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/7a/fe6d5257d2771ca0b48bd3d26035e6/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ee/eb56e06de4f0fbfff502cde020ad59/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.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/ee/eb56e06de4f0fbfff502cde020ad59/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7a/fe6d5257d2771ca0b48bd3d26035e6/.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 659_bQZ-T1-TRNA-1_B23MHV2LT4_1 + all_qc -bam 659_bQZ-T1-TRNA-1_B23MHV2LT4_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_bQZ-T1-TRNA-1_B23MHV2LT4_1 -reference ref_genome.fa -region chr20 mkdir -p 659_bQZ-T1-TRNA-1_B23MHV2LT4_1/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md/ cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > 659_bQZ-T1-TRNA-1_B23MHV2LT4_1/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md/full_bed.bed seqtool depth -bam 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bam -bed 659_bQZ-T1-TRNA-1_B23MHV2LT4_1/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > 659_bQZ-T1-TRNA-1_B23MHV2LT4_1/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz saturation_plot -bams 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bam -region chr20 -output 659_bQZ-T1-TRNA-1_B23MHV2LT4_1/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bQZ-T1-TRNA-1_B23MHV2LT4_1/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md/saturation_qc.tsv fragment_size -bams 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bam -region chr20 -output_prefix 659_bQZ-T1-TRNA-1_B23MHV2LT4_1/659_bQZ-T1-TRNA-1_B23MHV2LT4_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_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.mpileup && contamination -input 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > 659_bQZ-T1-TRNA-1_B23MHV2LT4_1/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai [mpileup] 1 samples in 1 input files [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_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_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai 0it [00:00, ?it/s] 155152it [00:00, 1551406.82it/s] 322027it [00:00, 1620392.42it/s] 492549it [00:00, 1659095.37it/s] 663524it [00:00, 1678908.43it/s] 833908it [00:00, 1687776.84it/s] 1004685it [00:00, 1694548.26it/s] 1174983it [00:00, 1697281.29it/s] 1345215it [00:00, 1698865.16it/s] 1517211it [00:00, 1705439.55it/s] 1687755it [00:01, 1704707.45it/s] 1858226it [00:01, 1704493.63it/s] 2028676it [00:01, 1702528.36it/s] 2199797it [00:01, 1705133.98it/s] 2370683it [00:01, 1706238.22it/s] 2543840it [00:01, 1713800.40it/s] 2722202it [00:01, 1734788.55it/s] 2895683it [00:01, 1731210.83it/s] 3068807it [00:01, 1724438.85it/s] 3241258it [00:01, 1716526.68it/s] 3412921it [00:02, 1709987.40it/s] 3583929it [00:02, 1709399.50it/s] 3754958it [00:02, 1709643.98it/s] 3926943it [00:02, 1712675.49it/s] 4098817it [00:02, 1714472.79it/s] 4270268it [00:02, 1710595.07it/s] 4442806it [00:02, 1715000.61it/s] 4614310it [00:02, 1709723.04it/s] 4785288it [00:02, 1704871.45it/s] 4955781it [00:02, 1700743.96it/s] 5125860it [00:03, 1692135.31it/s] 5295435it [00:03, 1693061.16it/s] 5464748it [00:03, 1689832.45it/s] 5636990it [00:03, 1699521.24it/s] 5807713it [00:03, 1701775.60it/s] 5978771it [00:03, 1704392.87it/s] 6149216it [00:03, 1704224.28it/s] 6319642it [00:03, 1697837.58it/s] 6489433it [00:03, 1692881.29it/s] 6658728it [00:03, 1688835.42it/s] 6827617it [00:04, 1682416.64it/s] 6995865it [00:04, 1678483.89it/s] 7163718it [00:04, 1676081.22it/s] 7332655it [00:04, 1680031.12it/s] 7503247it [00:04, 1687752.21it/s] 7676617it [00:04, 1701480.24it/s] 7847236it [00:04, 1702875.32it/s] 8017529it [00:04, 1702174.78it/s] 8187751it [00:04, 1700867.97it/s] 8357841it [00:04, 1696676.39it/s] 8527513it [00:05, 1695795.98it/s] 8697096it [00:05, 1691411.70it/s] 8866710it [00:05, 1692795.70it/s] 9037392it [00:05, 1696965.58it/s] 9209719it [00:05, 1704818.54it/s] 9383087it [00:05, 1713441.47it/s] 9555322it [00:05, 1716054.62it/s] 9726937it [00:05, 1716060.40it/s] 9898545it [00:05, 1712615.13it/s] 10069810it [00:05, 1704457.34it/s] 10240666it [00:06, 1705661.18it/s] 10411304it [00:06, 1705857.16it/s] 10581895it [00:06, 1705316.08it/s] 10752431it [00:06, 1700879.04it/s] 10922524it [00:06, 1694956.99it/s] 11092026it [00:06, 1692237.76it/s] 11261254it [00:06, 1689365.92it/s] 11430194it [00:06, 1685047.74it/s] 11601621it [00:06, 1693751.40it/s] 11771751it [00:06, 1695990.74it/s] 11942984it [00:07, 1700863.25it/s] 12115911it [00:07, 1709325.26it/s] 12286849it [00:07, 1703108.88it/s] 12457657it [00:07, 1704568.93it/s] 12628120it [00:07, 1702506.69it/s] 12685388it [00:07, 1700165.13it/s] [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai tabix -s 1 -b 2 -e 2 659_bQZ-T1-TRNA-1_B23MHV2LT4_1/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz seqtool depth_hist -nbins 500 659_bQZ-T1-TRNA-1_B23MHV2LT4_1/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz > 659_bQZ-T1-TRNA-1_B23MHV2LT4_1/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.depth_hist.tsv cat 659_bQZ-T1-TRNA-1_B23MHV2LT4_1/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md -output 659_bQZ-T1-TRNA-1_B23MHV2LT4_1/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md/659_bQZ-T1-TRNA-1_B23MHV2LT4_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_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bQZ-T1-TRNA-1_B23MHV2LT4_1/659_bQZ-T1-TRNA-1_B23MHV2LT4_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_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bQZ-T1-TRNA-1_B23MHV2LT4_1/659_bQZ-T1-TRNA-1_B23MHV2LT4_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_bQZ-T1-TRNA-1_B23MHV2LT4_1/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz> 659_bQZ-T1-TRNA-1_B23MHV2LT4_1/659_bQZ-T1-TRNA-1_B23MHV2LT4_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_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bQZ-T1-TRNA-1_B23MHV2LT4_1/659_bQZ-T1-TRNA-1_B23MHV2LT4_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_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai cat 659_bQZ-T1-TRNA-1_B23MHV2LT4_1/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "659_bQZ-T1-TRNA-1_B23MHV2LT4_1/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > 659_bQZ-T1-TRNA-1_B23MHV2LT4_1/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md/qc_complete.txt + merge_qc -folders 659_bQZ-T1-TRNA-1_B23MHV2LT4_1/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md -output 659_bQZ-T1-TRNA-1_B23MHV2LT4_1/659_bQZ-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv + head -n1 659_bQZ-T1-TRNA-1_B23MHV2LT4_1/659_bQZ-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed 659_bQZ-T1-TRNA-1_B23MHV2LT4_1/659_bQZ-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv