Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/81/055d16d900aa4f5d756bd4631fe78f/659_ciZ-T1-TRNA-1_B23WHTKLT4_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/f8/3cc1e1c746d5cb930b0f5903b1e19d/.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/f8/3cc1e1c746d5cb930b0f5903b1e19d/.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-rnd-pltf-dev-nextflow-scratch-01/work/81/055d16d900aa4f5d756bd4631fe78f/659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md.bai 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_ciZ-T1-TRNA-1_B23WHTKLT4_1 + all_qc -bam 659_ciZ-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_ciZ-T1-TRNA-1_B23WHTKLT4_1 -reference ref_genome.fa -region chr20 mkdir -p 659_ciZ-T1-TRNA-1_B23WHTKLT4_1/659_ciZ-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_ciZ-T1-TRNA-1_B23WHTKLT4_1/659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md/full_bed.bed seqtool depth -bam 659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md.bam -bed 659_ciZ-T1-TRNA-1_B23WHTKLT4_1/659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > 659_ciZ-T1-TRNA-1_B23WHTKLT4_1/659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md/659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md.depth.gz saturation_plot -bams 659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md.bam -region chr20 -output 659_ciZ-T1-TRNA-1_B23WHTKLT4_1/659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md.bam > 659_ciZ-T1-TRNA-1_B23WHTKLT4_1/659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md/saturation_qc.tsv fragment_size -bams 659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md.bam -region chr20 -output_prefix 659_ciZ-T1-TRNA-1_B23WHTKLT4_1/659_ciZ-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_ciZ-T1-TRNA-1_B23WHTKLT4_1.md.bam > 659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md.mpileup && contamination -input 659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > 659_ciZ-T1-TRNA-1_B23WHTKLT4_1/659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: 659_ciZ-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_ciZ-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_ciZ-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_ciZ-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md.bai 0it [00:00, ?it/s] 138055it [00:00, 1380307.79it/s] 297725it [00:00, 1507531.89it/s] 451354it [00:00, 1520519.32it/s] 603407it [00:00, 1478073.09it/s] 772843it [00:00, 1554620.47it/s] 943029it [00:00, 1604044.35it/s] 1103660it [00:00, 1582750.62it/s] 1275744it [00:00, 1626022.80it/s] 1438545it [00:00, 1620660.81it/s] 1604326it [00:01, 1631984.32it/s] 1773144it [00:01, 1649030.23it/s] 1939797it [00:01, 1654293.31it/s] 2110950it [00:01, 1671537.98it/s] 2278152it [00:01, 1613708.65it/s] 2439975it [00:01, 1605780.98it/s] 2610868it [00:01, 1636099.79it/s] 2783454it [00:01, 1662631.96it/s] 2957704it [00:01, 1686334.85it/s] 3130559it [00:01, 1698875.68it/s] 3300593it [00:02, 1643182.41it/s] 3470475it [00:02, 1659405.98it/s] 3644832it [00:02, 1684153.20it/s] 3813560it [00:02, 1641896.30it/s] 3978157it [00:02, 1548232.60it/s] 4135662it [00:02, 1555762.85it/s] 4292129it [00:02, 1558128.18it/s] 4458429it [00:02, 1588604.88it/s] 4617829it [00:02, 1558179.77it/s] 4781418it [00:02, 1580785.65it/s] 4950396it [00:03, 1612780.95it/s] 5112012it [00:03, 1590546.41it/s] 5271345it [00:03, 1589833.14it/s] 5430522it [00:03, 1564496.74it/s] 5600331it [00:03, 1603664.84it/s] 5764164it [00:03, 1613868.97it/s] 5938267it [00:03, 1651564.21it/s] 6110411it [00:03, 1672333.70it/s] 6281723it [00:03, 1684462.24it/s] 6450267it [00:03, 1642555.30it/s] 6614808it [00:04, 1590608.42it/s] 6774341it [00:04, 1580395.10it/s] 6937306it [00:04, 1594688.49it/s] 7106356it [00:04, 1622708.99it/s] 7273090it [00:04, 1635861.01it/s] 7436870it [00:04, 1597030.39it/s] 7596878it [00:04, 1570299.73it/s] 7754164it [00:04, 1559489.26it/s] 7910279it [00:04, 1550719.49it/s] 8073065it [00:05, 1573318.53it/s] 8233311it [00:05, 1581894.68it/s][W::hts_idx_load3] The index file is older than the data file: 659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md.bai 8395669it [00:05, 1594232.64it/s] 8555178it [00:05, 1591025.32it/s] 8717912it [00:05, 1601813.27it/s] 8878142it [00:05, 1575674.09it/s] 9035828it [00:05, 1557854.44it/s] 9199362it [00:05, 1580639.95it/s] 9357543it [00:05, 1569465.98it/s] 9519600it [00:05, 1584551.87it/s] 9680847it [00:06, 1592692.45it/s] 9840961it [00:06, 1595168.34it/s] 10006003it [00:06, 1611522.40it/s] 10167197it [00:06, 1515171.86it/s] 10322708it [00:06, 1526585.06it/s] 10476886it [00:06, 1530968.31it/s] 10630616it [00:06, 1518336.00it/s] 10782892it [00:06, 1515890.45it/s] 10949091it [00:06, 1558454.73it/s] 11105224it [00:06, 1504378.86it/s] 11263299it [00:07, 1526491.27it/s] 11416414it [00:07, 1491497.39it/s] 11565999it [00:07, 1470721.60it/s] 11717743it [00:07, 1484237.46it/s] 11866430it [00:07, 1451403.88it/s] 12011849it [00:07, 1446258.98it/s] 12160263it [00:07, 1457302.56it/s] 12307447it [00:07, 1461549.46it/s] 12463002it [00:07, 1489348.30it/s][W::hts_idx_load3] The index file is older than the data file: 659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md.bai 12612056it [00:08, 1469020.99it/s] 12759088it [00:08, 1458923.22it/s] 12921370it [00:08, 1507252.20it/s] 13072239it [00:08, 1448872.37it/s] 13222038it [00:08, 1463047.74it/s] 13370512it [00:08, 1469354.08it/s] 13517762it [00:08, 1437848.65it/s] 13661871it [00:08, 1431906.98it/s] 13805279it [00:08, 1429123.93it/s] 13951253it [00:08, 1438010.42it/s] 14095173it [00:09, 1380647.24it/s] 14236083it [00:09, 1388720.74it/s] 14382119it [00:09, 1409614.33it/s] 14529044it [00:09, 1427130.96it/s] 14638625it [00:09, 1554365.68it/s] [W::hts_idx_load3] The index file is older than the data file: 659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md.bai tabix -s 1 -b 2 -e 2 659_ciZ-T1-TRNA-1_B23WHTKLT4_1/659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md/659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md.depth.gz seqtool depth_hist -nbins 500 659_ciZ-T1-TRNA-1_B23WHTKLT4_1/659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md/659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md.depth.gz > 659_ciZ-T1-TRNA-1_B23WHTKLT4_1/659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md/659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md.depth_hist.tsv cat 659_ciZ-T1-TRNA-1_B23WHTKLT4_1/659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md/659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title 659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md -output 659_ciZ-T1-TRNA-1_B23WHTKLT4_1/659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md/659_ciZ-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_ciZ-T1-TRNA-1_B23WHTKLT4_1.md.bam > 659_ciZ-T1-TRNA-1_B23WHTKLT4_1/659_ciZ-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_ciZ-T1-TRNA-1_B23WHTKLT4_1.md.bam > 659_ciZ-T1-TRNA-1_B23WHTKLT4_1/659_ciZ-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_ciZ-T1-TRNA-1_B23WHTKLT4_1/659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md/659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md.depth.gz> 659_ciZ-T1-TRNA-1_B23WHTKLT4_1/659_ciZ-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_ciZ-T1-TRNA-1_B23WHTKLT4_1.md.bam > 659_ciZ-T1-TRNA-1_B23WHTKLT4_1/659_ciZ-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_ciZ-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md.bai cat 659_ciZ-T1-TRNA-1_B23WHTKLT4_1/659_ciZ-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_ciZ-T1-TRNA-1_B23WHTKLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "659_ciZ-T1-TRNA-1_B23WHTKLT4_1/659_ciZ-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_ciZ-T1-TRNA-1_B23WHTKLT4_1/659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md/qc_complete.txt + merge_qc -folders 659_ciZ-T1-TRNA-1_B23WHTKLT4_1/659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md -output 659_ciZ-T1-TRNA-1_B23WHTKLT4_1/659_ciZ-T1-TRNA-1_B23WHTKLT4_1_full_basic_stats.tsv + head -n1 659_ciZ-T1-TRNA-1_B23WHTKLT4_1/659_ciZ-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_ciZ-T1-TRNA-1_B23WHTKLT4_1/659_ciZ-T1-TRNA-1_B23WHTKLT4_1_full_basic_stats.tsv