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/62/912696f7c7b7d8bb92af09f941fda6/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/97/e022725fae0ac381fef6ce03b50cb6/aih-tih-sc-318819-R1_A23YTGFLT4_1.md.bai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/97/e022725fae0ac381fef6ce03b50cb6/aih-tih-sc-318819-R1_A23YTGFLT4_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/62/912696f7c7b7d8bb92af09f941fda6/.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 aih-tih-sc-318819-R1_A23YTGFLT4_1 + all_qc -bam aih-tih-sc-318819-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-318819-R1_A23YTGFLT4_1 -reference ref_genome.fa -region chr20 mkdir -p aih-tih-sc-318819-R1_A23YTGFLT4_1/aih-tih-sc-318819-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-318819-R1_A23YTGFLT4_1/aih-tih-sc-318819-R1_A23YTGFLT4_1.md/full_bed.bed seqtool depth -bam aih-tih-sc-318819-R1_A23YTGFLT4_1.md.bam -bed aih-tih-sc-318819-R1_A23YTGFLT4_1/aih-tih-sc-318819-R1_A23YTGFLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-318819-R1_A23YTGFLT4_1/aih-tih-sc-318819-R1_A23YTGFLT4_1.md/aih-tih-sc-318819-R1_A23YTGFLT4_1.md.depth.gz saturation_plot -bams aih-tih-sc-318819-R1_A23YTGFLT4_1.md.bam -region chr20 -output aih-tih-sc-318819-R1_A23YTGFLT4_1/aih-tih-sc-318819-R1_A23YTGFLT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-318819-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-318819-R1_A23YTGFLT4_1/aih-tih-sc-318819-R1_A23YTGFLT4_1.md/saturation_qc.tsv fragment_size -bams aih-tih-sc-318819-R1_A23YTGFLT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-318819-R1_A23YTGFLT4_1/aih-tih-sc-318819-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-318819-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-318819-R1_A23YTGFLT4_1.md.mpileup && contamination -input aih-tih-sc-318819-R1_A23YTGFLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-318819-R1_A23YTGFLT4_1/aih-tih-sc-318819-R1_A23YTGFLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-318819-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-318819-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-318819-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-318819-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-318819-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-318819-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-318819-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-318819-R1_A23YTGFLT4_1.md.bai 0it [00:00, ?it/s] 129681it [00:00, 1296755.59it/s] 269960it [00:00, 1359092.24it/s] 411218it [00:00, 1383494.82it/s] 554460it [00:00, 1402623.86it/s] 697469it [00:00, 1412474.42it/s] 840154it [00:00, 1417319.64it/s] 983248it [00:00, 1421757.03it/s] 1128152it [00:00, 1430428.41it/s] 1271195it [00:00, 1429697.30it/s] 1414165it [00:01, 1425312.93it/s] 1557185it [00:01, 1426792.99it/s] 1699899it [00:01, 1426883.29it/s] 1842589it [00:01, 1422700.26it/s] 1985830it [00:01, 1425612.78it/s] 2128602it [00:01, 1426236.86it/s] 2271229it [00:01, 1425674.07it/s] 2416837it [00:01, 1434689.85it/s] 2562965it [00:01, 1442660.38it/s] 2707234it [00:01, 1440641.87it/s] 2851301it [00:02, 1424219.93it/s] 2993765it [00:02, 1422279.51it/s] 3139051it [00:02, 1431370.95it/s] 3283886it [00:02, 1436426.90it/s] 3427550it [00:02, 1432267.46it/s] 3570793it [00:02, 1424379.90it/s] 3713250it [00:02, 1424422.77it/s] 3855705it [00:02, 1423912.88it/s] 3998105it [00:02, 1416952.10it/s] 4140310it [00:02, 1418461.54it/s] 4283993it [00:03, 1423856.83it/s] 4426388it [00:03, 1422651.48it/s] 4568659it [00:03, 1414150.69it/s] 4710298it [00:03, 1414806.72it/s] 4853734it [00:03, 1420635.84it/s] 4996587it [00:03, 1422985.19it/s] 5140143it [00:03, 1426736.83it/s] 5283329it [00:03, 1428260.68it/s] 5426160it [00:03, 1424288.66it/s] 5570004it [00:03, 1428363.09it/s] 5712845it [00:04, 1421438.02it/s] 5854999it [00:04, 1419491.42it/s] 5997586it [00:04, 1421332.35it/s] 6140718it [00:04, 1424308.71it/s] 6285101it [00:04, 1430089.64it/s] 6428115it [00:04, 1430016.28it/s] 6571274it [00:04, 1430474.99it/s] 6714622it [00:04, 1431208.44it/s] 6857745it [00:04, 1426617.27it/s] 7002160it [00:04, 1431850.04it/s] 7146200it [00:05, 1434308.19it/s] 7290285it [00:05, 1436219.20it/s] 7433910it [00:05, 1435809.22it/s] 7577493it [00:05, 1435491.70it/s] 7721044it [00:05, 1433828.28it/s] 7864916it [00:05, 1435280.88it/s] 8008446it [00:05, 1431704.30it/s] 8151619it [00:05, 1426814.48it/s] 8294305it [00:05, 1426689.25it/s] 8438133it [00:05, 1430143.42it/s] 8582588it [00:06, 1434442.56it/s] 8727018it [00:06, 1437383.59it/s] 8870907it [00:06, 1437734.79it/s] 9015598it [00:06, 1440473.30it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-318819-R1_A23YTGFLT4_1.md.bai 9159647it [00:06, 1439888.91it/s] 9303716it [00:06, 1440117.14it/s] 9447729it [00:06, 1419094.12it/s] 9589708it [00:06, 1408421.98it/s] 9732409it [00:06, 1413907.47it/s] 9875273it [00:06, 1418275.79it/s] 10017137it [00:07, 1417258.61it/s] 10158888it [00:07, 1416607.16it/s] 10300566it [00:07, 1415978.22it/s] 10442176it [00:07, 1412505.84it/s] 10584355it [00:07, 1415267.63it/s] 10726909it [00:07, 1418331.27it/s] 10869928it [00:07, 1421869.32it/s] 11012120it [00:07, 1421255.49it/s] 11155879it [00:07, 1426139.94it/s] 11300828it [00:07, 1433125.90it/s] 11444317it [00:08, 1433643.94it/s] 11589054it [00:08, 1437605.15it/s] 11732816it [00:08, 1434610.81it/s] 11876688it [00:08, 1435829.54it/s] 11890005it [00:08, 1425550.91it/s] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-318819-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-318819-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-318819-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-318819-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-318819-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-318819-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-318819-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-318819-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-318819-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-318819-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-318819-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-318819-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-318819-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-318819-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-318819-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-318819-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-318819-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-318819-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-318819-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-318819-R1_A23YTGFLT4_1.md.bai tabix -s 1 -b 2 -e 2 aih-tih-sc-318819-R1_A23YTGFLT4_1/aih-tih-sc-318819-R1_A23YTGFLT4_1.md/aih-tih-sc-318819-R1_A23YTGFLT4_1.md.depth.gz seqtool depth_hist -nbins 500 aih-tih-sc-318819-R1_A23YTGFLT4_1/aih-tih-sc-318819-R1_A23YTGFLT4_1.md/aih-tih-sc-318819-R1_A23YTGFLT4_1.md.depth.gz > aih-tih-sc-318819-R1_A23YTGFLT4_1/aih-tih-sc-318819-R1_A23YTGFLT4_1.md/aih-tih-sc-318819-R1_A23YTGFLT4_1.md.depth_hist.tsv cat aih-tih-sc-318819-R1_A23YTGFLT4_1/aih-tih-sc-318819-R1_A23YTGFLT4_1.md/aih-tih-sc-318819-R1_A23YTGFLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-318819-R1_A23YTGFLT4_1.md -output aih-tih-sc-318819-R1_A23YTGFLT4_1/aih-tih-sc-318819-R1_A23YTGFLT4_1.md/aih-tih-sc-318819-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-318819-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-318819-R1_A23YTGFLT4_1/aih-tih-sc-318819-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-318819-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-318819-R1_A23YTGFLT4_1/aih-tih-sc-318819-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-318819-R1_A23YTGFLT4_1/aih-tih-sc-318819-R1_A23YTGFLT4_1.md/aih-tih-sc-318819-R1_A23YTGFLT4_1.md.depth.gz> aih-tih-sc-318819-R1_A23YTGFLT4_1/aih-tih-sc-318819-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-318819-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-318819-R1_A23YTGFLT4_1/aih-tih-sc-318819-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-318819-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-318819-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-318819-R1_A23YTGFLT4_1.md.bai cat aih-tih-sc-318819-R1_A23YTGFLT4_1/aih-tih-sc-318819-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-318819-R1_A23YTGFLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "aih-tih-sc-318819-R1_A23YTGFLT4_1/aih-tih-sc-318819-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-318819-R1_A23YTGFLT4_1/aih-tih-sc-318819-R1_A23YTGFLT4_1.md/qc_complete.txt + merge_qc -folders aih-tih-sc-318819-R1_A23YTGFLT4_1/aih-tih-sc-318819-R1_A23YTGFLT4_1.md -output aih-tih-sc-318819-R1_A23YTGFLT4_1/aih-tih-sc-318819-R1_A23YTGFLT4_1_full_basic_stats.tsv + head -n1 aih-tih-sc-318819-R1_A23YTGFLT4_1/aih-tih-sc-318819-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-318819-R1_A23YTGFLT4_1/aih-tih-sc-318819-R1_A23YTGFLT4_1_full_basic_stats.tsv