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/43/c611db9d24bad4e6d774fd4e2f8f1b/.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/99/31d014da57bf3d6810accc6e29f56a/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bam Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/43/c611db9d24bad4e6d774fd4e2f8f1b/.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/99/31d014da57bf3d6810accc6e29f56a/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_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 aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1 + all_qc -bam aih-tih-sc-2b9bfa-R1_A23YTGFLT4_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 aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1 -reference ref_genome.fa -region chr20 mkdir -p aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md/ cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md/full_bed.bed seqtool depth -bam aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bam -bed aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.depth.gz saturation_plot -bams aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bam -region chr20 -output aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md/saturation_qc.tsv fragment_size -bams aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md/fragsize -threads 1 samtools mpileup -B --min-MQ 60 --min-BQ 30 -f ref_genome.fa -l dbsnp_hg38_contam_sites.bed aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.mpileup && contamination -input aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai [mpileup] 1 samples in 1 input files [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_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: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai 0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai 151442it [00:00, 1514255.37it/s] 317022it [00:00, 1597451.36it/s] 485743it [00:00, 1638387.74it/s] 655721it [00:00, 1662580.44it/s] 825323it [00:00, 1674597.26it/s] 995207it [00:00, 1682799.06it/s] 1164906it [00:00, 1687399.26it/s] 1336202it [00:00, 1695498.10it/s] 1508990it [00:00, 1705586.87it/s] 1679549it [00:01, 1702396.98it/s] 1849791it [00:01, 1690794.41it/s] 2020725it [00:01, 1696370.37it/s] 2192214it [00:01, 1701926.95it/s] 2362982it [00:01, 1703585.66it/s] 2533350it [00:01, 1697068.38it/s] 2706634it [00:01, 1707762.97it/s] 2883317it [00:01, 1725437.02it/s] 3055875it [00:01, 1720833.34it/s] 3227970it [00:01, 1713970.69it/s] 3399380it [00:02, 1691575.01it/s] 3572683it [00:02, 1703703.65it/s] 3743114it [00:02, 1700301.31it/s] 3913185it [00:02, 1693458.32it/s] 4082561it [00:02, 1691657.20it/s] 4253857it [00:02, 1697969.60it/s] 4424084it [00:02, 1699216.80it/s] 4595264it [00:02, 1702941.24it/s] 4765569it [00:02, 1682571.39it/s] 4936601it [00:02, 1690773.69it/s] 5107696it [00:03, 1696667.59it/s] 5279279it [00:03, 1702355.43it/s] 5450037it [00:03, 1703881.36it/s] 5621256it [00:03, 1706330.53it/s] 5791905it [00:03, 1705450.89it/s] 5962461it [00:03, 1697784.09it/s] 6132871it [00:03, 1699637.33it/s] 6302846it [00:03, 1692612.99it/s] 6474722it [00:03, 1700379.47it/s] 6644773it [00:03, 1698355.13it/s] 6814618it [00:04, 1687461.18it/s] 6983452it [00:04, 1687685.14it/s] 7153895it [00:04, 1692647.57it/s] 7323423it [00:04, 1693398.89it/s] 7494494it [00:04, 1698548.79it/s] 7665842it [00:04, 1702985.83it/s] 7836147it [00:04, 1701404.75it/s] 8007407it [00:04, 1704724.70it/s] 8179065it [00:04, 1708241.39it/s] 8351175it [00:04, 1712062.28it/s] 8522936it [00:05, 1713689.43it/s] 8694307it [00:05, 1712738.48it/s] 8865583it [00:05, 1711547.74it/s] 9036739it [00:05, 1699673.72it/s] 9207191it [00:05, 1701074.06it/s] 9377313it [00:05, 1697897.95it/s] 9547618it [00:05, 1699401.46it/s] 9719789it [00:05, 1706037.66it/s] 9891713it [00:05, 1709957.90it/s] 10064577it [00:05, 1715514.59it/s] 10236134it [00:06, 1713353.76it/s] 10410635it [00:06, 1722800.26it/s] 10582920it [00:06, 1718876.10it/s] 10754813it [00:06, 1716084.94it/s] 10926426it [00:06, 1714146.43it/s] 11097844it [00:06, 1709296.03it/s] 11268778it [00:06, 1699342.02it/s] 11441898it [00:06, 1708799.38it/s] 11613440it [00:06, 1710632.82it/s] 11784515it [00:06, 1710609.82it/s] 11955584it [00:07, 1709376.82it/s] 12126528it [00:07, 1706321.39it/s] 12297165it [00:07, 1703799.02it/s] 12467549it [00:07, 1701545.17it/s] 12639009it [00:07, 1705414.94it/s] 12810453it [00:07, 1708078.13it/s] 12983497it [00:07, 1714748.84it/s] 13154975it [00:07, 1710136.33it/s] 13325993it [00:07, 1708716.40it/s] 13496868it [00:07, 1704663.28it/s] 13508536it [00:07, 1700660.67it/s] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai tabix -s 1 -b 2 -e 2 aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.depth.gz seqtool depth_hist -nbins 500 aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.depth.gz > aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.depth_hist.tsv cat aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md -output aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_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 aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_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 aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md/reads_per_target.Twist_rna_exome_AND_fusion_hg38.bed.tsv seqtool depth_stats -bed Twist_rna_exome_AND_fusion_hg38.bed aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.depth.gz> aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_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 aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_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: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bai cat aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md/qc_complete.txt + merge_qc -folders aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md -output aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1_full_basic_stats.tsv + head -n1 aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1_full_basic_stats.tsv