582_B23MVV7LT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00582_B23MVV7LT4_1.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_00582_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00582_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00582_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00582_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00582_B23MVV7LT4_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: tih_rna_sample_00582_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00582_B23MVV7LT4_1.md.bai 0it [00:00, ?it/s] 146332it [00:00, 1463080.71it/s] 309828it [00:00, 1563895.13it/s] 471248it [00:00, 1586831.88it/s] 639790it [00:00, 1625724.33it/s] 808171it [00:00, 1646645.48it/s] 977316it [00:00, 1661846.42it/s] 1143906it [00:00, 1663140.97it/s] 1310221it [00:00, 1656784.12it/s] 1479945it [00:00, 1669374.47it/s] 1648494it [00:01, 1674156.45it/s] 1820876it [00:01, 1689284.14it/s] 1989811it [00:01, 1689025.61it/s] 2158718it [00:01, 1679601.82it/s] 2328528it [00:01, 1685060.85it/s] 2498299it [00:01, 1688736.31it/s] 2667183it [00:01, 1678739.60it/s] 2837513it [00:01, 1686057.75it/s] 3010585it [00:01, 1699401.61it/s] 3180543it [00:01, 1699206.80it/s] 3350476it [00:02, 1685225.79it/s] 3522952it [00:02, 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1671760.13it/s] 8492068it [00:05, 1677799.90it/s] 8660163it [00:05, 1670728.86it/s] 8830935it [00:05, 1681729.73it/s] 8999750it [00:05, 1683622.35it/s] 9168875it [00:05, 1685878.56it/s] 9337481it [00:05, 1680063.20it/s] 9505504it [00:05, 1679303.62it/s] 9674789it [00:05, 1683267.60it/s] 9843125it [00:05, 1675667.46it/s] 10012663it [00:06, 1681430.35it/s] 10181469it [00:06, 1683248.63it/s] 10352970it [00:06, 1692710.84it/s] 10524658it [00:06, 1699922.88it/s] 10696164it [00:06, 1704326.26it/s] 10868604it [00:06, 1710322.63it/s] 11039641it [00:06, 1694901.49it/s] 11212459it [00:06, 1704792.38it/s] 11382969it [00:06, 1703411.44it/s] 11554015it [00:06, 1705496.28it/s] 11724581it [00:07, 1694275.48it/s] 11894034it [00:07, 1687632.95it/s] 12062817it [00:07, 1683556.42it/s] 12232746it [00:07, 1688203.68it/s] 12402137it [00:07, 1689887.31it/s] 12571355it [00:07, 1690405.76it/s] 12740997it [00:07, 1692181.94it/s] 12910496it [00:07, 1692999.20it/s] 13079800it [00:07, 1689204.66it/s] 13251224it [00:07, 1696557.07it/s] 13420885it [00:08, 1684703.45it/s] 13589376it [00:08, 1671990.85it/s] 13758871it [00:08, 1678790.28it/s] 13926777it [00:08, 1665748.54it/s] 14096242it [00:08, 1674308.43it/s] 14266554it [00:08, 1682856.89it/s] 14435495it [00:08, 1684789.40it/s] 14605838it [00:08, 1690339.32it/s] 14774889it [00:08, 1689468.76it/s] 14943848it [00:09, 1678973.35it/s] 14968872it [00:09, 1658920.94it/s] [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00582_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00582_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00582_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00582_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00582_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00582_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00582_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00582_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00582_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00582_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00582_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00582_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00582_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00582_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00582_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00582_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00582_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00582_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00582_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00582_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00582_B23MVV7LT4_1.md.bai tabix -s 1 -b 2 -e 2 tih_rna_sample_00582_B23MVV7LT4_1/tih_rna_sample_00582_B23MVV7LT4_1.md/tih_rna_sample_00582_B23MVV7LT4_1.md.depth.gz seqtool depth_hist -nbins 500 tih_rna_sample_00582_B23MVV7LT4_1/tih_rna_sample_00582_B23MVV7LT4_1.md/tih_rna_sample_00582_B23MVV7LT4_1.md.depth.gz > tih_rna_sample_00582_B23MVV7LT4_1/tih_rna_sample_00582_B23MVV7LT4_1.md/tih_rna_sample_00582_B23MVV7LT4_1.md.depth_hist.tsv cat tih_rna_sample_00582_B23MVV7LT4_1/tih_rna_sample_00582_B23MVV7LT4_1.md/tih_rna_sample_00582_B23MVV7LT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title tih_rna_sample_00582_B23MVV7LT4_1.md -output tih_rna_sample_00582_B23MVV7LT4_1/tih_rna_sample_00582_B23MVV7LT4_1.md/tih_rna_sample_00582_B23MVV7LT4_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 tih_rna_sample_00582_B23MVV7LT4_1.md.bam > tih_rna_sample_00582_B23MVV7LT4_1/tih_rna_sample_00582_B23MVV7LT4_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 tih_rna_sample_00582_B23MVV7LT4_1.md.bam > tih_rna_sample_00582_B23MVV7LT4_1/tih_rna_sample_00582_B23MVV7LT4_1.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_00582_B23MVV7LT4_1/tih_rna_sample_00582_B23MVV7LT4_1.md/tih_rna_sample_00582_B23MVV7LT4_1.md.depth.gz> tih_rna_sample_00582_B23MVV7LT4_1/tih_rna_sample_00582_B23MVV7LT4_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 tih_rna_sample_00582_B23MVV7LT4_1.md.bam > tih_rna_sample_00582_B23MVV7LT4_1/tih_rna_sample_00582_B23MVV7LT4_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: tih_rna_sample_00582_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00582_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00582_B23MVV7LT4_1.md.bai cat tih_rna_sample_00582_B23MVV7LT4_1/tih_rna_sample_00582_B23MVV7LT4_1.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "tih_rna_sample_00582_B23MVV7LT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "tih_rna_sample_00582_B23MVV7LT4_1/tih_rna_sample_00582_B23MVV7LT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > tih_rna_sample_00582_B23MVV7LT4_1/tih_rna_sample_00582_B23MVV7LT4_1.md/qc_complete.txt + merge_qc -folders tih_rna_sample_00582_B23MVV7LT4_1/tih_rna_sample_00582_B23MVV7LT4_1.md -output tih_rna_sample_00582_B23MVV7LT4_1/tih_rna_sample_00582_B23MVV7LT4_1_full_basic_stats.tsv + head -n1 tih_rna_sample_00582_B23MVV7LT4_1/tih_rna_sample_00582_B23MVV7LT4_1_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed tih_rna_sample_00582_B23MVV7LT4_1/tih_rna_sample_00582_B23MVV7LT4_1_full_basic_stats.tsv