Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/97/66490b76973a9679d6c0934a160dc6/tih_rna_sample_00581_B23MVV7LT4_1.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/9f/43b97d82548ce57ddc3f9a0b978c1e/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/97/66490b76973a9679d6c0934a160dc6/tih_rna_sample_00581_B23MVV7LT4_1.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/9f/43b97d82548ce57ddc3f9a0b978c1e/.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 tih_rna_sample_00581_B23MVV7LT4_1 + all_qc -bam tih_rna_sample_00581_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_00581_B23MVV7LT4_1 -reference ref_genome.fa -region chr20 mkdir -p tih_rna_sample_00581_B23MVV7LT4_1/tih_rna_sample_00581_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_00581_B23MVV7LT4_1/tih_rna_sample_00581_B23MVV7LT4_1.md/full_bed.bed seqtool depth -bam tih_rna_sample_00581_B23MVV7LT4_1.md.bam -bed tih_rna_sample_00581_B23MVV7LT4_1/tih_rna_sample_00581_B23MVV7LT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > tih_rna_sample_00581_B23MVV7LT4_1/tih_rna_sample_00581_B23MVV7LT4_1.md/tih_rna_sample_00581_B23MVV7LT4_1.md.depth.gz saturation_plot -bams tih_rna_sample_00581_B23MVV7LT4_1.md.bam -region chr20 -output tih_rna_sample_00581_B23MVV7LT4_1/tih_rna_sample_00581_B23MVV7LT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 tih_rna_sample_00581_B23MVV7LT4_1.md.bam > tih_rna_sample_00581_B23MVV7LT4_1/tih_rna_sample_00581_B23MVV7LT4_1.md/saturation_qc.tsv samtools mpileup -B --min-MQ 60 --min-BQ 30 -f ref_genome.fa -l dbsnp_hg38_contam_sites.bed tih_rna_sample_00581_B23MVV7LT4_1.md.bam > tih_rna_sample_00581_B23MVV7LT4_1.md.mpileup && contamination -input tih_rna_sample_00581_B23MVV7LT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > tih_rna_sample_00581_B23MVV7LT4_1/tih_rna_sample_00581_B23MVV7LT4_1.md/contamination.tsv fragment_size -bams tih_rna_sample_00581_B23MVV7LT4_1.md.bam -region chr20 -output_prefix tih_rna_sample_00581_B23MVV7LT4_1/tih_rna_sample_00581_B23MVV7LT4_1.md/fragsize -threads 1 [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00581_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_00581_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00581_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00581_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00581_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00581_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_00581_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00581_B23MVV7LT4_1.md.bai 0it [00:00, ?it/s] 157656it [00:00, 1576369.83it/s] 320691it [00:00, 1608068.07it/s] 496969it [00:00, 1678670.14it/s] 672276it [00:00, 1708004.82it/s] 848105it [00:00, 1726106.72it/s] 1022234it [00:00, 1731241.35it/s] 1197308it [00:00, 1737590.49it/s] 1373067it [00:00, 1743932.54it/s] 1549105it [00:00, 1749049.85it/s] 1724011it [00:01, 1739506.17it/s] 1897974it [00:01, 1727954.87it/s] 2071471it [00:01, 1730048.96it/s] 2249125it [00:01, 1744037.49it/s] 2424267it [00:01, 1746232.32it/s] 2598904it [00:01, 1742787.32it/s] 2774322it [00:01, 1746183.72it/s] 2948949it [00:01, 1746022.76it/s] 3123557it [00:01, 1735321.41it/s] 3298257it [00:01, 1738712.58it/s] 3472143it [00:02, 1726267.94it/s] 3645267it [00:02, 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1730739.91it/s] 8819643it [00:05, 1727294.06it/s] 8992380it [00:05, 1723974.37it/s] 9164784it [00:05, 1716788.97it/s] 9336473it [00:05, 1715152.15it/s] 9511738it [00:05, 1726340.54it/s] 9685826it [00:05, 1730653.12it/s] 9859880it [00:05, 1733597.49it/s] 10033246it [00:05, 1723350.17it/s] 10205598it [00:05, 1722346.14it/s] 10377844it [00:06, 1721182.75it/s] 10549970it [00:06, 1714638.76it/s] 10721443it [00:06, 1678335.24it/s] 10889438it [00:06, 1671503.51it/s] 11056696it [00:06, 1650704.72it/s] 11223258it [00:06, 1655074.94it/s] 11394384it [00:06, 1671677.42it/s] 11561633it [00:06, 1668366.63it/s] 11730504it [00:06, 1674401.85it/s] 11897988it [00:06, 1666896.94it/s] 12064712it [00:07, 1656525.03it/s] 12230870it [00:07, 1657991.09it/s] 12396693it [00:07, 1650836.93it/s] 12561796it [00:07, 1644957.30it/s][W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00581_B23MVV7LT4_1.md.bai 12727628it [00:07, 1648920.64it/s][W::hts_idx_load3] The index file is older than 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17506116it [00:10, 1579690.27it/s] 17666255it [00:10, 1569417.06it/s] 17839019it [00:10, 1614477.90it/s] 18010731it [00:10, 1644190.40it/s] 18181136it [00:10, 1661693.20it/s] 18355173it [00:10, 1684875.17it/s] 18530128it [00:10, 1704025.53it/s] 18701299it [00:11, 1706294.72it/s] 18872951it [00:11, 1709328.58it/s] 19046650it [00:11, 1717576.62it/s] 19218556it [00:11, 1676182.35it/s] 19390889it [00:11, 1690025.55it/s] 19560208it [00:11, 1690946.99it/s] 19654060it [00:11, 1695011.25it/s] [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00581_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00581_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00581_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00581_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00581_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00581_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00581_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00581_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00581_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00581_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00581_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00581_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00581_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00581_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00581_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00581_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00581_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00581_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00581_B23MVV7LT4_1.md.bai tabix -s 1 -b 2 -e 2 tih_rna_sample_00581_B23MVV7LT4_1/tih_rna_sample_00581_B23MVV7LT4_1.md/tih_rna_sample_00581_B23MVV7LT4_1.md.depth.gz seqtool depth_hist -nbins 500 tih_rna_sample_00581_B23MVV7LT4_1/tih_rna_sample_00581_B23MVV7LT4_1.md/tih_rna_sample_00581_B23MVV7LT4_1.md.depth.gz > tih_rna_sample_00581_B23MVV7LT4_1/tih_rna_sample_00581_B23MVV7LT4_1.md/tih_rna_sample_00581_B23MVV7LT4_1.md.depth_hist.tsv cat tih_rna_sample_00581_B23MVV7LT4_1/tih_rna_sample_00581_B23MVV7LT4_1.md/tih_rna_sample_00581_B23MVV7LT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title tih_rna_sample_00581_B23MVV7LT4_1.md -output tih_rna_sample_00581_B23MVV7LT4_1/tih_rna_sample_00581_B23MVV7LT4_1.md/tih_rna_sample_00581_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_00581_B23MVV7LT4_1.md.bam > tih_rna_sample_00581_B23MVV7LT4_1/tih_rna_sample_00581_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_00581_B23MVV7LT4_1.md.bam > tih_rna_sample_00581_B23MVV7LT4_1/tih_rna_sample_00581_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_00581_B23MVV7LT4_1/tih_rna_sample_00581_B23MVV7LT4_1.md/tih_rna_sample_00581_B23MVV7LT4_1.md.depth.gz> tih_rna_sample_00581_B23MVV7LT4_1/tih_rna_sample_00581_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_00581_B23MVV7LT4_1.md.bam > tih_rna_sample_00581_B23MVV7LT4_1/tih_rna_sample_00581_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_00581_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00581_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00581_B23MVV7LT4_1.md.bai cat tih_rna_sample_00581_B23MVV7LT4_1/tih_rna_sample_00581_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_00581_B23MVV7LT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "tih_rna_sample_00581_B23MVV7LT4_1/tih_rna_sample_00581_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_00581_B23MVV7LT4_1/tih_rna_sample_00581_B23MVV7LT4_1.md/qc_complete.txt + merge_qc -folders tih_rna_sample_00581_B23MVV7LT4_1/tih_rna_sample_00581_B23MVV7LT4_1.md -output tih_rna_sample_00581_B23MVV7LT4_1/tih_rna_sample_00581_B23MVV7LT4_1_full_basic_stats.tsv + head -n1 tih_rna_sample_00581_B23MVV7LT4_1/tih_rna_sample_00581_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_00581_B23MVV7LT4_1/tih_rna_sample_00581_B23MVV7LT4_1_full_basic_stats.tsv