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/54/c4544dca98748c1a6ab0262a46b0be/.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/a3/83249b178d76b14274cb018dfecf28/aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/54/c4544dca98748c1a6ab0262a46b0be/.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-rnd-pltf-dev-nextflow-scratch-01/work/a3/83249b178d76b14274cb018dfecf28/aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bam Downloading: s3://natera-platform-sandbox/pipeline-resources/Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi ==> STAGING COMPLETE (11 inputs) + mkdir aih-tih-sc-242a7d-R1_A23YTGFLT4_1 + all_qc -bam aih-tih-sc-242a7d-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-242a7d-R1_A23YTGFLT4_1 -reference ref_genome.fa -region chr20 mkdir -p aih-tih-sc-242a7d-R1_A23YTGFLT4_1/aih-tih-sc-242a7d-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-242a7d-R1_A23YTGFLT4_1/aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md/full_bed.bed seqtool depth -bam aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bam -bed aih-tih-sc-242a7d-R1_A23YTGFLT4_1/aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-242a7d-R1_A23YTGFLT4_1/aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md/aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.depth.gz saturation_plot -bams aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bam -region chr20 -output aih-tih-sc-242a7d-R1_A23YTGFLT4_1/aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-242a7d-R1_A23YTGFLT4_1/aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md/saturation_qc.tsv fragment_size -bams aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-242a7d-R1_A23YTGFLT4_1/aih-tih-sc-242a7d-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-242a7d-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.mpileup && contamination -input aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-242a7d-R1_A23YTGFLT4_1/aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-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-242a7d-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-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-242a7d-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bai 0it [00:00, ?it/s] 144180it [00:00, 1441674.20it/s] 305382it [00:00, 1541831.63it/s] 470161it [00:00, 1590177.12it/s] 631140it [00:00, 1597891.82it/s] 805374it [00:00, 1649949.93it/s] 981964it [00:00, 1689344.88it/s] 1158188it [00:00, 1713084.96it/s] 1338491it [00:00, 1741695.55it/s] 1516978it [00:00, 1755094.30it/s] 1692598it [00:01, 1755411.60it/s] 1870536it [00:01, 1762722.80it/s] 2046809it [00:01, 1724390.02it/s] 2223822it [00:01, 1738012.57it/s] 2402739it [00:01, 1753275.51it/s] 2579899it [00:01, 1758602.45it/s] 2757649it [00:01, 1764239.35it/s] 2935649it [00:01, 1768932.26it/s] 3115012it [00:01, 1776306.69it/s] 3292678it [00:01, 1763618.69it/s] 3469083it [00:02, 1754572.57it/s] 3644576it [00:02, 1700044.88it/s] 3820976it [00:02, 1718563.80it/s] 3995467it [00:02, 1726283.16it/s] 4174125it [00:02, 1744100.00it/s] 4350269it [00:02, 1749200.75it/s] 4525323it [00:02, 1732723.28it/s] 4698715it [00:02, 1731073.83it/s] 4871905it [00:02, 1703170.55it/s] 5042359it [00:02, 1701551.67it/s] 5212608it [00:03, 1678436.89it/s] 5382295it [00:03, 1683826.13it/s] 5558517it [00:03, 1706986.89it/s] 5729308it [00:03, 1700743.56it/s] 5902592it [00:03, 1710237.85it/s] 6080035it [00:03, 1729325.12it/s] 6253018it [00:03, 1706492.56it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bai 6426805it [00:03, 1715764.03it/s] 6599326it [00:03, 1718518.50it/s] 6771235it [00:03, 1699956.30it/s] 6941306it [00:04, 1699813.80it/s] 7111693it [00:04, 1700999.00it/s] 7285945it [00:04, 1713240.65it/s] 7462409it [00:04, 1728570.29it/s] 7639362it [00:04, 1740747.21it/s] 7814624it [00:04, 1744263.33it/s] 7993114it [00:04, 1756407.53it/s] 8173069it [00:04, 1769311.62it/s] 8351598it [00:04, 1773940.98it/s] 8531595it [00:04, 1781648.75it/s] 8713290it [00:05, 1792210.48it/s] 8892516it [00:05, 1791092.45it/s] 9071629it [00:05, 1786499.55it/s] 9250284it [00:05, 1756519.96it/s] 9426047it [00:05, 1735138.32it/s] 9603288it [00:05, 1746089.09it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bai 9781987it [00:05, 1758164.13it/s] 9959335it [00:05, 1762692.04it/s] 10136321it [00:05, 1764735.33it/s] 10313602it [00:05, 1767119.77it/s] 10493989it [00:06, 1778085.49it/s] 10671824it [00:06, 1742969.60it/s] 10849985it [00:06, 1754222.31it/s] 11029130it [00:06, 1765245.19it/s] 11209258it [00:06, 1775918.77it/s] 11388276it [00:06, 1780149.13it/s] 11556068it [00:06, 1735326.47it/s] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bai tabix -s 1 -b 2 -e 2 aih-tih-sc-242a7d-R1_A23YTGFLT4_1/aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md/aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.depth.gz seqtool depth_hist -nbins 500 aih-tih-sc-242a7d-R1_A23YTGFLT4_1/aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md/aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.depth.gz > aih-tih-sc-242a7d-R1_A23YTGFLT4_1/aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md/aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.depth_hist.tsv cat aih-tih-sc-242a7d-R1_A23YTGFLT4_1/aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md/aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md -output aih-tih-sc-242a7d-R1_A23YTGFLT4_1/aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md/aih-tih-sc-242a7d-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-242a7d-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-242a7d-R1_A23YTGFLT4_1/aih-tih-sc-242a7d-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-242a7d-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-242a7d-R1_A23YTGFLT4_1/aih-tih-sc-242a7d-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-242a7d-R1_A23YTGFLT4_1/aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md/aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.depth.gz> aih-tih-sc-242a7d-R1_A23YTGFLT4_1/aih-tih-sc-242a7d-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-242a7d-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-242a7d-R1_A23YTGFLT4_1/aih-tih-sc-242a7d-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-242a7d-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md.bai cat aih-tih-sc-242a7d-R1_A23YTGFLT4_1/aih-tih-sc-242a7d-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-242a7d-R1_A23YTGFLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "aih-tih-sc-242a7d-R1_A23YTGFLT4_1/aih-tih-sc-242a7d-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-242a7d-R1_A23YTGFLT4_1/aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md/qc_complete.txt + merge_qc -folders aih-tih-sc-242a7d-R1_A23YTGFLT4_1/aih-tih-sc-242a7d-R1_A23YTGFLT4_1.md -output aih-tih-sc-242a7d-R1_A23YTGFLT4_1/aih-tih-sc-242a7d-R1_A23YTGFLT4_1_full_basic_stats.tsv + head -n1 aih-tih-sc-242a7d-R1_A23YTGFLT4_1/aih-tih-sc-242a7d-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-242a7d-R1_A23YTGFLT4_1/aih-tih-sc-242a7d-R1_A23YTGFLT4_1_full_basic_stats.tsv