Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f3/67ec575eab1b85319d951586af5c3e/aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bai 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/3c/0bb5aa371672e6a7bf55c63c76772a/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f3/67ec575eab1b85319d951586af5c3e/aih-tih-sc-4f4d6e-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/3c/0bb5aa371672e6a7bf55c63c76772a/.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-4f4d6e-R1_B23WHYVLT4_1 + all_qc -bam aih-tih-sc-4f4d6e-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-4f4d6e-R1_B23WHYVLT4_1 -reference ref_genome.fa -region chr20 mkdir -p aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1/aih-tih-sc-4f4d6e-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-4f4d6e-R1_B23WHYVLT4_1/aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md/full_bed.bed saturation_plot -bams aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bam -region chr20 -output aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1/aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md/saturation_plot.png -threads 1 seqtool depth -bam aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bam -bed aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1/aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1/aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md/aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.depth.gz seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1/aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md/saturation_qc.tsv fragment_size -bams aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1/aih-tih-sc-4f4d6e-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-4f4d6e-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.mpileup && contamination -input aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1/aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-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-4f4d6e-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-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-4f4d6e-R1_B23WHYVLT4_1.md.bai 0it [00:00, ?it/s] 121358it [00:00, 1213101.04it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bai 246414it [00:00, 1235101.66it/s] 382958it [00:00, 1294583.21it/s] 517556it [00:00, 1314845.84it/s] 649042it [00:00, 1303104.12it/s] 779506it [00:00, 1303600.52it/s] 909879it [00:00, 1301213.69it/s] 1040009it [00:00, 1263481.73it/s] 1166571it [00:00, 1235272.16it/s] 1290322it [00:01, 1213419.94it/s] 1411840it [00:01, 1206323.12it/s] 1535895it [00:01, 1216415.76it/s] 1657641it [00:01, 1211074.91it/s] 1785342it [00:01, 1230625.59it/s] 1919160it [00:01, 1262626.78it/s] 2051013it [00:01, 1279290.15it/s] 2180834it [00:01, 1284926.10it/s] 2314610it [00:01, 1300715.62it/s] 2445097it [00:01, 1301777.85it/s] 2577087it [00:02, 1307187.70it/s] 2711532it [00:02, 1318204.12it/s] 2843372it [00:02, 1317866.68it/s] 2978149it [00:02, 1326732.72it/s] 3112761it [00:02, 1332528.79it/s] 3246022it [00:02, 1290519.39it/s] 3375901it [00:02, 1292920.51it/s] 3505403it [00:02, 1279338.28it/s] 3633497it [00:02, 1234893.92it/s] 3757365it [00:02, 1192175.34it/s] 3877036it [00:03, 1138663.64it/s] 3991513it [00:03, 1104063.19it/s] 4102374it [00:03, 1075627.72it/s] 4210238it [00:03, 1060160.51it/s] 4327688it [00:03, 1092377.43it/s] 4458247it [00:03, 1153596.39it/s] 4574099it [00:03, 1118026.95it/s] 4686402it [00:03, 1094157.91it/s] 4813844it [00:03, 1145661.61it/s] 4946010it [00:04, 1196685.65it/s] 5071892it [00:04, 1214865.61it/s] 5195974it [00:04, 1222492.54it/s] 5318528it [00:04, 1215247.19it/s] 5441469it [00:04, 1219412.57it/s] 5563567it [00:04, 1203488.04it/s] 5684061it [00:04, 1162741.96it/s] 5802892it [00:04, 1169998.85it/s] 5923018it [00:04, 1179121.58it/s] 6044186it [00:04, 1188693.40it/s] 6166183it [00:05, 1197855.52it/s] 6291423it [00:05, 1213971.59it/s] 6413186it [00:05, 1215041.91it/s] 6537672it [00:05, 1223926.81it/s] 6660120it [00:05, 1219439.75it/s] 6787631it [00:05, 1236037.89it/s] 6911272it [00:05, 1219324.89it/s] 7036487it [00:05, 1228999.73it/s] 7159449it [00:05, 1223759.10it/s] 7284804it [00:05, 1232593.70it/s] 7418401it [00:06, 1263293.35it/s] 7544777it [00:06, 1250519.32it/s] 7673843it [00:06, 1262408.17it/s] 7800136it [00:06, 1252039.63it/s] 7936119it [00:06, 1283995.67it/s] 8064829it [00:06, 1229635.11it/s] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bai tabix -s 1 -b 2 -e 2 aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1/aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md/aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.depth.gz seqtool depth_hist -nbins 500 aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1/aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md/aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.depth.gz > aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1/aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md/aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.depth_hist.tsv cat aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1/aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md/aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md -output aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1/aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md/aih-tih-sc-4f4d6e-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-4f4d6e-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1/aih-tih-sc-4f4d6e-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-4f4d6e-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1/aih-tih-sc-4f4d6e-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-4f4d6e-R1_B23WHYVLT4_1/aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md/aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.depth.gz> aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1/aih-tih-sc-4f4d6e-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-4f4d6e-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1/aih-tih-sc-4f4d6e-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-4f4d6e-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md.bai cat aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1/aih-tih-sc-4f4d6e-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-4f4d6e-R1_B23WHYVLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1/aih-tih-sc-4f4d6e-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-4f4d6e-R1_B23WHYVLT4_1/aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md/qc_complete.txt + merge_qc -folders aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1/aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1.md -output aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1/aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1_full_basic_stats.tsv + head -n1 aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1/aih-tih-sc-4f4d6e-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-4f4d6e-R1_B23WHYVLT4_1/aih-tih-sc-4f4d6e-R1_B23WHYVLT4_1_full_basic_stats.tsv