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/9a/9cbaae03cd53b419e6e5c234397533/.command.sh 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/50/84a17fbf8b15d10dfb1c34a2725f20/aih-tih-sc-1274d4-R1_A23YTGFLT4_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/9a/9cbaae03cd53b419e6e5c234397533/.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/50/84a17fbf8b15d10dfb1c34a2725f20/aih-tih-sc-1274d4-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-1274d4-R1_A23YTGFLT4_1 + all_qc -bam aih-tih-sc-1274d4-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-1274d4-R1_A23YTGFLT4_1 -reference ref_genome.fa -region chr20 mkdir -p aih-tih-sc-1274d4-R1_A23YTGFLT4_1/aih-tih-sc-1274d4-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-1274d4-R1_A23YTGFLT4_1/aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md/full_bed.bed seqtool depth -bam aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bam -bed aih-tih-sc-1274d4-R1_A23YTGFLT4_1/aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-1274d4-R1_A23YTGFLT4_1/aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md/aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.depth.gz saturation_plot -bams aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bam -region chr20 -output aih-tih-sc-1274d4-R1_A23YTGFLT4_1/aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-1274d4-R1_A23YTGFLT4_1/aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md/saturation_qc.tsv fragment_size -bams aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-1274d4-R1_A23YTGFLT4_1/aih-tih-sc-1274d4-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-1274d4-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.mpileup && contamination -input aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-1274d4-R1_A23YTGFLT4_1/aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-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-1274d4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-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-1274d4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bai 0it [00:00, ?it/s] 127265it [00:00, 1272508.62it/s] 262791it [00:00, 1321004.72it/s] 401821it [00:00, 1352618.84it/s] 539701it [00:00, 1362930.28it/s] 679366it [00:00, 1375069.55it/s] 818485it [00:00, 1380533.92it/s] 957167it [00:00, 1382573.17it/s] 1096375it [00:00, 1385584.24it/s] 1236602it [00:00, 1390785.16it/s] 1375681it [00:01, 1386695.30it/s] 1515553it [00:01, 1390354.12it/s] 1654592it [00:01, 1379045.35it/s] 1793276it [00:01, 1381374.37it/s] 1931430it [00:01, 1378652.75it/s] 2071434it [00:01, 1384967.72it/s] 2216040it [00:01, 1403279.68it/s] 2357319it [00:01, 1406115.04it/s] 2497941it [00:01, 1399657.82it/s] 2637920it [00:01, 1392169.44it/s] 2777153it [00:02, 1384199.46it/s] 2918478it [00:02, 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1374888.81it/s] 11192373it [00:08, 1384014.87it/s] 11331250it [00:08, 1385417.01it/s] 11471895it [00:08, 1391682.38it/s] 11611123it [00:08, 1382986.64it/s] 11751559it [00:08, 1389332.67it/s] 11891592it [00:08, 1392596.00it/s] 12035744it [00:08, 1407210.24it/s] 12177411it [00:08, 1410026.91it/s] 12320748it [00:08, 1416873.15it/s] 12462450it [00:08, 1410005.51it/s] 12603739it [00:09, 1410849.48it/s] 12745074it [00:09, 1411579.67it/s] 12888449it [00:09, 1418202.97it/s] 13030277it [00:09, 1415761.32it/s] 13173081it [00:09, 1419420.81it/s] 13315028it [00:09, 1409092.59it/s] 13456767it [00:09, 1411548.67it/s] 13600905it [00:09, 1420444.18it/s] 13742964it [00:09, 1420138.83it/s] 13884988it [00:09, 1416003.43it/s] 14026598it [00:10, 1413609.97it/s] 14167966it [00:10, 1409862.02it/s] 14308958it [00:10, 1407555.59it/s] 14449718it [00:10, 1403398.52it/s] 14590062it [00:10, 1390694.51it/s] 14729155it [00:10, 1142445.29it/s] 14850615it [00:10, 1081685.20it/s] 14988825it [00:10, 1158564.45it/s] 15127350it [00:10, 1219247.05it/s] 15266040it [00:11, 1265618.95it/s] 15404699it [00:11, 1299870.27it/s] 15544534it [00:11, 1328153.91it/s] 15684202it [00:11, 1348119.79it/s] 15824259it [00:11, 1363521.13it/s] 15963472it [00:11, 1371970.29it/s] 16103413it [00:11, 1380102.82it/s] 16244125it [00:11, 1388138.37it/s] 16384103it [00:11, 1391599.38it/s] 16524472it [00:11, 1395199.64it/s] 16664172it [00:12, 1395673.12it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bai 16804401it [00:12, 1397544.41it/s] 16944244it [00:12, 1372016.64it/s] 17081610it [00:12, 1359154.72it/s] 17223084it [00:12, 1375542.40it/s] 17362208it [00:12, 1380182.63it/s] 17504898it [00:12, 1394068.73it/s] 17646689it [00:12, 1401165.45it/s] 17786861it [00:12, 1401279.63it/s] 17927028it [00:12, 1401093.03it/s] 18068037it [00:13, 1403617.41it/s] 18208418it [00:13, 1331393.12it/s] 18342337it [00:13, 1318523.19it/s] 18481728it [00:13, 1340186.47it/s] 18578339it [00:13, 1379157.70it/s] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bai tabix -s 1 -b 2 -e 2 aih-tih-sc-1274d4-R1_A23YTGFLT4_1/aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md/aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.depth.gz seqtool depth_hist -nbins 500 aih-tih-sc-1274d4-R1_A23YTGFLT4_1/aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md/aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.depth.gz > aih-tih-sc-1274d4-R1_A23YTGFLT4_1/aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md/aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.depth_hist.tsv cat aih-tih-sc-1274d4-R1_A23YTGFLT4_1/aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md/aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md -output aih-tih-sc-1274d4-R1_A23YTGFLT4_1/aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md/aih-tih-sc-1274d4-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-1274d4-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-1274d4-R1_A23YTGFLT4_1/aih-tih-sc-1274d4-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-1274d4-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-1274d4-R1_A23YTGFLT4_1/aih-tih-sc-1274d4-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-1274d4-R1_A23YTGFLT4_1/aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md/aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.depth.gz> aih-tih-sc-1274d4-R1_A23YTGFLT4_1/aih-tih-sc-1274d4-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-1274d4-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-1274d4-R1_A23YTGFLT4_1/aih-tih-sc-1274d4-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-1274d4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md.bai cat aih-tih-sc-1274d4-R1_A23YTGFLT4_1/aih-tih-sc-1274d4-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-1274d4-R1_A23YTGFLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "aih-tih-sc-1274d4-R1_A23YTGFLT4_1/aih-tih-sc-1274d4-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-1274d4-R1_A23YTGFLT4_1/aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md/qc_complete.txt + merge_qc -folders aih-tih-sc-1274d4-R1_A23YTGFLT4_1/aih-tih-sc-1274d4-R1_A23YTGFLT4_1.md -output aih-tih-sc-1274d4-R1_A23YTGFLT4_1/aih-tih-sc-1274d4-R1_A23YTGFLT4_1_full_basic_stats.tsv + head -n1 aih-tih-sc-1274d4-R1_A23YTGFLT4_1/aih-tih-sc-1274d4-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-1274d4-R1_A23YTGFLT4_1/aih-tih-sc-1274d4-R1_A23YTGFLT4_1_full_basic_stats.tsv