Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/08/294a374d3afa19c4a39cc95cda9671/659_bua-T1-TRNA-1_A23MVY2LT4_2.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/27/4086efc2035ef30c8fe624dc74b130/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/08/294a374d3afa19c4a39cc95cda9671/659_bua-T1-TRNA-1_A23MVY2LT4_2.md.bai 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/27/4086efc2035ef30c8fe624dc74b130/.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_bua-T1-TRNA-1_A23MVY2LT4_2 + all_qc -bam 659_bua-T1-TRNA-1_A23MVY2LT4_2.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_bua-T1-TRNA-1_A23MVY2LT4_2 -reference ref_genome.fa -region chr20 mkdir -p 659_bua-T1-TRNA-1_A23MVY2LT4_2/659_bua-T1-TRNA-1_A23MVY2LT4_2.md/ cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > 659_bua-T1-TRNA-1_A23MVY2LT4_2/659_bua-T1-TRNA-1_A23MVY2LT4_2.md/full_bed.bed seqtool depth -bam 659_bua-T1-TRNA-1_A23MVY2LT4_2.md.bam -bed 659_bua-T1-TRNA-1_A23MVY2LT4_2/659_bua-T1-TRNA-1_A23MVY2LT4_2.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > 659_bua-T1-TRNA-1_A23MVY2LT4_2/659_bua-T1-TRNA-1_A23MVY2LT4_2.md/659_bua-T1-TRNA-1_A23MVY2LT4_2.md.depth.gz saturation_plot -bams 659_bua-T1-TRNA-1_A23MVY2LT4_2.md.bam -region chr20 -output 659_bua-T1-TRNA-1_A23MVY2LT4_2/659_bua-T1-TRNA-1_A23MVY2LT4_2.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 659_bua-T1-TRNA-1_A23MVY2LT4_2.md.bam > 659_bua-T1-TRNA-1_A23MVY2LT4_2/659_bua-T1-TRNA-1_A23MVY2LT4_2.md/saturation_qc.tsv fragment_size -bams 659_bua-T1-TRNA-1_A23MVY2LT4_2.md.bam -region chr20 -output_prefix 659_bua-T1-TRNA-1_A23MVY2LT4_2/659_bua-T1-TRNA-1_A23MVY2LT4_2.md/fragsize -threads 1 samtools mpileup -B --min-MQ 60 --min-BQ 30 -f ref_genome.fa -l dbsnp_hg38_contam_sites.bed 659_bua-T1-TRNA-1_A23MVY2LT4_2.md.bam > 659_bua-T1-TRNA-1_A23MVY2LT4_2.md.mpileup && contamination -input 659_bua-T1-TRNA-1_A23MVY2LT4_2.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > 659_bua-T1-TRNA-1_A23MVY2LT4_2/659_bua-T1-TRNA-1_A23MVY2LT4_2.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_A23MVY2LT4_2.md.bai [mpileup] 1 samples in 1 input files [W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_A23MVY2LT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_A23MVY2LT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_A23MVY2LT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_A23MVY2LT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_A23MVY2LT4_2.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_bua-T1-TRNA-1_A23MVY2LT4_2.md.bai 0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_A23MVY2LT4_2.md.bai 149226it [00:00, 1492190.27it/s] 313852it [00:00, 1582674.39it/s] 478434it [00:00, 1611468.39it/s] 644263it [00:00, 1629813.13it/s] 813391it [00:00, 1651960.13it/s] 983591it [00:00, 1668959.65it/s] 1153971it [00:00, 1680199.16it/s] 1323676it [00:00, 1685547.04it/s] 1495457it [00:00, 1695618.82it/s] 1665952it [00:01, 1698486.14it/s] 1837248it [00:01, 1702901.28it/s] 2007539it [00:01, 1700642.33it/s] 2177604it [00:01, 1664387.95it/s] 2344964it [00:01, 1667115.59it/s] 2518153it [00:01, 1686414.75it/s] 2696071it [00:01, 1714049.25it/s] 2871433it [00:01, 1725740.08it/s] 3044282it [00:01, 1726407.23it/s] 3216974it [00:01, 1720015.98it/s] 3389016it [00:02, 1712224.11it/s] 3560271it [00:02, 1702275.44it/s] 3731165it [00:02, 1704246.75it/s] 3903750it [00:02, 1710535.07it/s] 4076875it [00:02, 1716583.85it/s] 4251042it [00:02, 1724075.75it/s] 4423464it [00:02, 1718547.93it/s] 4595332it [00:02, 1713087.19it/s] 4767961it [00:02, 1717017.13it/s] 4939673it [00:02, 1711178.83it/s] 5110801it [00:03, 1705518.00it/s] 5281361it [00:03, 1688852.31it/s] 5451627it [00:03, 1692935.85it/s] 5623420it [00:03, 1700359.40it/s] 5796879it [00:03, 1710558.33it/s] 5970237it [00:03, 1717428.37it/s] 6142211it [00:03, 1718108.26it/s] 6314231it [00:03, 1718721.61it/s] 6486634it [00:03, 1720230.22it/s] 6658664it [00:03, 1719520.53it/s] 6830621it [00:04, 1717547.61it/s] 7002940it [00:04, 1719205.16it/s] 7175152it [00:04, 1719951.38it/s] 7347150it [00:04, 1717134.15it/s] 7518866it [00:04, 1715184.08it/s] 7690387it [00:04, 1711914.87it/s] 7862959it [00:04, 1716032.12it/s][W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_A23MVY2LT4_2.md.bai 8035305it [00:04, 1718241.98it/s] 8207132it [00:04, 1707620.85it/s] 8377910it [00:04, 1695046.94it/s] 8548465it [00:05, 1698078.88it/s] 8720756it [00:05, 1705472.32it/s] 8892061it [00:05, 1707723.95it/s] 9063369it [00:05, 1709287.28it/s] 9234309it [00:05, 1708626.43it/s] 9405179it [00:05, 1705741.98it/s] 9575759it [00:05, 1701572.51it/s] 9748568it [00:05, 1709347.36it/s] 9922217it [00:05, 1717459.47it/s] 10095150it [00:05, 1721002.65it/s] 10267266it [00:06, 1721012.18it/s] 10439371it [00:06, 1719938.69it/s] 10614577it [00:06, 1729551.86it/s] 10790543it [00:06, 1738564.44it/s] 10964403it [00:06, 1736901.81it/s] 11138096it [00:06, 1730677.11it/s] 11311170it [00:06, 1712974.96it/s] 11482684it [00:06, 1713607.89it/s] 11654074it [00:06, 1702959.41it/s] 11824399it [00:06, 1696150.37it/s] 11994035it [00:07, 1694212.83it/s] 12165646it [00:07, 1700722.69it/s] 12341679it [00:07, 1718461.63it/s] 12516140it [00:07, 1726204.61it/s] 12689134it [00:07, 1727310.54it/s] 12863621it [00:07, 1732548.41it/s] 13038977it [00:07, 1738798.47it/s] 13212864it [00:07, 1733252.90it/s] 13386198it [00:07, 1723600.16it/s] 13558574it [00:07, 1719089.12it/s] 13730494it [00:08, 1717442.53it/s] 13903100it [00:08, 1719891.97it/s] 14075096it [00:08, 1717139.40it/s] 14250961it [00:08, 1729532.64it/s] 14423922it [00:08, 1724068.98it/s] 14596995it [00:08, 1725922.12it/s] 14771723it [00:08, 1732298.18it/s] 14944959it [00:08, 1724686.64it/s] 15047527it [00:08, 1708963.71it/s] [W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_A23MVY2LT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_A23MVY2LT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_A23MVY2LT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_A23MVY2LT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_A23MVY2LT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_A23MVY2LT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_A23MVY2LT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_A23MVY2LT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_A23MVY2LT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_A23MVY2LT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_A23MVY2LT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_A23MVY2LT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_A23MVY2LT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_A23MVY2LT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_A23MVY2LT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_A23MVY2LT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_A23MVY2LT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_A23MVY2LT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_A23MVY2LT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_A23MVY2LT4_2.md.bai tabix -s 1 -b 2 -e 2 659_bua-T1-TRNA-1_A23MVY2LT4_2/659_bua-T1-TRNA-1_A23MVY2LT4_2.md/659_bua-T1-TRNA-1_A23MVY2LT4_2.md.depth.gz seqtool depth_hist -nbins 500 659_bua-T1-TRNA-1_A23MVY2LT4_2/659_bua-T1-TRNA-1_A23MVY2LT4_2.md/659_bua-T1-TRNA-1_A23MVY2LT4_2.md.depth.gz > 659_bua-T1-TRNA-1_A23MVY2LT4_2/659_bua-T1-TRNA-1_A23MVY2LT4_2.md/659_bua-T1-TRNA-1_A23MVY2LT4_2.md.depth_hist.tsv cat 659_bua-T1-TRNA-1_A23MVY2LT4_2/659_bua-T1-TRNA-1_A23MVY2LT4_2.md/659_bua-T1-TRNA-1_A23MVY2LT4_2.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title 659_bua-T1-TRNA-1_A23MVY2LT4_2.md -output 659_bua-T1-TRNA-1_A23MVY2LT4_2/659_bua-T1-TRNA-1_A23MVY2LT4_2.md/659_bua-T1-TRNA-1_A23MVY2LT4_2.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_bua-T1-TRNA-1_A23MVY2LT4_2.md.bam > 659_bua-T1-TRNA-1_A23MVY2LT4_2/659_bua-T1-TRNA-1_A23MVY2LT4_2.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_bua-T1-TRNA-1_A23MVY2LT4_2.md.bam > 659_bua-T1-TRNA-1_A23MVY2LT4_2/659_bua-T1-TRNA-1_A23MVY2LT4_2.md/reads_per_target.Twist_rna_exome_AND_fusion_hg38.bed.tsv seqtool depth_stats -bed Twist_rna_exome_AND_fusion_hg38.bed 659_bua-T1-TRNA-1_A23MVY2LT4_2/659_bua-T1-TRNA-1_A23MVY2LT4_2.md/659_bua-T1-TRNA-1_A23MVY2LT4_2.md.depth.gz> 659_bua-T1-TRNA-1_A23MVY2LT4_2/659_bua-T1-TRNA-1_A23MVY2LT4_2.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_bua-T1-TRNA-1_A23MVY2LT4_2.md.bam > 659_bua-T1-TRNA-1_A23MVY2LT4_2/659_bua-T1-TRNA-1_A23MVY2LT4_2.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_bua-T1-TRNA-1_A23MVY2LT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_A23MVY2LT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_A23MVY2LT4_2.md.bai cat 659_bua-T1-TRNA-1_A23MVY2LT4_2/659_bua-T1-TRNA-1_A23MVY2LT4_2.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "659_bua-T1-TRNA-1_A23MVY2LT4_2.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "659_bua-T1-TRNA-1_A23MVY2LT4_2/659_bua-T1-TRNA-1_A23MVY2LT4_2.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > 659_bua-T1-TRNA-1_A23MVY2LT4_2/659_bua-T1-TRNA-1_A23MVY2LT4_2.md/qc_complete.txt + merge_qc -folders 659_bua-T1-TRNA-1_A23MVY2LT4_2/659_bua-T1-TRNA-1_A23MVY2LT4_2.md -output 659_bua-T1-TRNA-1_A23MVY2LT4_2/659_bua-T1-TRNA-1_A23MVY2LT4_2_full_basic_stats.tsv + head -n1 659_bua-T1-TRNA-1_A23MVY2LT4_2/659_bua-T1-TRNA-1_A23MVY2LT4_2_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed 659_bua-T1-TRNA-1_A23MVY2LT4_2/659_bua-T1-TRNA-1_A23MVY2LT4_2_full_basic_stats.tsv