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/d3/14da0cbee785608d44170ecd3eddef/.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/c1/a027bcb16d65edbca2386be9628273/aih-tih-sc-446670-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/d3/14da0cbee785608d44170ecd3eddef/.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/c1/a027bcb16d65edbca2386be9628273/aih-tih-sc-446670-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-446670-R1_B23WHYVLT4_1 + all_qc -bam aih-tih-sc-446670-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-446670-R1_B23WHYVLT4_1 -reference ref_genome.fa -region chr20 mkdir -p aih-tih-sc-446670-R1_B23WHYVLT4_1/aih-tih-sc-446670-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-446670-R1_B23WHYVLT4_1/aih-tih-sc-446670-R1_B23WHYVLT4_1.md/full_bed.bed seqtool depth -bam aih-tih-sc-446670-R1_B23WHYVLT4_1.md.bam -bed aih-tih-sc-446670-R1_B23WHYVLT4_1/aih-tih-sc-446670-R1_B23WHYVLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-446670-R1_B23WHYVLT4_1/aih-tih-sc-446670-R1_B23WHYVLT4_1.md/aih-tih-sc-446670-R1_B23WHYVLT4_1.md.depth.gz saturation_plot -bams aih-tih-sc-446670-R1_B23WHYVLT4_1.md.bam -region chr20 -output aih-tih-sc-446670-R1_B23WHYVLT4_1/aih-tih-sc-446670-R1_B23WHYVLT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-446670-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-446670-R1_B23WHYVLT4_1/aih-tih-sc-446670-R1_B23WHYVLT4_1.md/saturation_qc.tsv fragment_size -bams aih-tih-sc-446670-R1_B23WHYVLT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-446670-R1_B23WHYVLT4_1/aih-tih-sc-446670-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-446670-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-446670-R1_B23WHYVLT4_1.md.mpileup && contamination -input aih-tih-sc-446670-R1_B23WHYVLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-446670-R1_B23WHYVLT4_1/aih-tih-sc-446670-R1_B23WHYVLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-446670-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-446670-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-446670-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-446670-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-446670-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-446670-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-446670-R1_B23WHYVLT4_1.md.bai 0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-446670-R1_B23WHYVLT4_1.md.bai 127883it [00:00, 1278730.61it/s] 275939it [00:00, 1397386.09it/s] 435763it [00:00, 1489019.17it/s] 593517it [00:00, 1523920.33it/s] 758041it [00:00, 1567630.83it/s] 926644it [00:00, 1607846.00it/s] 1097106it [00:00, 1639439.16it/s] 1267473it [00:00, 1659843.80it/s] 1433458it [00:00, 1654274.67it/s] 1602649it [00:01, 1665827.40it/s] 1769238it [00:01, 1656972.67it/s] 1936773it [00:01, 1662501.75it/s] 2103679it [00:01, 1664340.82it/s] 2271265it [00:01, 1667778.61it/s] 2438050it [00:01, 1649654.92it/s] 2606196it [00:01, 1659111.18it/s] 2774794it [00:01, 1666958.08it/s] 2941524it [00:01, 1548909.54it/s] 3103552it [00:01, 1557253.77it/s] 3268211it [00:02, 1582885.58it/s] 3428485it [00:02, 1588542.15it/s] 3593497it [00:02, 1606582.19it/s] 3757380it [00:02, 1616084.71it/s] 3919366it [00:02, 1603461.17it/s] 4086154it [00:02, 1622501.91it/s] 4248624it [00:02, 1578099.52it/s] 4406931it [00:02, 1579524.62it/s] 4565158it [00:02, 1573930.07it/s] 4722739it [00:02, 1521265.37it/s] 4875312it [00:03, 1513695.38it/s] 5026978it [00:03, 1504255.35it/s] 5177599it [00:03, 1495919.24it/s] 5333870it [00:03, 1515489.87it/s] 5485552it [00:03, 1414819.59it/s] 5628373it [00:03, 1299622.94it/s] 5780264it [00:03, 1358791.64it/s] 5934991it [00:03, 1411219.05it/s] 6096011it [00:03, 1467787.58it/s] 6257752it [00:04, 1510782.30it/s] 6424959it [00:04, 1557874.76it/s] 6592960it [00:04, 1593737.65it/s] 6761729it [00:04, 1621526.61it/s] 6924498it [00:04, 1611000.15it/s] 7092631it [00:04, 1631826.05it/s] 7261524it [00:04, 1648787.91it/s] 7428858it [00:04, 1655973.39it/s] 7597097it [00:04, 1663842.36it/s] 7763609it [00:04, 1656112.05it/s] 7929316it [00:05, 1646450.05it/s] 8097085it [00:05, 1655591.07it/s] 8264565it [00:05, 1661293.04it/s] 8433522it [00:05, 1669640.33it/s] 8603394it [00:05, 1678309.92it/s] 8774269it [00:05, 1687395.17it/s] 8943030it [00:05, 1666266.43it/s] 9110332it [00:05, 1668245.91it/s] 9277209it [00:05, 1665806.47it/s] 9446505it [00:05, 1673876.16it/s] 9613923it [00:06, 1671712.19it/s] 9781115it [00:06, 1643523.25it/s] 9947585it [00:06, 1649755.06it/s] 10113039it [00:06, 1651145.89it/s] 10280778it [00:06, 1658926.25it/s] 10449573it [00:06, 1667557.59it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-446670-R1_B23WHYVLT4_1.md.bai 10616368it [00:06, 1659315.61it/s] 10782334it [00:06, 1654700.17it/s] 10800915it [00:06, 1598700.42it/s] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-446670-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-446670-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-446670-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-446670-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-446670-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-446670-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-446670-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-446670-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-446670-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-446670-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-446670-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-446670-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-446670-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-446670-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-446670-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-446670-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-446670-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-446670-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-446670-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-446670-R1_B23WHYVLT4_1.md.bai tabix -s 1 -b 2 -e 2 aih-tih-sc-446670-R1_B23WHYVLT4_1/aih-tih-sc-446670-R1_B23WHYVLT4_1.md/aih-tih-sc-446670-R1_B23WHYVLT4_1.md.depth.gz seqtool depth_hist -nbins 500 aih-tih-sc-446670-R1_B23WHYVLT4_1/aih-tih-sc-446670-R1_B23WHYVLT4_1.md/aih-tih-sc-446670-R1_B23WHYVLT4_1.md.depth.gz > aih-tih-sc-446670-R1_B23WHYVLT4_1/aih-tih-sc-446670-R1_B23WHYVLT4_1.md/aih-tih-sc-446670-R1_B23WHYVLT4_1.md.depth_hist.tsv cat aih-tih-sc-446670-R1_B23WHYVLT4_1/aih-tih-sc-446670-R1_B23WHYVLT4_1.md/aih-tih-sc-446670-R1_B23WHYVLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-446670-R1_B23WHYVLT4_1.md -output aih-tih-sc-446670-R1_B23WHYVLT4_1/aih-tih-sc-446670-R1_B23WHYVLT4_1.md/aih-tih-sc-446670-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-446670-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-446670-R1_B23WHYVLT4_1/aih-tih-sc-446670-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-446670-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-446670-R1_B23WHYVLT4_1/aih-tih-sc-446670-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-446670-R1_B23WHYVLT4_1/aih-tih-sc-446670-R1_B23WHYVLT4_1.md/aih-tih-sc-446670-R1_B23WHYVLT4_1.md.depth.gz> aih-tih-sc-446670-R1_B23WHYVLT4_1/aih-tih-sc-446670-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-446670-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-446670-R1_B23WHYVLT4_1/aih-tih-sc-446670-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-446670-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-446670-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-446670-R1_B23WHYVLT4_1.md.bai cat aih-tih-sc-446670-R1_B23WHYVLT4_1/aih-tih-sc-446670-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-446670-R1_B23WHYVLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "aih-tih-sc-446670-R1_B23WHYVLT4_1/aih-tih-sc-446670-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-446670-R1_B23WHYVLT4_1/aih-tih-sc-446670-R1_B23WHYVLT4_1.md/qc_complete.txt + merge_qc -folders aih-tih-sc-446670-R1_B23WHYVLT4_1/aih-tih-sc-446670-R1_B23WHYVLT4_1.md -output aih-tih-sc-446670-R1_B23WHYVLT4_1/aih-tih-sc-446670-R1_B23WHYVLT4_1_full_basic_stats.tsv + head -n1 aih-tih-sc-446670-R1_B23WHYVLT4_1/aih-tih-sc-446670-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-446670-R1_B23WHYVLT4_1/aih-tih-sc-446670-R1_B23WHYVLT4_1_full_basic_stats.tsv