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/a0/bc4aa29c21e835c2b504178faf635a/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/43/d826b00de827d340c50c373cb99bb1/tih_rna_sample_00087_B23WHTKLT4_2.md.bai 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/43/d826b00de827d340c50c373cb99bb1/tih_rna_sample_00087_B23WHTKLT4_2.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/a0/bc4aa29c21e835c2b504178faf635a/.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 tih_rna_sample_00087_B23WHTKLT4_2 + all_qc -bam tih_rna_sample_00087_B23WHTKLT4_2.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 tih_rna_sample_00087_B23WHTKLT4_2 -reference ref_genome.fa -region chr20 mkdir -p tih_rna_sample_00087_B23WHTKLT4_2/tih_rna_sample_00087_B23WHTKLT4_2.md/ cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > tih_rna_sample_00087_B23WHTKLT4_2/tih_rna_sample_00087_B23WHTKLT4_2.md/full_bed.bed seqtool depth -bam tih_rna_sample_00087_B23WHTKLT4_2.md.bam -bed tih_rna_sample_00087_B23WHTKLT4_2/tih_rna_sample_00087_B23WHTKLT4_2.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > tih_rna_sample_00087_B23WHTKLT4_2/tih_rna_sample_00087_B23WHTKLT4_2.md/tih_rna_sample_00087_B23WHTKLT4_2.md.depth.gz saturation_plot -bams tih_rna_sample_00087_B23WHTKLT4_2.md.bam -region chr20 -output tih_rna_sample_00087_B23WHTKLT4_2/tih_rna_sample_00087_B23WHTKLT4_2.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 tih_rna_sample_00087_B23WHTKLT4_2.md.bam > tih_rna_sample_00087_B23WHTKLT4_2/tih_rna_sample_00087_B23WHTKLT4_2.md/saturation_qc.tsv fragment_size -bams tih_rna_sample_00087_B23WHTKLT4_2.md.bam -region chr20 -output_prefix tih_rna_sample_00087_B23WHTKLT4_2/tih_rna_sample_00087_B23WHTKLT4_2.md/fragsize -threads 1 samtools mpileup -B --min-MQ 60 --min-BQ 30 -f ref_genome.fa -l dbsnp_hg38_contam_sites.bed tih_rna_sample_00087_B23WHTKLT4_2.md.bam > tih_rna_sample_00087_B23WHTKLT4_2.md.mpileup && contamination -input tih_rna_sample_00087_B23WHTKLT4_2.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > tih_rna_sample_00087_B23WHTKLT4_2/tih_rna_sample_00087_B23WHTKLT4_2.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00087_B23WHTKLT4_2.md.bai [mpileup] 1 samples in 1 input files [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00087_B23WHTKLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00087_B23WHTKLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00087_B23WHTKLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00087_B23WHTKLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00087_B23WHTKLT4_2.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: tih_rna_sample_00087_B23WHTKLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00087_B23WHTKLT4_2.md.bai 0it [00:00, ?it/s] 147144it [00:00, 1470894.33it/s] 306651it [00:00, 1543885.25it/s] 471999it [00:00, 1593799.39it/s] 635512it [00:00, 1610081.79it/s] 800865it [00:00, 1625719.47it/s] 968210it [00:00, 1641919.41it/s] 1134256it [00:00, 1647947.55it/s] 1299051it [00:00, 1645555.88it/s] 1464320it [00:00, 1647758.53it/s] 1629228it [00:01, 1648143.65it/s] 1796056it [00:01, 1654277.19it/s] 1962284it [00:01, 1656686.09it/s] 2127954it [00:01, 1649851.57it/s] 2292946it [00:01, 1616128.65it/s] 2454707it [00:01, 1503453.42it/s] 2616772it [00:01, 1536554.14it/s] 2783659it [00:01, 1574500.74it/s] 2949299it [00:01, 1598328.02it/s] 3109963it [00:01, 1596051.69it/s] 3275053it [00:02, 1612208.54it/s] 3439099it [00:02, 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1625567.83it/s] 8208967it [00:05, 1624890.18it/s] 8374841it [00:05, 1634946.91it/s] 8541289it [00:05, 1643636.36it/s] 8705832it [00:05, 1641459.89it/s] 8870942it [00:05, 1644316.20it/s] 9037293it [00:05, 1650031.97it/s] 9202360it [00:05, 1647175.19it/s] 9367123it [00:06, 1644183.31it/s] 9533075it [00:06, 1648739.91it/s] 9697973it [00:06, 1641728.26it/s] 9864746it [00:06, 1649469.15it/s] 10031623it [00:06, 1655214.23it/s] 10197160it [00:06, 1520642.16it/s] 10359869it [00:06, 1550641.94it/s] 10527724it [00:06, 1587352.81it/s] 10692786it [00:06, 1605734.19it/s] 10861203it [00:06, 1628740.16it/s] 11027472it [00:07, 1638738.44it/s] 11192849it [00:07, 1643177.22it/s] 11357550it [00:07, 1637394.46it/s][W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00087_B23WHTKLT4_2.md.bai 11525663it [00:07, 1650371.94it/s] 11690900it [00:07, 1624752.96it/s] 11853593it [00:07, 1611223.43it/s] 12014875it [00:07, 1611539.56it/s] 12179000it [00:07, 1620320.00it/s] 12344106it [00:07, 1629302.61it/s] 12508468it [00:07, 1633491.55it/s] 12673639it [00:08, 1638905.48it/s] 12843636it [00:08, 1657135.87it/s] 13009382it [00:08, 1656620.87it/s] 13175067it [00:08, 1644123.98it/s] 13342094it [00:08, 1651890.12it/s] 13507313it [00:08, 1645767.53it/s] 13675241it [00:08, 1655613.48it/s] 13840825it [00:08, 1655165.25it/s] 14006357it [00:08, 1643444.78it/s] 14172113it [00:08, 1647622.52it/s] 14340065it [00:09, 1657118.01it/s] 14509354it [00:09, 1667789.42it/s] 14677460it [00:09, 1671737.28it/s] 14844648it [00:09, 1666612.51it/s] 15011322it [00:09, 1654544.51it/s] 15176802it [00:09, 1649241.14it/s] 15191438it [00:09, 1586847.84it/s] [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00087_B23WHTKLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00087_B23WHTKLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00087_B23WHTKLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00087_B23WHTKLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00087_B23WHTKLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00087_B23WHTKLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00087_B23WHTKLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00087_B23WHTKLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00087_B23WHTKLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00087_B23WHTKLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00087_B23WHTKLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00087_B23WHTKLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00087_B23WHTKLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00087_B23WHTKLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00087_B23WHTKLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00087_B23WHTKLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00087_B23WHTKLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00087_B23WHTKLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00087_B23WHTKLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00087_B23WHTKLT4_2.md.bai tabix -s 1 -b 2 -e 2 tih_rna_sample_00087_B23WHTKLT4_2/tih_rna_sample_00087_B23WHTKLT4_2.md/tih_rna_sample_00087_B23WHTKLT4_2.md.depth.gz seqtool depth_hist -nbins 500 tih_rna_sample_00087_B23WHTKLT4_2/tih_rna_sample_00087_B23WHTKLT4_2.md/tih_rna_sample_00087_B23WHTKLT4_2.md.depth.gz > tih_rna_sample_00087_B23WHTKLT4_2/tih_rna_sample_00087_B23WHTKLT4_2.md/tih_rna_sample_00087_B23WHTKLT4_2.md.depth_hist.tsv cat tih_rna_sample_00087_B23WHTKLT4_2/tih_rna_sample_00087_B23WHTKLT4_2.md/tih_rna_sample_00087_B23WHTKLT4_2.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title tih_rna_sample_00087_B23WHTKLT4_2.md -output tih_rna_sample_00087_B23WHTKLT4_2/tih_rna_sample_00087_B23WHTKLT4_2.md/tih_rna_sample_00087_B23WHTKLT4_2.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 tih_rna_sample_00087_B23WHTKLT4_2.md.bam > tih_rna_sample_00087_B23WHTKLT4_2/tih_rna_sample_00087_B23WHTKLT4_2.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 tih_rna_sample_00087_B23WHTKLT4_2.md.bam > tih_rna_sample_00087_B23WHTKLT4_2/tih_rna_sample_00087_B23WHTKLT4_2.md/reads_per_target.Twist_rna_exome_AND_fusion_hg38.bed.tsv seqtool depth_stats -bed Twist_rna_exome_AND_fusion_hg38.bed tih_rna_sample_00087_B23WHTKLT4_2/tih_rna_sample_00087_B23WHTKLT4_2.md/tih_rna_sample_00087_B23WHTKLT4_2.md.depth.gz> tih_rna_sample_00087_B23WHTKLT4_2/tih_rna_sample_00087_B23WHTKLT4_2.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 tih_rna_sample_00087_B23WHTKLT4_2.md.bam > tih_rna_sample_00087_B23WHTKLT4_2/tih_rna_sample_00087_B23WHTKLT4_2.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: tih_rna_sample_00087_B23WHTKLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00087_B23WHTKLT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00087_B23WHTKLT4_2.md.bai cat tih_rna_sample_00087_B23WHTKLT4_2/tih_rna_sample_00087_B23WHTKLT4_2.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "tih_rna_sample_00087_B23WHTKLT4_2.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "tih_rna_sample_00087_B23WHTKLT4_2/tih_rna_sample_00087_B23WHTKLT4_2.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > tih_rna_sample_00087_B23WHTKLT4_2/tih_rna_sample_00087_B23WHTKLT4_2.md/qc_complete.txt + merge_qc -folders tih_rna_sample_00087_B23WHTKLT4_2/tih_rna_sample_00087_B23WHTKLT4_2.md -output tih_rna_sample_00087_B23WHTKLT4_2/tih_rna_sample_00087_B23WHTKLT4_2_full_basic_stats.tsv + head -n1 tih_rna_sample_00087_B23WHTKLT4_2/tih_rna_sample_00087_B23WHTKLT4_2_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed tih_rna_sample_00087_B23WHTKLT4_2/tih_rna_sample_00087_B23WHTKLT4_2_full_basic_stats.tsv