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/20/683d2163eed793b6598adab0638d7f/.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/ea/e13a5beb79ba31e2f8a88cb79fa5d4/aih-tih-sc-97c26d-R1_B23WHYVLT4_1.md.bai 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/20/683d2163eed793b6598adab0638d7f/.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/ea/e13a5beb79ba31e2f8a88cb79fa5d4/aih-tih-sc-97c26d-R1_B23WHYVLT4_1.md.bam 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-97c26d-R1_B23WHYVLT4_1 + all_qc -bam aih-tih-sc-97c26d-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-97c26d-R1_B23WHYVLT4_1 -reference ref_genome.fa -region chr20 mkdir -p aih-tih-sc-97c26d-R1_B23WHYVLT4_1/aih-tih-sc-97c26d-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-97c26d-R1_B23WHYVLT4_1/aih-tih-sc-97c26d-R1_B23WHYVLT4_1.md/full_bed.bed seqtool depth -bam aih-tih-sc-97c26d-R1_B23WHYVLT4_1.md.bam -bed aih-tih-sc-97c26d-R1_B23WHYVLT4_1/aih-tih-sc-97c26d-R1_B23WHYVLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-97c26d-R1_B23WHYVLT4_1/aih-tih-sc-97c26d-R1_B23WHYVLT4_1.md/aih-tih-sc-97c26d-R1_B23WHYVLT4_1.md.depth.gz saturation_plot -bams aih-tih-sc-97c26d-R1_B23WHYVLT4_1.md.bam -region chr20 -output aih-tih-sc-97c26d-R1_B23WHYVLT4_1/aih-tih-sc-97c26d-R1_B23WHYVLT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-97c26d-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-97c26d-R1_B23WHYVLT4_1/aih-tih-sc-97c26d-R1_B23WHYVLT4_1.md/saturation_qc.tsv fragment_size -bams aih-tih-sc-97c26d-R1_B23WHYVLT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-97c26d-R1_B23WHYVLT4_1/aih-tih-sc-97c26d-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-97c26d-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-97c26d-R1_B23WHYVLT4_1.md.mpileup && contamination -input aih-tih-sc-97c26d-R1_B23WHYVLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-97c26d-R1_B23WHYVLT4_1/aih-tih-sc-97c26d-R1_B23WHYVLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97c26d-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-97c26d-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97c26d-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97c26d-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97c26d-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97c26d-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-97c26d-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97c26d-R1_B23WHYVLT4_1.md.bai 0it [00:00, ?it/s] 134322it [00:00, 1343122.01it/s] 271182it [00:00, 1358042.72it/s] 406987it [00:00, 1327281.62it/s] 547924it [00:00, 1359210.26it/s] 686392it [00:00, 1368284.22it/s] 823289it [00:00, 1349750.95it/s] 963634it [00:00, 1367052.28it/s] 1107205it [00:00, 1388519.51it/s] 1252229it [00:00, 1407670.25it/s] 1394428it [00:01, 1412043.00it/s] 1536519it [00:01, 1414724.12it/s] 1678024it [00:01, 1405906.09it/s] 1821429it [00:01, 1414355.56it/s] 1964334it [00:01, 1418679.38it/s] 2108859it [00:01, 1426604.10it/s] 2252289it [00:01, 1428887.48it/s] 2395191it [00:01, 1427619.54it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97c26d-R1_B23WHYVLT4_1.md.bai 2538406it [00:01, 1428819.61it/s] 2681295it [00:01, 1423378.71it/s] 2823642it [00:02, 1403205.54it/s] 2967175it [00:02, 1412698.68it/s] 3108502it [00:02, 1412135.89it/s] 3252019it [00:02, 1418975.19it/s] 3395916it [00:02, 1424922.35it/s] 3543116it [00:02, 1438902.93it/s] 3690370it [00:02, 1448949.40it/s] 3838017it [00:02, 1457169.18it/s] 3984037it [00:02, 1457982.01it/s] 4129845it [00:02, 1454511.81it/s] 4275305it [00:03, 1452837.22it/s] 4421233it [00:03, 1454746.12it/s] 4567695it [00:03, 1457483.06it/s] 4713447it [00:03, 1452772.71it/s] 4858730it [00:03, 1451321.91it/s] 5003866it [00:03, 1445169.47it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97c26d-R1_B23WHYVLT4_1.md.bai 5148390it [00:03, 1440558.10it/s] 5293770it [00:03, 1444341.79it/s] 5441159it [00:03, 1453150.46it/s] 5586483it [00:03, 1452034.39it/s] 5732215it [00:04, 1453592.55it/s] 5858385it [00:04, 1425021.72it/s] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97c26d-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97c26d-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97c26d-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97c26d-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97c26d-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97c26d-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97c26d-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97c26d-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97c26d-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97c26d-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97c26d-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97c26d-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97c26d-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97c26d-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97c26d-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97c26d-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97c26d-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97c26d-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97c26d-R1_B23WHYVLT4_1.md.bai tabix -s 1 -b 2 -e 2 aih-tih-sc-97c26d-R1_B23WHYVLT4_1/aih-tih-sc-97c26d-R1_B23WHYVLT4_1.md/aih-tih-sc-97c26d-R1_B23WHYVLT4_1.md.depth.gz seqtool depth_hist -nbins 500 aih-tih-sc-97c26d-R1_B23WHYVLT4_1/aih-tih-sc-97c26d-R1_B23WHYVLT4_1.md/aih-tih-sc-97c26d-R1_B23WHYVLT4_1.md.depth.gz > aih-tih-sc-97c26d-R1_B23WHYVLT4_1/aih-tih-sc-97c26d-R1_B23WHYVLT4_1.md/aih-tih-sc-97c26d-R1_B23WHYVLT4_1.md.depth_hist.tsv cat aih-tih-sc-97c26d-R1_B23WHYVLT4_1/aih-tih-sc-97c26d-R1_B23WHYVLT4_1.md/aih-tih-sc-97c26d-R1_B23WHYVLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-97c26d-R1_B23WHYVLT4_1.md -output aih-tih-sc-97c26d-R1_B23WHYVLT4_1/aih-tih-sc-97c26d-R1_B23WHYVLT4_1.md/aih-tih-sc-97c26d-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-97c26d-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-97c26d-R1_B23WHYVLT4_1/aih-tih-sc-97c26d-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-97c26d-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-97c26d-R1_B23WHYVLT4_1/aih-tih-sc-97c26d-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-97c26d-R1_B23WHYVLT4_1/aih-tih-sc-97c26d-R1_B23WHYVLT4_1.md/aih-tih-sc-97c26d-R1_B23WHYVLT4_1.md.depth.gz> aih-tih-sc-97c26d-R1_B23WHYVLT4_1/aih-tih-sc-97c26d-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-97c26d-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-97c26d-R1_B23WHYVLT4_1/aih-tih-sc-97c26d-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-97c26d-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97c26d-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-97c26d-R1_B23WHYVLT4_1.md.bai cat aih-tih-sc-97c26d-R1_B23WHYVLT4_1/aih-tih-sc-97c26d-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-97c26d-R1_B23WHYVLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "aih-tih-sc-97c26d-R1_B23WHYVLT4_1/aih-tih-sc-97c26d-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-97c26d-R1_B23WHYVLT4_1/aih-tih-sc-97c26d-R1_B23WHYVLT4_1.md/qc_complete.txt + merge_qc -folders aih-tih-sc-97c26d-R1_B23WHYVLT4_1/aih-tih-sc-97c26d-R1_B23WHYVLT4_1.md -output aih-tih-sc-97c26d-R1_B23WHYVLT4_1/aih-tih-sc-97c26d-R1_B23WHYVLT4_1_full_basic_stats.tsv + head -n1 aih-tih-sc-97c26d-R1_B23WHYVLT4_1/aih-tih-sc-97c26d-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-97c26d-R1_B23WHYVLT4_1/aih-tih-sc-97c26d-R1_B23WHYVLT4_1_full_basic_stats.tsv