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/eb/c359c97e28e760ad2df8a0e6078ae4/.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/39/b62f15a4561d0fc1ce19a04264433c/659_cTi-T1-TRNA-1_B23WHTKLT4_1.md.bam 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/eb/c359c97e28e760ad2df8a0e6078ae4/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/39/b62f15a4561d0fc1ce19a04264433c/659_cTi-T1-TRNA-1_B23WHTKLT4_1.md.bai 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 659_cTi-T1-TRNA-1_B23WHTKLT4_1 + all_qc -bam 659_cTi-T1-TRNA-1_B23WHTKLT4_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 659_cTi-T1-TRNA-1_B23WHTKLT4_1 -reference ref_genome.fa -region chr20 mkdir -p 659_cTi-T1-TRNA-1_B23WHTKLT4_1/659_cTi-T1-TRNA-1_B23WHTKLT4_1.md/ cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > 659_cTi-T1-TRNA-1_B23WHTKLT4_1/659_cTi-T1-TRNA-1_B23WHTKLT4_1.md/full_bed.bed seqtool depth -bam 659_cTi-T1-TRNA-1_B23WHTKLT4_1.md.bam -bed 659_cTi-T1-TRNA-1_B23WHTKLT4_1/659_cTi-T1-TRNA-1_B23WHTKLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > 659_cTi-T1-TRNA-1_B23WHTKLT4_1/659_cTi-T1-TRNA-1_B23WHTKLT4_1.md/659_cTi-T1-TRNA-1_B23WHTKLT4_1.md.depth.gz saturation_plot -bams 659_cTi-T1-TRNA-1_B23WHTKLT4_1.md.bam -region chr20 -output 659_cTi-T1-TRNA-1_B23WHTKLT4_1/659_cTi-T1-TRNA-1_B23WHTKLT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 659_cTi-T1-TRNA-1_B23WHTKLT4_1.md.bam > 659_cTi-T1-TRNA-1_B23WHTKLT4_1/659_cTi-T1-TRNA-1_B23WHTKLT4_1.md/saturation_qc.tsv fragment_size -bams 659_cTi-T1-TRNA-1_B23WHTKLT4_1.md.bam -region chr20 -output_prefix 659_cTi-T1-TRNA-1_B23WHTKLT4_1/659_cTi-T1-TRNA-1_B23WHTKLT4_1.md/fragsize -threads 1 samtools mpileup -B --min-MQ 60 --min-BQ 30 -f ref_genome.fa -l dbsnp_hg38_contam_sites.bed 659_cTi-T1-TRNA-1_B23WHTKLT4_1.md.bam > 659_cTi-T1-TRNA-1_B23WHTKLT4_1.md.mpileup && contamination -input 659_cTi-T1-TRNA-1_B23WHTKLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > 659_cTi-T1-TRNA-1_B23WHTKLT4_1/659_cTi-T1-TRNA-1_B23WHTKLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: 659_cTi-T1-TRNA-1_B23WHTKLT4_1.md.bai [mpileup] 1 samples in 1 input files [W::hts_idx_load3] The index file is older than the data file: 659_cTi-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cTi-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cTi-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cTi-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cTi-T1-TRNA-1_B23WHTKLT4_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: 659_cTi-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cTi-T1-TRNA-1_B23WHTKLT4_1.md.bai 0it [00:00, ?it/s] 146131it [00:00, 1461252.17it/s] 306191it [00:00, 1543182.05it/s] 460510it [00:00, 1519257.26it/s] 627831it [00:00, 1579416.32it/s] 794661it [00:00, 1611231.26it/s] 964727it [00:00, 1641494.87it/s] 1132100it [00:00, 1651987.04it/s] 1303527it [00:00, 1671737.85it/s] 1470734it [00:00, 1635095.31it/s] 1640163it [00:01, 1653055.36it/s] 1809379it [00:01, 1664868.23it/s] 1979434it [00:01, 1675619.67it/s] 2147091it [00:01, 1673167.61it/s] 2315780it [00:01, 1677270.55it/s] 2483555it [00:01, 1536153.08it/s] 2652767it [00:01, 1580130.82it/s] 2823993it [00:01, 1618061.46it/s] 2993024it [00:01, 1639061.26it/s] 3158056it [00:01, 1637404.30it/s] 3326003it [00:02, 1649755.17it/s] 3499628it [00:02, 1675370.97it/s] 3671652it [00:02, 1688573.07it/s] 3840824it [00:02, 1687080.69it/s] 4009752it [00:02, 1685099.75it/s] 4181315it [00:02, 1694197.69it/s] 4352699it [00:02, 1699920.93it/s] 4523869it [00:02, 1703418.69it/s] 4694896it [00:02, 1705326.19it/s] 4865469it [00:02, 1704849.69it/s] 5035983it [00:03, 1699250.60it/s] 5205932it [00:03, 1693755.23it/s] 5377530it [00:03, 1700371.50it/s] 5549321it [00:03, 1705596.30it/s] 5720523it [00:03, 1707501.35it/s] 5891283it [00:03, 1698182.35it/s] 6061419it [00:03, 1699097.57it/s] 6231342it [00:03, 1694458.75it/s] 6401451it [00:03, 1696421.82it/s] 6572025it [00:03, 1699038.38it/s] 6741936it [00:04, 1691490.14it/s] 6912289it [00:04, 1695070.02it/s] 7081806it [00:04, 1693404.22it/s] 7253864it [00:04, 1701517.22it/s] 7424023it [00:04, 1692833.99it/s] 7594635it [00:04, 1696782.00it/s] 7768806it [00:04, 1710198.36it/s] 7939839it [00:04, 1708994.54it/s] 8111453it [00:04, 1711054.45it/s] 8282736it [00:04, 1711503.64it/s] 8453892it [00:05, 1709379.00it/s] 8624834it [00:05, 1704887.50it/s] 8796396it [00:05, 1708080.93it/s] 8968934it [00:05, 1713185.51it/s] 9141020it [00:05, 1715468.92it/s] 9312570it [00:05, 1711293.42it/s] 9483704it [00:05, 1703654.72it/s] 9654079it [00:05, 1700526.91it/s] 9824138it [00:05, 1700351.34it/s] 9994178it [00:05, 1699218.09it/s] 10164103it [00:06, 1694056.81it/s] 10335134it [00:06, 1698897.45it/s] 10505029it [00:06, 1689829.11it/s][W::hts_idx_load3] The index file is older than the data file: 659_cTi-T1-TRNA-1_B23WHTKLT4_1.md.bai 10679026it [00:06, 1704768.10it/s] 10849958it [00:06, 1706112.82it/s] 11020582it [00:06, 1694455.30it/s] 11190052it [00:06, 1689954.66it/s] 11361926it [00:06, 1698518.81it/s] 11532895it [00:06, 1701838.03it/s] 11703093it [00:06, 1696476.01it/s] 11872753it [00:07, 1691344.78it/s] 12043185it [00:07, 1695197.90it/s] 12214098it [00:07, 1699341.86it/s] 12384040it [00:07, 1697585.52it/s] 12553804it [00:07, 1697161.58it/s] 12723999it [00:07, 1698571.49it/s] 12893859it [00:07, 1696795.32it/s] 13063541it [00:07, 1695438.85it/s] 13233087it [00:07, 1693878.26it/s] 13403420it [00:07, 1696684.71it/s] 13574068it [00:08, 1699595.60it/s] 13744029it [00:08, 1699391.53it/s] 13915881it [00:08, 1705105.58it/s] 14086393it [00:08, 1700046.13it/s] 14256989it [00:08, 1701743.58it/s] 14427167it [00:08, 1697699.05it/s] 14492868it [00:08, 1683755.90it/s] [W::hts_idx_load3] The index file is older than the data file: 659_cTi-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cTi-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cTi-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cTi-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cTi-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cTi-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cTi-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cTi-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cTi-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cTi-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cTi-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cTi-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cTi-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cTi-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cTi-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cTi-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cTi-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cTi-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cTi-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cTi-T1-TRNA-1_B23WHTKLT4_1.md.bai tabix -s 1 -b 2 -e 2 659_cTi-T1-TRNA-1_B23WHTKLT4_1/659_cTi-T1-TRNA-1_B23WHTKLT4_1.md/659_cTi-T1-TRNA-1_B23WHTKLT4_1.md.depth.gz seqtool depth_hist -nbins 500 659_cTi-T1-TRNA-1_B23WHTKLT4_1/659_cTi-T1-TRNA-1_B23WHTKLT4_1.md/659_cTi-T1-TRNA-1_B23WHTKLT4_1.md.depth.gz > 659_cTi-T1-TRNA-1_B23WHTKLT4_1/659_cTi-T1-TRNA-1_B23WHTKLT4_1.md/659_cTi-T1-TRNA-1_B23WHTKLT4_1.md.depth_hist.tsv cat 659_cTi-T1-TRNA-1_B23WHTKLT4_1/659_cTi-T1-TRNA-1_B23WHTKLT4_1.md/659_cTi-T1-TRNA-1_B23WHTKLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title 659_cTi-T1-TRNA-1_B23WHTKLT4_1.md -output 659_cTi-T1-TRNA-1_B23WHTKLT4_1/659_cTi-T1-TRNA-1_B23WHTKLT4_1.md/659_cTi-T1-TRNA-1_B23WHTKLT4_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 2 659_cTi-T1-TRNA-1_B23WHTKLT4_1.md.bam > 659_cTi-T1-TRNA-1_B23WHTKLT4_1/659_cTi-T1-TRNA-1_B23WHTKLT4_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 2 659_cTi-T1-TRNA-1_B23WHTKLT4_1.md.bam > 659_cTi-T1-TRNA-1_B23WHTKLT4_1/659_cTi-T1-TRNA-1_B23WHTKLT4_1.md/reads_per_target.Twist_rna_exome_AND_fusion_hg38.bed.tsv seqtool depth_stats -bed Twist_rna_exome_AND_fusion_hg38.bed 659_cTi-T1-TRNA-1_B23WHTKLT4_1/659_cTi-T1-TRNA-1_B23WHTKLT4_1.md/659_cTi-T1-TRNA-1_B23WHTKLT4_1.md.depth.gz> 659_cTi-T1-TRNA-1_B23WHTKLT4_1/659_cTi-T1-TRNA-1_B23WHTKLT4_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 2 659_cTi-T1-TRNA-1_B23WHTKLT4_1.md.bam > 659_cTi-T1-TRNA-1_B23WHTKLT4_1/659_cTi-T1-TRNA-1_B23WHTKLT4_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: 659_cTi-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cTi-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_cTi-T1-TRNA-1_B23WHTKLT4_1.md.bai cat 659_cTi-T1-TRNA-1_B23WHTKLT4_1/659_cTi-T1-TRNA-1_B23WHTKLT4_1.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "659_cTi-T1-TRNA-1_B23WHTKLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "659_cTi-T1-TRNA-1_B23WHTKLT4_1/659_cTi-T1-TRNA-1_B23WHTKLT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > 659_cTi-T1-TRNA-1_B23WHTKLT4_1/659_cTi-T1-TRNA-1_B23WHTKLT4_1.md/qc_complete.txt + merge_qc -folders 659_cTi-T1-TRNA-1_B23WHTKLT4_1/659_cTi-T1-TRNA-1_B23WHTKLT4_1.md -output 659_cTi-T1-TRNA-1_B23WHTKLT4_1/659_cTi-T1-TRNA-1_B23WHTKLT4_1_full_basic_stats.tsv + head -n1 659_cTi-T1-TRNA-1_B23WHTKLT4_1/659_cTi-T1-TRNA-1_B23WHTKLT4_1_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed 659_cTi-T1-TRNA-1_B23WHTKLT4_1/659_cTi-T1-TRNA-1_B23WHTKLT4_1_full_basic_stats.tsv