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/58/29f431948ddecb06336b79f4067883/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/99/eb5677357d9af5f07600c3c60fb026/659_bCu-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.dict Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/99/eb5677357d9af5f07600c3c60fb026/659_bCu-T1-TRNA-1_B23MHV2LT4_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/58/29f431948ddecb06336b79f4067883/.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_bCu-T1-TRNA-1_B23MHV2LT4_1 + all_qc -bam 659_bCu-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_bCu-T1-TRNA-1_B23MHV2LT4_1 -reference ref_genome.fa -region chr20 mkdir -p 659_bCu-T1-TRNA-1_B23MHV2LT4_1/659_bCu-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_bCu-T1-TRNA-1_B23MHV2LT4_1/659_bCu-T1-TRNA-1_B23MHV2LT4_1.md/full_bed.bed seqtool depth -bam 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bam -bed 659_bCu-T1-TRNA-1_B23MHV2LT4_1/659_bCu-T1-TRNA-1_B23MHV2LT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > 659_bCu-T1-TRNA-1_B23MHV2LT4_1/659_bCu-T1-TRNA-1_B23MHV2LT4_1.md/659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz saturation_plot -bams 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bam -region chr20 -output 659_bCu-T1-TRNA-1_B23MHV2LT4_1/659_bCu-T1-TRNA-1_B23MHV2LT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bCu-T1-TRNA-1_B23MHV2LT4_1/659_bCu-T1-TRNA-1_B23MHV2LT4_1.md/saturation_qc.tsv fragment_size -bams 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bam -region chr20 -output_prefix 659_bCu-T1-TRNA-1_B23MHV2LT4_1/659_bCu-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_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.mpileup && contamination -input 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > 659_bCu-T1-TRNA-1_B23MHV2LT4_1/659_bCu-T1-TRNA-1_B23MHV2LT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: 659_bCu-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_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-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_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai 0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai 141988it [00:00, 1419773.03it/s] 300931it [00:00, 1519434.76it/s] 463613it [00:00, 1568434.19it/s] 627437it [00:00, 1595861.25it/s] 794871it [00:00, 1624131.49it/s] 961441it [00:00, 1638237.84it/s] 1130542it [00:00, 1655460.18it/s] 1296089it [00:00, 1645954.62it/s] 1460697it [00:00, 1643283.52it/s] 1631516it [00:01, 1663214.59it/s] 1797851it [00:01, 1642544.62it/s] 1962167it [00:01, 1642654.87it/s] 2127279it [00:01, 1645168.83it/s] 2291828it [00:01, 1623383.36it/s] 2459071it [00:01, 1637940.45it/s] 2622938it [00:01, 1616934.15it/s] 2784726it [00:01, 1610248.45it/s] 2945813it [00:01, 1561282.65it/s] 3102252it [00:01, 1519816.82it/s] 3254583it [00:02, 1483075.18it/s] 3403200it [00:02, 1463699.26it/s] 3560452it [00:02, 1494955.35it/s] 3730954it [00:02, 1556082.88it/s] 3886940it [00:02, 1544849.24it/s] 4041687it [00:02, 1517104.97it/s] 4209451it [00:02, 1563931.96it/s] 4379614it [00:02, 1604423.76it/s] 4540348it [00:02, 1455633.20it/s] 4688649it [00:03, 1430828.97it/s] 4847327it [00:03, 1474309.14it/s] 5011178it [00:03, 1521076.52it/s] 5168613it [00:03, 1536430.98it/s] 5323281it [00:03, 1452347.31it/s] 5473358it [00:03, 1466003.70it/s] 5624229it [00:03, 1478255.99it/s] 5788392it [00:03, 1525727.51it/s] 5941712it [00:03, 1515241.11it/s] 6105004it [00:03, 1549787.99it/s] 6273711it [00:04, 1589931.20it/s] 6433066it [00:04, 1509285.15it/s] 6585048it [00:04, 1427077.73it/s] 6749142it [00:04, 1486676.37it/s] 6904121it [00:04, 1504603.70it/s] 7055687it [00:04, 1385497.85it/s] 7202085it [00:04, 1407053.64it/s] 7370859it [00:04, 1486185.36it/s] 7540379it [00:04, 1546195.93it/s] 7708385it [00:04, 1585086.43it/s] 7868082it [00:05, 1532042.69it/s] 8022431it [00:05, 1463416.75it/s] 8170030it [00:05, 1463857.16it/s] 8335507it [00:05, 1518535.81it/s] 8502164it [00:05, 1561506.72it/s] 8674151it [00:05, 1607915.84it/s] 8844145it [00:05, 1635058.09it/s] 9008139it [00:05, 1571428.17it/s] 9179642it [00:05, 1612934.52it/s] 9353775it [00:06, 1650448.04it/s] 9527234it [00:06, 1675204.09it/s] 9698605it [00:06, 1686580.54it/s] 9867608it [00:06, 1681154.46it/s] 10036258it [00:06, 1682564.20it/s] 10205557it [00:06, 1685579.18it/s] 10375328it [00:06, 1689172.54it/s] 10544823it [00:06, 1690861.02it/s] 10715884it [00:06, 1696728.22it/s][W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai 10886758it [00:06, 1700299.84it/s] 11057911it [00:07, 1703613.29it/s] 11228295it [00:07, 1693883.23it/s] 11397712it [00:07, 1652721.66it/s] 11563209it [00:07, 1616982.62it/s] 11725174it [00:07, 1592214.27it/s] 11739404it [00:07, 1570513.80it/s] [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai tabix -s 1 -b 2 -e 2 659_bCu-T1-TRNA-1_B23MHV2LT4_1/659_bCu-T1-TRNA-1_B23MHV2LT4_1.md/659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz seqtool depth_hist -nbins 500 659_bCu-T1-TRNA-1_B23MHV2LT4_1/659_bCu-T1-TRNA-1_B23MHV2LT4_1.md/659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz > 659_bCu-T1-TRNA-1_B23MHV2LT4_1/659_bCu-T1-TRNA-1_B23MHV2LT4_1.md/659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.depth_hist.tsv cat 659_bCu-T1-TRNA-1_B23MHV2LT4_1/659_bCu-T1-TRNA-1_B23MHV2LT4_1.md/659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md -output 659_bCu-T1-TRNA-1_B23MHV2LT4_1/659_bCu-T1-TRNA-1_B23MHV2LT4_1.md/659_bCu-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_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bCu-T1-TRNA-1_B23MHV2LT4_1/659_bCu-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_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bCu-T1-TRNA-1_B23MHV2LT4_1/659_bCu-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_bCu-T1-TRNA-1_B23MHV2LT4_1/659_bCu-T1-TRNA-1_B23MHV2LT4_1.md/659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz> 659_bCu-T1-TRNA-1_B23MHV2LT4_1/659_bCu-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_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bCu-T1-TRNA-1_B23MHV2LT4_1/659_bCu-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_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.md.bai cat 659_bCu-T1-TRNA-1_B23MHV2LT4_1/659_bCu-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_bCu-T1-TRNA-1_B23MHV2LT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "659_bCu-T1-TRNA-1_B23MHV2LT4_1/659_bCu-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_bCu-T1-TRNA-1_B23MHV2LT4_1/659_bCu-T1-TRNA-1_B23MHV2LT4_1.md/qc_complete.txt + merge_qc -folders 659_bCu-T1-TRNA-1_B23MHV2LT4_1/659_bCu-T1-TRNA-1_B23MHV2LT4_1.md -output 659_bCu-T1-TRNA-1_B23MHV2LT4_1/659_bCu-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv + head -n1 659_bCu-T1-TRNA-1_B23MHV2LT4_1/659_bCu-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_bCu-T1-TRNA-1_B23MHV2LT4_1/659_bCu-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv