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/ac/76534499db58ae8eaa81d88da3d3d3/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/67/e00c42f8a68df19dbf51d6f8de308b/aih-tih-sc-1ba302-R1_B23WHYVLT4_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/67/e00c42f8a68df19dbf51d6f8de308b/aih-tih-sc-1ba302-R1_B23WHYVLT4_1.md.bai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ac/76534499db58ae8eaa81d88da3d3d3/.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-1ba302-R1_B23WHYVLT4_1 + all_qc -bam aih-tih-sc-1ba302-R1_B23WHYVLT4_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-1ba302-R1_B23WHYVLT4_1 -reference ref_genome.fa -region chr20 mkdir -p aih-tih-sc-1ba302-R1_B23WHYVLT4_1/aih-tih-sc-1ba302-R1_B23WHYVLT4_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-1ba302-R1_B23WHYVLT4_1/aih-tih-sc-1ba302-R1_B23WHYVLT4_1.md/full_bed.bed seqtool depth -bam aih-tih-sc-1ba302-R1_B23WHYVLT4_1.md.bam -bed aih-tih-sc-1ba302-R1_B23WHYVLT4_1/aih-tih-sc-1ba302-R1_B23WHYVLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-1ba302-R1_B23WHYVLT4_1/aih-tih-sc-1ba302-R1_B23WHYVLT4_1.md/aih-tih-sc-1ba302-R1_B23WHYVLT4_1.md.depth.gz saturation_plot -bams aih-tih-sc-1ba302-R1_B23WHYVLT4_1.md.bam -region chr20 -output aih-tih-sc-1ba302-R1_B23WHYVLT4_1/aih-tih-sc-1ba302-R1_B23WHYVLT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-1ba302-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-1ba302-R1_B23WHYVLT4_1/aih-tih-sc-1ba302-R1_B23WHYVLT4_1.md/saturation_qc.tsv fragment_size -bams aih-tih-sc-1ba302-R1_B23WHYVLT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-1ba302-R1_B23WHYVLT4_1/aih-tih-sc-1ba302-R1_B23WHYVLT4_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-1ba302-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-1ba302-R1_B23WHYVLT4_1.md.mpileup && contamination -input aih-tih-sc-1ba302-R1_B23WHYVLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-1ba302-R1_B23WHYVLT4_1/aih-tih-sc-1ba302-R1_B23WHYVLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1ba302-R1_B23WHYVLT4_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-1ba302-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1ba302-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1ba302-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1ba302-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1ba302-R1_B23WHYVLT4_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-1ba302-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1ba302-R1_B23WHYVLT4_1.md.bai 0it [00:00, ?it/s] 144858it [00:00, 1448505.40it/s] 295849it [00:00, 1484592.51it/s] 444309it [00:00, 1484554.56it/s] 601030it [00:00, 1517141.29it/s] 755448it [00:00, 1526868.17it/s] 912851it [00:00, 1542881.90it/s] 1068406it [00:00, 1547003.25it/s] 1228746it [00:00, 1564937.01it/s] 1386963it [00:00, 1570308.23it/s] 1543994it [00:01, 1568893.52it/s] 1704495it [00:01, 1579806.72it/s] 1862477it [00:01, 1400533.33it/s] 2006220it [00:01, 1119615.78it/s] 2128917it [00:01, 1001258.91it/s] 2237710it [00:01, 927902.17it/s] 2336537it [00:01, 931495.68it/s] 2463775it [00:01, 1015136.01it/s] 2570934it [00:02, 1029634.51it/s] 2700309it [00:02, 1101057.68it/s] 2821749it [00:02, 1132634.60it/s] 2969593it [00:02, 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1381066.61it/s] 7488591it [00:05, 1384040.62it/s] 7629031it [00:05, 1390006.29it/s] 7768091it [00:05, 1387132.82it/s] 7908599it [00:05, 1392347.72it/s] 8047866it [00:05, 1390484.27it/s] 8188547it [00:05, 1395342.94it/s] 8329147it [00:06, 1398378.57it/s] 8470513it [00:06, 1402935.64it/s] 8612020it [00:06, 1406552.27it/s] 8754886it [00:06, 1413159.10it/s] 8896209it [00:06, 1410892.88it/s] 9038774it [00:06, 1415294.66it/s] 9180763it [00:06, 1416654.80it/s] 9322432it [00:06, 1412613.55it/s] 9463698it [00:06, 1410324.84it/s] 9604734it [00:06, 1404710.92it/s] 9745212it [00:07, 1393459.80it/s] 9884578it [00:07, 1377195.54it/s] 10024196it [00:07, 1382784.10it/s] 10164923it [00:07, 1389987.20it/s] 10305607it [00:07, 1394987.13it/s] 10446316it [00:07, 1398579.06it/s] 10587034it [00:07, 1401131.57it/s] 10727655it [00:07, 1402632.66it/s] 10869134it [00:07, 1406254.74it/s] 11009769it [00:07, 1403362.37it/s] 11150113it [00:08, 1400869.89it/s] 11292113it [00:08, 1406573.71it/s] 11433139it [00:08, 1407658.66it/s] 11575272it [00:08, 1411609.41it/s] 11716437it [00:08, 1393490.53it/s] 11857361it [00:08, 1398151.76it/s] 11998771it [00:08, 1402885.82it/s] 12117820it [00:08, 1392742.64it/s] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1ba302-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1ba302-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1ba302-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1ba302-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1ba302-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1ba302-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1ba302-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1ba302-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1ba302-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1ba302-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1ba302-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1ba302-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1ba302-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1ba302-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1ba302-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1ba302-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1ba302-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1ba302-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1ba302-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1ba302-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1ba302-R1_B23WHYVLT4_1.md.bai tabix -s 1 -b 2 -e 2 aih-tih-sc-1ba302-R1_B23WHYVLT4_1/aih-tih-sc-1ba302-R1_B23WHYVLT4_1.md/aih-tih-sc-1ba302-R1_B23WHYVLT4_1.md.depth.gz seqtool depth_hist -nbins 500 aih-tih-sc-1ba302-R1_B23WHYVLT4_1/aih-tih-sc-1ba302-R1_B23WHYVLT4_1.md/aih-tih-sc-1ba302-R1_B23WHYVLT4_1.md.depth.gz > aih-tih-sc-1ba302-R1_B23WHYVLT4_1/aih-tih-sc-1ba302-R1_B23WHYVLT4_1.md/aih-tih-sc-1ba302-R1_B23WHYVLT4_1.md.depth_hist.tsv cat aih-tih-sc-1ba302-R1_B23WHYVLT4_1/aih-tih-sc-1ba302-R1_B23WHYVLT4_1.md/aih-tih-sc-1ba302-R1_B23WHYVLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-1ba302-R1_B23WHYVLT4_1.md -output aih-tih-sc-1ba302-R1_B23WHYVLT4_1/aih-tih-sc-1ba302-R1_B23WHYVLT4_1.md/aih-tih-sc-1ba302-R1_B23WHYVLT4_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-1ba302-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-1ba302-R1_B23WHYVLT4_1/aih-tih-sc-1ba302-R1_B23WHYVLT4_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-1ba302-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-1ba302-R1_B23WHYVLT4_1/aih-tih-sc-1ba302-R1_B23WHYVLT4_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-1ba302-R1_B23WHYVLT4_1/aih-tih-sc-1ba302-R1_B23WHYVLT4_1.md/aih-tih-sc-1ba302-R1_B23WHYVLT4_1.md.depth.gz> aih-tih-sc-1ba302-R1_B23WHYVLT4_1/aih-tih-sc-1ba302-R1_B23WHYVLT4_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-1ba302-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-1ba302-R1_B23WHYVLT4_1/aih-tih-sc-1ba302-R1_B23WHYVLT4_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-1ba302-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1ba302-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-1ba302-R1_B23WHYVLT4_1.md.bai cat aih-tih-sc-1ba302-R1_B23WHYVLT4_1/aih-tih-sc-1ba302-R1_B23WHYVLT4_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-1ba302-R1_B23WHYVLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "aih-tih-sc-1ba302-R1_B23WHYVLT4_1/aih-tih-sc-1ba302-R1_B23WHYVLT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > aih-tih-sc-1ba302-R1_B23WHYVLT4_1/aih-tih-sc-1ba302-R1_B23WHYVLT4_1.md/qc_complete.txt + merge_qc -folders aih-tih-sc-1ba302-R1_B23WHYVLT4_1/aih-tih-sc-1ba302-R1_B23WHYVLT4_1.md -output aih-tih-sc-1ba302-R1_B23WHYVLT4_1/aih-tih-sc-1ba302-R1_B23WHYVLT4_1_full_basic_stats.tsv + head -n1 aih-tih-sc-1ba302-R1_B23WHYVLT4_1/aih-tih-sc-1ba302-R1_B23WHYVLT4_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-1ba302-R1_B23WHYVLT4_1/aih-tih-sc-1ba302-R1_B23WHYVLT4_1_full_basic_stats.tsv