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/5f/7f3bc5ff735419a1a4ebd5e852b05d/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/15/1583358bf761ffb33374f0a0b1e427/659_bMa-T1-TRNA-1_B23MHV2LT4_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-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/gatk4/dbsnp_hg38_contam_sites.bed Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5f/7f3bc5ff735419a1a4ebd5e852b05d/.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-rnd-pltf-dev-nextflow-scratch-01/work/15/1583358bf761ffb33374f0a0b1e427/659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bam Downloading: s3://natera-platform-sandbox/pipeline-resources/Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi ==> STAGING COMPLETE (11 inputs) + mkdir 659_bMa-T1-TRNA-1_B23MHV2LT4_1 + all_qc -bam 659_bMa-T1-TRNA-1_B23MHV2LT4_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 659_bMa-T1-TRNA-1_B23MHV2LT4_1 -reference ref_genome.fa -region chr20 mkdir -p 659_bMa-T1-TRNA-1_B23MHV2LT4_1/659_bMa-T1-TRNA-1_B23MHV2LT4_1.md/ cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > 659_bMa-T1-TRNA-1_B23MHV2LT4_1/659_bMa-T1-TRNA-1_B23MHV2LT4_1.md/full_bed.bed saturation_plot -bams 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bam -region chr20 -output 659_bMa-T1-TRNA-1_B23MHV2LT4_1/659_bMa-T1-TRNA-1_B23MHV2LT4_1.md/saturation_plot.png -threads 1 seqtool depth -bam 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bam -bed 659_bMa-T1-TRNA-1_B23MHV2LT4_1/659_bMa-T1-TRNA-1_B23MHV2LT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > 659_bMa-T1-TRNA-1_B23MHV2LT4_1/659_bMa-T1-TRNA-1_B23MHV2LT4_1.md/659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz fragment_size -bams 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bam -region chr20 -output_prefix 659_bMa-T1-TRNA-1_B23MHV2LT4_1/659_bMa-T1-TRNA-1_B23MHV2LT4_1.md/fragsize -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bMa-T1-TRNA-1_B23MHV2LT4_1/659_bMa-T1-TRNA-1_B23MHV2LT4_1.md/saturation_qc.tsv samtools mpileup -B --min-MQ 60 --min-BQ 30 -f ref_genome.fa -l dbsnp_hg38_contam_sites.bed 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.mpileup && contamination -input 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > 659_bMa-T1-TRNA-1_B23MHV2LT4_1/659_bMa-T1-TRNA-1_B23MHV2LT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai [mpileup] 1 samples in 1 input files [W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_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: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai 0it [00:00, ?it/s] 133978it [00:00, 1339666.29it/s] 284194it [00:00, 1435161.75it/s] 442535it [00:00, 1502788.38it/s] 608959it [00:00, 1566483.37it/s] 777859it [00:00, 1610609.36it/s] 945569it [00:00, 1633175.77it/s] 1108887it [00:00, 1563639.41it/s] 1265812it [00:00, 1549023.84it/s] 1429256it [00:00, 1574954.29it/s] 1595294it [00:01, 1600775.23it/s] 1765257it [00:01, 1630584.93it/s] 1933991it [00:01, 1647593.77it/s] 2098929it [00:01, 1642424.79it/s] 2269070it [00:01, 1660072.32it/s] 2440248it [00:01, 1675537.67it/s] 2610002it [00:01, 1682095.70it/s] 2779254it [00:01, 1685180.89it/s] 2947813it [00:01, 1679148.32it/s][W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai 3117130it [00:01, 1683308.20it/s] 3285485it [00:02, 1665215.61it/s] 3452064it [00:02, 1635724.86it/s] 3615769it [00:02, 1628242.60it/s] 3778680it [00:02, 1606689.42it/s] 3940723it [00:02, 1610669.19it/s] 4101863it [00:02, 1584093.06it/s] 4267938it [00:02, 1603129.99it/s] 4428364it [00:02, 1588239.08it/s] 4598195it [00:02, 1620531.94it/s] 4770669it [00:02, 1651332.82it/s][W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai 4939526it [00:03, 1662222.03it/s] 5111235it [00:03, 1678413.73it/s] 5279156it [00:03, 1677517.44it/s] 5449754it [00:03, 1685911.75it/s] 5618387it [00:03, 1684487.28it/s] 5788750it [00:03, 1690063.00it/s] 5961584it [00:03, 1701422.36it/s] 6132306it [00:03, 1703102.67it/s] 6302629it [00:03, 1701501.13it/s] 6472788it [00:03, 1660439.89it/s] 6639053it [00:04, 1480371.52it/s] 6790705it [00:04, 1371886.86it/s] 6931426it [00:04, 1307081.69it/s] 7064682it [00:04, 1260209.32it/s] 7192376it [00:04, 1242557.48it/s] 7317662it [00:04, 1227281.69it/s] 7441012it [00:04, 1222399.25it/s] 7563653it [00:04, 1215439.88it/s] 7685445it [00:04, 1205552.80it/s] 7806322it [00:05, 1206447.55it/s] 7927073it [00:05, 1193407.72it/s] 8046486it [00:05, 1183098.55it/s] 8113870it [00:05, 1514749.63it/s] [W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai tabix -s 1 -b 2 -e 2 659_bMa-T1-TRNA-1_B23MHV2LT4_1/659_bMa-T1-TRNA-1_B23MHV2LT4_1.md/659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz seqtool depth_hist -nbins 500 659_bMa-T1-TRNA-1_B23MHV2LT4_1/659_bMa-T1-TRNA-1_B23MHV2LT4_1.md/659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz > 659_bMa-T1-TRNA-1_B23MHV2LT4_1/659_bMa-T1-TRNA-1_B23MHV2LT4_1.md/659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.depth_hist.tsv cat 659_bMa-T1-TRNA-1_B23MHV2LT4_1/659_bMa-T1-TRNA-1_B23MHV2LT4_1.md/659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md -output 659_bMa-T1-TRNA-1_B23MHV2LT4_1/659_bMa-T1-TRNA-1_B23MHV2LT4_1.md/659_bMa-T1-TRNA-1_B23MHV2LT4_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 2 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bMa-T1-TRNA-1_B23MHV2LT4_1/659_bMa-T1-TRNA-1_B23MHV2LT4_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 2 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bMa-T1-TRNA-1_B23MHV2LT4_1/659_bMa-T1-TRNA-1_B23MHV2LT4_1.md/reads_per_target.Twist_rna_exome_AND_fusion_hg38.bed.tsv seqtool depth_stats -bed Twist_rna_exome_AND_fusion_hg38.bed 659_bMa-T1-TRNA-1_B23MHV2LT4_1/659_bMa-T1-TRNA-1_B23MHV2LT4_1.md/659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz> 659_bMa-T1-TRNA-1_B23MHV2LT4_1/659_bMa-T1-TRNA-1_B23MHV2LT4_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 2 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bMa-T1-TRNA-1_B23MHV2LT4_1/659_bMa-T1-TRNA-1_B23MHV2LT4_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: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bai cat 659_bMa-T1-TRNA-1_B23MHV2LT4_1/659_bMa-T1-TRNA-1_B23MHV2LT4_1.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "659_bMa-T1-TRNA-1_B23MHV2LT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "659_bMa-T1-TRNA-1_B23MHV2LT4_1/659_bMa-T1-TRNA-1_B23MHV2LT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > 659_bMa-T1-TRNA-1_B23MHV2LT4_1/659_bMa-T1-TRNA-1_B23MHV2LT4_1.md/qc_complete.txt + merge_qc -folders 659_bMa-T1-TRNA-1_B23MHV2LT4_1/659_bMa-T1-TRNA-1_B23MHV2LT4_1.md -output 659_bMa-T1-TRNA-1_B23MHV2LT4_1/659_bMa-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv + head -n1 659_bMa-T1-TRNA-1_B23MHV2LT4_1/659_bMa-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed 659_bMa-T1-TRNA-1_B23MHV2LT4_1/659_bMa-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv