Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f9/b2b41b68398ceec482172096b4b95d/659_bNS-T1-TRNA-1_B23MHV2LT4_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-rnd-pltf-dev-nextflow-scratch-01/work/a9/b1693f0f6611bb071a2d338c79cdb7/.command.sh Downloading: s3://natera-platform-sandbox/pipeline-resources/Homo_sapiens_assembly38.dbsnp138.vcf.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f9/b2b41b68398ceec482172096b4b95d/659_bNS-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/a9/b1693f0f6611bb071a2d338c79cdb7/.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_bNS-T1-TRNA-1_B23MHV2LT4_1 + all_qc -bam 659_bNS-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_bNS-T1-TRNA-1_B23MHV2LT4_1 -reference ref_genome.fa -region chr20 mkdir -p 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-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_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md/full_bed.bed seqtool depth -bam 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bam -bed 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz saturation_plot -bams 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bam -region chr20 -output 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md/saturation_qc.tsv fragment_size -bams 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bam -region chr20 -output_prefix 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-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_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.mpileup && contamination -input 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: 659_bNS-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_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-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_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai 0it [00:00, ?it/s] 132448it [00:00, 1324386.54it/s] 292701it [00:00, 1487881.65it/s] 459607it [00:00, 1570569.81it/s] 616665it [00:00, 1568865.97it/s] 773552it [00:00, 1561127.83it/s] 932165it [00:00, 1569541.52it/s] 1095042it [00:00, 1588822.58it/s] 1253934it [00:00, 1555704.56it/s] 1423639it [00:00, 1599167.12it/s] 1591326it [00:01, 1622862.21it/s] 1753754it [00:01, 1486581.95it/s] 1921037it [00:01, 1539432.97it/s] 2090391it [00:01, 1583922.45it/s] 2265110it [00:01, 1631590.82it/s] 2438755it [00:01, 1662439.68it/s] 2610215it [00:01, 1677855.28it/s] 2778684it [00:01, 1548312.33it/s] 2935890it [00:01, 1514141.61it/s] 3099428it [00:01, 1548102.73it/s] 3271037it [00:02, 1596225.93it/s] 3431861it [00:02, 1592404.34it/s] 3591934it [00:02, 1556121.85it/s] 3748239it [00:02, 1467635.90it/s] 3896309it [00:02, 1383957.17it/s] 4036215it [00:02, 1316239.48it/s] 4202308it [00:02, 1409389.33it/s] 4369412it [00:02, 1482222.43it/s] 4521151it [00:02, 1492206.64it/s] 4677128it [00:03, 1511713.13it/s] 4833286it [00:03, 1526258.25it/s] 4989126it [00:03, 1535573.58it/s] 5143240it [00:03, 1533954.78it/s] 5297024it [00:03, 1424542.49it/s] 5466996it [00:03, 1502228.03it/s] 5637770it [00:03, 1561169.43it/s] 5809055it [00:03, 1605284.75it/s] 5977737it [00:03, 1629201.50it/s] 6144205it [00:03, 1637149.95it/s] 6309322it [00:04, 1641251.27it/s] 6473881it [00:04, 1638505.57it/s] 6639743it [00:04, 1644365.00it/s] 6804396it [00:04, 1643701.72it/s] 6968918it [00:04, 1613799.06it/s] 7140561it [00:04, 1644069.11it/s] 7312113it [00:04, 1665233.65it/s] 7480734it [00:04, 1671451.25it/s] 7654156it [00:04, 1690057.62it/s] 7825454it [00:04, 1696879.91it/s] 7995211it [00:05, 1674309.14it/s] 8162753it [00:05, 1660813.98it/s] 8330982it [00:05, 1667092.23it/s] 8497762it [00:05, 1650058.93it/s] 8664406it [00:05, 1654873.21it/s] 8829952it [00:05, 1532797.09it/s] 9002290it [00:05, 1586533.99it/s] 9178075it [00:05, 1635608.79it/s] 9352791it [00:05, 1668030.92it/s] 9526572it [00:06, 1688485.38it/s] 9700565it [00:06, 1703658.25it/s] 9873047it [00:06, 1709894.04it/s] 10044432it [00:06, 1694937.74it/s] 10214224it [00:06, 1695057.95it/s] 10383939it [00:06, 1693658.23it/s] 10553816it [00:06, 1695042.02it/s] 10723423it [00:06, 1690322.81it/s] 10892529it [00:06, 1687603.38it/s] 11062790it [00:06, 1692015.59it/s] 11234283it [00:07, 1698816.13it/s] 11406486it [00:07, 1705735.17it/s] 11577601it [00:07, 1707332.83it/s] 11751308it [00:07, 1716101.03it/s] 11922930it [00:07, 1703756.65it/s] 12093334it [00:07, 1655898.38it/s] 12229420it [00:07, 1604664.37it/s] [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai tabix -s 1 -b 2 -e 2 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz seqtool depth_hist -nbins 500 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz > 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.depth_hist.tsv cat 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md -output 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md/659_bNS-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_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md/read_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv seqtool depth_stats -bed Twist_rna_exome_AND_fusion_hg38.bed 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz> 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md/depth_stats.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_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md/reads_per_target.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_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-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_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.md.bai cat 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-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_bNS-T1-TRNA-1_B23MHV2LT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-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_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md/qc_complete.txt + merge_qc -folders 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1.md -output 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv + head -n1 659_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-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_bNS-T1-TRNA-1_B23MHV2LT4_1/659_bNS-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv