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/c3/0c8cf6f2cfdd23a0307ccf70cb8715/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/02/d01c59f31cbc545a07fa7cad6f31d9/aih-tih-sc-027d27-R1_B23WHYVLT4_1.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/02/d01c59f31cbc545a07fa7cad6f31d9/aih-tih-sc-027d27-R1_B23WHYVLT4_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/c3/0c8cf6f2cfdd23a0307ccf70cb8715/.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-027d27-R1_B23WHYVLT4_1 + all_qc -bam aih-tih-sc-027d27-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-027d27-R1_B23WHYVLT4_1 -reference ref_genome.fa -region chr20 mkdir -p aih-tih-sc-027d27-R1_B23WHYVLT4_1/aih-tih-sc-027d27-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-027d27-R1_B23WHYVLT4_1/aih-tih-sc-027d27-R1_B23WHYVLT4_1.md/full_bed.bed seqtool depth -bam aih-tih-sc-027d27-R1_B23WHYVLT4_1.md.bam -bed aih-tih-sc-027d27-R1_B23WHYVLT4_1/aih-tih-sc-027d27-R1_B23WHYVLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-027d27-R1_B23WHYVLT4_1/aih-tih-sc-027d27-R1_B23WHYVLT4_1.md/aih-tih-sc-027d27-R1_B23WHYVLT4_1.md.depth.gz saturation_plot -bams aih-tih-sc-027d27-R1_B23WHYVLT4_1.md.bam -region chr20 -output aih-tih-sc-027d27-R1_B23WHYVLT4_1/aih-tih-sc-027d27-R1_B23WHYVLT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-027d27-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-027d27-R1_B23WHYVLT4_1/aih-tih-sc-027d27-R1_B23WHYVLT4_1.md/saturation_qc.tsv fragment_size -bams aih-tih-sc-027d27-R1_B23WHYVLT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-027d27-R1_B23WHYVLT4_1/aih-tih-sc-027d27-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-027d27-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-027d27-R1_B23WHYVLT4_1.md.mpileup && contamination -input aih-tih-sc-027d27-R1_B23WHYVLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-027d27-R1_B23WHYVLT4_1/aih-tih-sc-027d27-R1_B23WHYVLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-027d27-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-027d27-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-027d27-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-027d27-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-027d27-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-027d27-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-027d27-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-027d27-R1_B23WHYVLT4_1.md.bai 0it [00:00, ?it/s] 151702it [00:00, 1516862.32it/s] 319362it [00:00, 1610768.33it/s] 489544it [00:00, 1652194.15it/s] 654990it [00:00, 1652989.67it/s] 828855it [00:00, 1683836.70it/s] 1000830it [00:00, 1696015.27it/s] 1175876it [00:00, 1713661.70it/s] 1349315it [00:00, 1720227.81it/s] 1521352it [00:00, 1720245.85it/s] 1693377it [00:01, 1720071.66it/s] 1865385it [00:01, 1718655.27it/s] 2037251it [00:01, 1708618.42it/s] 2215667it [00:01, 1731376.93it/s] 2390097it [00:01, 1735241.01it/s] 2563636it [00:01, 1733467.80it/s] 2736994it [00:01, 1733030.47it/s] 2910478it [00:01, 1733550.54it/s] 3083839it [00:01, 1725430.58it/s] 3256394it [00:01, 1693615.18it/s] 3425883it [00:02, 1655658.51it/s] 3591674it [00:02, 1646340.71it/s] 3757607it [00:02, 1650047.41it/s] 3927552it [00:02, 1664608.18it/s] 4095547it [00:02, 1669137.62it/s] 4266219it [00:02, 1680301.21it/s] 4434312it [00:02, 1673351.94it/s] 4601694it [00:02, 1663612.95it/s] 4768934it [00:02, 1666188.09it/s] 4935583it [00:02, 1658860.19it/s] 5101906it [00:03, 1660075.69it/s] 5274109it [00:03, 1678530.02it/s] 5448227it [00:03, 1697094.21it/s] 5621592it [00:03, 1707995.35it/s] 5793995it [00:03, 1712765.30it/s] 5966624it [00:03, 1716785.86it/s] 6138313it [00:03, 1701131.67it/s] 6308465it [00:03, 1698023.19it/s] 6482521it [00:03, 1710585.31it/s] 6656170it [00:03, 1718280.95it/s] 6828020it [00:04, 1657138.92it/s] 6994203it [00:04, 1647696.61it/s] 7164398it [00:04, 1663563.00it/s] 7334469it [00:04, 1674491.89it/s] 7502119it [00:04, 1667593.93it/s] 7669019it [00:04, 1645468.08it/s] 7835854it [00:04, 1652127.14it/s] 8003028it [00:04, 1657900.19it/s] 8168903it [00:04, 1657100.63it/s] 8336795it [00:04, 1663586.37it/s] 8504962it [00:05, 1668967.99it/s] 8675937it [00:05, 1681053.31it/s] 8847055it [00:05, 1690043.20it/s] 9016081it [00:05, 1675573.38it/s] 9185413it [00:05, 1680841.76it/s] 9353530it [00:05, 1636574.36it/s] 9517448it [00:05, 1531621.74it/s] 9672000it [00:05, 1508670.57it/s] 9832692it [00:05, 1536487.45it/s] 10002212it [00:05, 1582175.34it/s] 10173723it [00:06, 1620775.74it/s] 10344280it [00:06, 1645625.15it/s] 10515893it [00:06, 1666407.04it/s] 10687461it [00:06, 1681019.15it/s] 10856686it [00:06, 1684340.29it/s] 11027933it [00:06, 1692708.25it/s] 11200250it [00:06, 1701787.88it/s] 11372190it [00:06, 1706908.17it/s] 11546883it [00:06, 1718868.30it/s] 11718824it [00:06, 1713716.75it/s] 11890237it [00:07, 1712686.72it/s] 12052807it [00:07, 1676739.97it/s] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-027d27-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-027d27-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-027d27-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-027d27-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-027d27-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-027d27-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-027d27-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-027d27-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-027d27-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-027d27-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-027d27-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-027d27-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-027d27-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-027d27-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-027d27-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-027d27-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-027d27-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-027d27-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-027d27-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-027d27-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-027d27-R1_B23WHYVLT4_1.md.bai tabix -s 1 -b 2 -e 2 aih-tih-sc-027d27-R1_B23WHYVLT4_1/aih-tih-sc-027d27-R1_B23WHYVLT4_1.md/aih-tih-sc-027d27-R1_B23WHYVLT4_1.md.depth.gz seqtool depth_hist -nbins 500 aih-tih-sc-027d27-R1_B23WHYVLT4_1/aih-tih-sc-027d27-R1_B23WHYVLT4_1.md/aih-tih-sc-027d27-R1_B23WHYVLT4_1.md.depth.gz > aih-tih-sc-027d27-R1_B23WHYVLT4_1/aih-tih-sc-027d27-R1_B23WHYVLT4_1.md/aih-tih-sc-027d27-R1_B23WHYVLT4_1.md.depth_hist.tsv cat aih-tih-sc-027d27-R1_B23WHYVLT4_1/aih-tih-sc-027d27-R1_B23WHYVLT4_1.md/aih-tih-sc-027d27-R1_B23WHYVLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-027d27-R1_B23WHYVLT4_1.md -output aih-tih-sc-027d27-R1_B23WHYVLT4_1/aih-tih-sc-027d27-R1_B23WHYVLT4_1.md/aih-tih-sc-027d27-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-027d27-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-027d27-R1_B23WHYVLT4_1/aih-tih-sc-027d27-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-027d27-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-027d27-R1_B23WHYVLT4_1/aih-tih-sc-027d27-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-027d27-R1_B23WHYVLT4_1/aih-tih-sc-027d27-R1_B23WHYVLT4_1.md/aih-tih-sc-027d27-R1_B23WHYVLT4_1.md.depth.gz> aih-tih-sc-027d27-R1_B23WHYVLT4_1/aih-tih-sc-027d27-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-027d27-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-027d27-R1_B23WHYVLT4_1/aih-tih-sc-027d27-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-027d27-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-027d27-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-027d27-R1_B23WHYVLT4_1.md.bai cat aih-tih-sc-027d27-R1_B23WHYVLT4_1/aih-tih-sc-027d27-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-027d27-R1_B23WHYVLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "aih-tih-sc-027d27-R1_B23WHYVLT4_1/aih-tih-sc-027d27-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-027d27-R1_B23WHYVLT4_1/aih-tih-sc-027d27-R1_B23WHYVLT4_1.md/qc_complete.txt + merge_qc -folders aih-tih-sc-027d27-R1_B23WHYVLT4_1/aih-tih-sc-027d27-R1_B23WHYVLT4_1.md -output aih-tih-sc-027d27-R1_B23WHYVLT4_1/aih-tih-sc-027d27-R1_B23WHYVLT4_1_full_basic_stats.tsv + head -n1 aih-tih-sc-027d27-R1_B23WHYVLT4_1/aih-tih-sc-027d27-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-027d27-R1_B23WHYVLT4_1/aih-tih-sc-027d27-R1_B23WHYVLT4_1_full_basic_stats.tsv