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/61/bf1693f032ef2f79bc706695e547b5/.command.sh Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.dict Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/df/3a7a270cd2fe019fc3a84b11f997a7/tih_rna_sample_00569_B23MVV7LT4_1.md.bai 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/61/bf1693f032ef2f79bc706695e547b5/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/df/3a7a270cd2fe019fc3a84b11f997a7/tih_rna_sample_00569_B23MVV7LT4_1.md.bam 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_00569_B23MVV7LT4_1 + all_qc -bam tih_rna_sample_00569_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_00569_B23MVV7LT4_1 -reference ref_genome.fa -region chr20 mkdir -p tih_rna_sample_00569_B23MVV7LT4_1/tih_rna_sample_00569_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_00569_B23MVV7LT4_1/tih_rna_sample_00569_B23MVV7LT4_1.md/full_bed.bed seqtool depth -bam tih_rna_sample_00569_B23MVV7LT4_1.md.bam -bed tih_rna_sample_00569_B23MVV7LT4_1/tih_rna_sample_00569_B23MVV7LT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > tih_rna_sample_00569_B23MVV7LT4_1/tih_rna_sample_00569_B23MVV7LT4_1.md/tih_rna_sample_00569_B23MVV7LT4_1.md.depth.gz saturation_plot -bams tih_rna_sample_00569_B23MVV7LT4_1.md.bam -region chr20 -output tih_rna_sample_00569_B23MVV7LT4_1/tih_rna_sample_00569_B23MVV7LT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 tih_rna_sample_00569_B23MVV7LT4_1.md.bam > tih_rna_sample_00569_B23MVV7LT4_1/tih_rna_sample_00569_B23MVV7LT4_1.md/saturation_qc.tsv fragment_size -bams tih_rna_sample_00569_B23MVV7LT4_1.md.bam -region chr20 -output_prefix tih_rna_sample_00569_B23MVV7LT4_1/tih_rna_sample_00569_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_00569_B23MVV7LT4_1.md.bam > tih_rna_sample_00569_B23MVV7LT4_1.md.mpileup && contamination -input tih_rna_sample_00569_B23MVV7LT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > tih_rna_sample_00569_B23MVV7LT4_1/tih_rna_sample_00569_B23MVV7LT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00569_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_00569_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00569_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00569_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00569_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00569_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_00569_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00569_B23MVV7LT4_1.md.bai 0it [00:00, ?it/s] 148430it [00:00, 1484028.97it/s] 308837it [00:00, 1554597.66it/s] 477206it [00:00, 1613371.07it/s] 647716it [00:00, 1649552.26it/s] 819973it [00:00, 1675860.03it/s] 991211it [00:00, 1688256.17it/s] 1161123it [00:00, 1691689.51it/s] 1332701it [00:00, 1699339.34it/s] 1503972it [00:00, 1703431.86it/s] 1675210it [00:01, 1706173.27it/s] 1848426it [00:01, 1714107.80it/s] 2019837it [00:01, 1705352.28it/s] 2194275it [00:01, 1717114.52it/s] 2366727it [00:01, 1719327.66it/s] 2538669it [00:01, 1717096.75it/s] 2711969it [00:01, 1721855.30it/s] 2884160it [00:01, 1721741.58it/s] 3056338it [00:01, 1715444.89it/s] 3227890it [00:01, 1711197.18it/s] 3399563it [00:02, 1712715.31it/s] 3573277it [00:02, 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1729518.82it/s] 8765871it [00:05, 1724734.36it/s] 8938350it [00:05, 1724104.53it/s] 9110764it [00:05, 1714563.90it/s] 9284062it [00:05, 1720043.81it/s] 9458174it [00:05, 1726327.46it/s] 9630818it [00:05, 1724693.27it/s] 9803295it [00:05, 1722539.03it/s] 9975555it [00:05, 1722098.31it/s] 10148419it [00:05, 1723909.64it/s] 10320813it [00:06, 1719711.41it/s] 10492960it [00:06, 1720222.07it/s] 10664985it [00:06, 1702122.32it/s] 10837004it [00:06, 1707481.20it/s] 11010092it [00:06, 1714443.60it/s] 11181565it [00:06, 1714463.70it/s] 11355669it [00:06, 1722363.65it/s] 11530292it [00:06, 1729493.80it/s] 11703361it [00:06, 1729799.49it/s] 11879790it [00:06, 1740118.53it/s] 12053810it [00:07, 1737653.41it/s] 12227582it [00:07, 1734925.73it/s] 12401080it [00:07, 1731101.37it/s] 12574195it [00:07, 1719910.89it/s] 12747553it [00:07, 1723969.98it/s] 12922606it [00:07, 1731885.01it/s] 13097625it [00:07, 1737241.22it/s] 13271361it [00:07, 1732336.42it/s] 13444605it [00:07, 1732014.86it/s] 13617814it [00:07, 1728216.20it/s] 13790642it [00:08, 1723933.66it/s] 13963041it [00:08, 1714733.17it/s] 14134526it [00:08, 1699831.25it/s] 14306423it [00:08, 1705434.35it/s] 14481511it [00:08, 1718951.66it/s] 14653920it [00:08, 1720469.53it/s] 14825988it [00:08, 1717424.47it/s] 14997746it [00:08, 1708195.09it/s] 15168584it [00:08, 1699003.83it/s] 15338691it [00:08, 1699603.32it/s] 15508665it [00:09, 1696391.34it/s] 15638009it [00:09, 1715057.38it/s] [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00569_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00569_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00569_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00569_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00569_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00569_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00569_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00569_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00569_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00569_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00569_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00569_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00569_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00569_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00569_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00569_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00569_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00569_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00569_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00569_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00569_B23MVV7LT4_1.md.bai tabix -s 1 -b 2 -e 2 tih_rna_sample_00569_B23MVV7LT4_1/tih_rna_sample_00569_B23MVV7LT4_1.md/tih_rna_sample_00569_B23MVV7LT4_1.md.depth.gz seqtool depth_hist -nbins 500 tih_rna_sample_00569_B23MVV7LT4_1/tih_rna_sample_00569_B23MVV7LT4_1.md/tih_rna_sample_00569_B23MVV7LT4_1.md.depth.gz > tih_rna_sample_00569_B23MVV7LT4_1/tih_rna_sample_00569_B23MVV7LT4_1.md/tih_rna_sample_00569_B23MVV7LT4_1.md.depth_hist.tsv cat tih_rna_sample_00569_B23MVV7LT4_1/tih_rna_sample_00569_B23MVV7LT4_1.md/tih_rna_sample_00569_B23MVV7LT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title tih_rna_sample_00569_B23MVV7LT4_1.md -output tih_rna_sample_00569_B23MVV7LT4_1/tih_rna_sample_00569_B23MVV7LT4_1.md/tih_rna_sample_00569_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_00569_B23MVV7LT4_1.md.bam > tih_rna_sample_00569_B23MVV7LT4_1/tih_rna_sample_00569_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_00569_B23MVV7LT4_1.md.bam > tih_rna_sample_00569_B23MVV7LT4_1/tih_rna_sample_00569_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_00569_B23MVV7LT4_1/tih_rna_sample_00569_B23MVV7LT4_1.md/tih_rna_sample_00569_B23MVV7LT4_1.md.depth.gz> tih_rna_sample_00569_B23MVV7LT4_1/tih_rna_sample_00569_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_00569_B23MVV7LT4_1.md.bam > tih_rna_sample_00569_B23MVV7LT4_1/tih_rna_sample_00569_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_00569_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00569_B23MVV7LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00569_B23MVV7LT4_1.md.bai cat tih_rna_sample_00569_B23MVV7LT4_1/tih_rna_sample_00569_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_00569_B23MVV7LT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "tih_rna_sample_00569_B23MVV7LT4_1/tih_rna_sample_00569_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_00569_B23MVV7LT4_1/tih_rna_sample_00569_B23MVV7LT4_1.md/qc_complete.txt + merge_qc -folders tih_rna_sample_00569_B23MVV7LT4_1/tih_rna_sample_00569_B23MVV7LT4_1.md -output tih_rna_sample_00569_B23MVV7LT4_1/tih_rna_sample_00569_B23MVV7LT4_1_full_basic_stats.tsv + head -n1 tih_rna_sample_00569_B23MVV7LT4_1/tih_rna_sample_00569_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_00569_B23MVV7LT4_1/tih_rna_sample_00569_B23MVV7LT4_1_full_basic_stats.tsv