Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e6/8bbe66d59a7eace64d482eecd90ce8/659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md.bai 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/ad/a89b0ff5d0d476a98487a02fcb1ae0/.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/ad/a89b0ff5d0d476a98487a02fcb1ae0/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e6/8bbe66d59a7eace64d482eecd90ce8/659_bQZ-T1-TRNA-1_A23MVY2LT4_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 659_bQZ-T1-TRNA-1_A23MVY2LT4_1 + all_qc -bam 659_bQZ-T1-TRNA-1_A23MVY2LT4_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_A23MVY2LT4_1 -reference ref_genome.fa -region chr20 mkdir -p 659_bQZ-T1-TRNA-1_A23MVY2LT4_1/659_bQZ-T1-TRNA-1_A23MVY2LT4_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_A23MVY2LT4_1/659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md/full_bed.bed seqtool depth -bam 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md.bam -bed 659_bQZ-T1-TRNA-1_A23MVY2LT4_1/659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > 659_bQZ-T1-TRNA-1_A23MVY2LT4_1/659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md/659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md.depth.gz saturation_plot -bams 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md.bam -region chr20 -output 659_bQZ-T1-TRNA-1_A23MVY2LT4_1/659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md.bam > 659_bQZ-T1-TRNA-1_A23MVY2LT4_1/659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md/saturation_qc.tsv fragment_size -bams 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md.bam -region chr20 -output_prefix 659_bQZ-T1-TRNA-1_A23MVY2LT4_1/659_bQZ-T1-TRNA-1_A23MVY2LT4_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_A23MVY2LT4_1.md.bam > 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md.mpileup && contamination -input 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > 659_bQZ-T1-TRNA-1_A23MVY2LT4_1/659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_A23MVY2LT4_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_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_A23MVY2LT4_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_A23MVY2LT4_1.md.bai 0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md.bai 141035it [00:00, 1410263.92it/s] 285916it [00:00, 1432904.16it/s] 438345it [00:00, 1471932.34it/s] 595499it [00:00, 1511073.45it/s] 756961it [00:00, 1548235.60it/s] 920033it [00:00, 1576236.60it/s] 1084078it [00:00, 1597033.68it/s] 1248749it [00:00, 1612819.91it/s] 1413248it [00:00, 1622854.16it/s] 1577212it [00:01, 1627910.04it/s] 1741151it [00:01, 1631399.54it/s] 1905941it [00:01, 1636272.99it/s] 2069569it [00:01, 1616948.41it/s] 2233692it [00:01, 1624203.06it/s] 2400555it [00:01, 1637420.54it/s] 2571896it [00:01, 1660178.62it/s] 2738020it [00:01, 1660383.38it/s] 2904084it [00:01, 1654460.39it/s] 3069552it [00:01, 1652068.67it/s] 3234774it [00:02, 1644416.26it/s] 3399232it [00:02, 1644319.37it/s] 3564687it [00:02, 1647243.43it/s] 3729421it [00:02, 1644129.85it/s] 3895578it [00:02, 1649325.32it/s] 4062599it [00:02, 1655557.92it/s] 4228161it [00:02, 1646322.34it/s] 4392808it [00:02, 1643464.03it/s] 4557907it [00:02, 1645690.43it/s] 4725957it [00:02, 1656077.51it/s] 4891574it [00:03, 1647076.98it/s] 5056298it [00:03, 1498333.17it/s] 5210920it [00:03, 1511674.67it/s] 5372078it [00:03, 1540141.40it/s] 5529585it [00:03, 1550224.72it/s] 5697449it [00:03, 1587768.15it/s] 5857065it [00:03, 1577363.14it/s] 6018576it [00:03, 1588462.51it/s] 6181384it [00:03, 1600088.66it/s] 6341711it [00:03, 1597563.95it/s] 6501689it [00:04, 1562262.15it/s] 6658222it [00:04, 1512714.73it/s] 6809966it [00:04, 1504788.87it/s] 6960757it [00:04, 1494531.79it/s] 7121751it [00:04, 1528163.78it/s] 7287090it [00:04, 1564972.10it/s] 7451681it [00:04, 1588735.28it/s] 7615005it [00:04, 1601943.09it/s] 7782484it [00:04, 1623633.03it/s] 7946576it [00:04, 1628686.23it/s] 8109531it [00:05, 1521883.68it/s] 8263175it [00:05, 1403547.46it/s] 8419014it [00:05, 1445645.56it/s] 8586370it [00:05, 1509504.43it/s] 8752675it [00:05, 1553339.22it/s] 8920224it [00:05, 1588740.86it/s] 9086048it [00:05, 1609075.18it/s] 9250018it [00:05, 1618087.31it/s] 9412482it [00:05, 1619224.74it/s] 9576061it [00:06, 1624130.24it/s] 9738801it [00:06, 1622444.67it/s] 9901274it [00:06, 1617308.61it/s] 10066371it [00:06, 1627301.32it/s] 10231707it [00:06, 1635062.73it/s] 10398604it [00:06, 1645180.32it/s] 10563186it [00:06, 1641288.86it/s] 10729091it [00:06, 1646582.65it/s] 10894343it [00:06, 1648336.71it/s] 11063286it [00:06, 1660625.05it/s] 11231251it [00:07, 1666189.60it/s] 11397884it [00:07, 1657708.46it/s] 11563674it [00:07, 1654133.83it/s] 11729101it [00:07, 1648059.75it/s] 11746866it [00:07, 1599263.27it/s] [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md.bai tabix -s 1 -b 2 -e 2 659_bQZ-T1-TRNA-1_A23MVY2LT4_1/659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md/659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md.depth.gz seqtool depth_hist -nbins 500 659_bQZ-T1-TRNA-1_A23MVY2LT4_1/659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md/659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md.depth.gz > 659_bQZ-T1-TRNA-1_A23MVY2LT4_1/659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md/659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md.depth_hist.tsv cat 659_bQZ-T1-TRNA-1_A23MVY2LT4_1/659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md/659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md -output 659_bQZ-T1-TRNA-1_A23MVY2LT4_1/659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md/659_bQZ-T1-TRNA-1_A23MVY2LT4_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_A23MVY2LT4_1.md.bam > 659_bQZ-T1-TRNA-1_A23MVY2LT4_1/659_bQZ-T1-TRNA-1_A23MVY2LT4_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_A23MVY2LT4_1.md.bam > 659_bQZ-T1-TRNA-1_A23MVY2LT4_1/659_bQZ-T1-TRNA-1_A23MVY2LT4_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_A23MVY2LT4_1/659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md/659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md.depth.gz> 659_bQZ-T1-TRNA-1_A23MVY2LT4_1/659_bQZ-T1-TRNA-1_A23MVY2LT4_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_A23MVY2LT4_1.md.bam > 659_bQZ-T1-TRNA-1_A23MVY2LT4_1/659_bQZ-T1-TRNA-1_A23MVY2LT4_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_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md.bai cat 659_bQZ-T1-TRNA-1_A23MVY2LT4_1/659_bQZ-T1-TRNA-1_A23MVY2LT4_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_A23MVY2LT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "659_bQZ-T1-TRNA-1_A23MVY2LT4_1/659_bQZ-T1-TRNA-1_A23MVY2LT4_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_A23MVY2LT4_1/659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md/qc_complete.txt + merge_qc -folders 659_bQZ-T1-TRNA-1_A23MVY2LT4_1/659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md -output 659_bQZ-T1-TRNA-1_A23MVY2LT4_1/659_bQZ-T1-TRNA-1_A23MVY2LT4_1_full_basic_stats.tsv + head -n1 659_bQZ-T1-TRNA-1_A23MVY2LT4_1/659_bQZ-T1-TRNA-1_A23MVY2LT4_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_A23MVY2LT4_1/659_bQZ-T1-TRNA-1_A23MVY2LT4_1_full_basic_stats.tsv