Downloading: s3://natera-platform-sandbox/pipeline-resources/Homo_sapiens_assembly38.dbsnp138.vcf.gz Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/22/002d345fc6e6f6badd104e29e63806/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/74/d254f3b61aa5406dab68e9add3fbc5/659_bR4-T1-TRNA-1_B23MHV2LT4_1.md.bam 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/22/002d345fc6e6f6badd104e29e63806/.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/74/d254f3b61aa5406dab68e9add3fbc5/659_bR4-T1-TRNA-1_B23MHV2LT4_1.md.bai Downloading: s3://natera-platform-sandbox/pipeline-resources/Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi ==> STAGING COMPLETE (11 inputs) + mkdir 659_bR4-T1-TRNA-1_B23MHV2LT4_1 + all_qc -bam 659_bR4-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_bR4-T1-TRNA-1_B23MHV2LT4_1 -reference ref_genome.fa -region chr20 mkdir -p 659_bR4-T1-TRNA-1_B23MHV2LT4_1/659_bR4-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_bR4-T1-TRNA-1_B23MHV2LT4_1/659_bR4-T1-TRNA-1_B23MHV2LT4_1.md/full_bed.bed saturation_plot -bams 659_bR4-T1-TRNA-1_B23MHV2LT4_1.md.bam -region chr20 -output 659_bR4-T1-TRNA-1_B23MHV2LT4_1/659_bR4-T1-TRNA-1_B23MHV2LT4_1.md/saturation_plot.png -threads 1 seqtool depth -bam 659_bR4-T1-TRNA-1_B23MHV2LT4_1.md.bam -bed 659_bR4-T1-TRNA-1_B23MHV2LT4_1/659_bR4-T1-TRNA-1_B23MHV2LT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > 659_bR4-T1-TRNA-1_B23MHV2LT4_1/659_bR4-T1-TRNA-1_B23MHV2LT4_1.md/659_bR4-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 659_bR4-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bR4-T1-TRNA-1_B23MHV2LT4_1/659_bR4-T1-TRNA-1_B23MHV2LT4_1.md/saturation_qc.tsv fragment_size -bams 659_bR4-T1-TRNA-1_B23MHV2LT4_1.md.bam -region chr20 -output_prefix 659_bR4-T1-TRNA-1_B23MHV2LT4_1/659_bR4-T1-TRNA-1_B23MHV2LT4_1.md/fragsize -threads 1 samtools mpileup -B --min-MQ 60 --min-BQ 30 -f ref_genome.fa -l dbsnp_hg38_contam_sites.bed 659_bR4-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bR4-T1-TRNA-1_B23MHV2LT4_1.md.mpileup && contamination -input 659_bR4-T1-TRNA-1_B23MHV2LT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > 659_bR4-T1-TRNA-1_B23MHV2LT4_1/659_bR4-T1-TRNA-1_B23MHV2LT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: 659_bR4-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_bR4-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bR4-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bR4-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bR4-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bR4-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_bR4-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bR4-T1-TRNA-1_B23MHV2LT4_1.md.bai 0it [00:00, ?it/s] 157683it [00:00, 1576436.86it/s] 326559it [00:00, 1642339.91it/s] 498734it [00:00, 1678569.58it/s] 669545it [00:00, 1690207.69it/s] 841860it [00:00, 1702063.42it/s] 1015155it [00:00, 1712545.51it/s] 1187217it [00:00, 1715168.30it/s] 1358813it [00:00, 1715405.23it/s] 1530497it [00:00, 1715836.36it/s] 1702081it [00:01, 1713846.18it/s] 1873467it [00:01, 1701496.45it/s] 2048552it [00:01, 1716411.91it/s] 2220672it [00:01, 1717841.14it/s] 2392995it [00:01, 1719448.81it/s] 2565813it [00:01, 1722060.04it/s] 2738028it [00:01, 1717195.68it/s] 2909757it [00:01, 1715354.54it/s] 3082287it [00:01, 1718319.17it/s] 3254298it [00:01, 1718840.49it/s] 3426186it [00:02, 1708010.87it/s] 3597004it [00:02, 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1591077.75it/s] 8601177it [00:05, 1602750.27it/s] 8771262it [00:05, 1631649.83it/s] 8938643it [00:05, 1644066.33it/s] 9103175it [00:05, 1621062.96it/s] 9270098it [00:05, 1635216.34it/s] 9433743it [00:05, 1630500.98it/s] 9596878it [00:05, 1603823.99it/s] 9757394it [00:05, 1572937.90it/s] 9914863it [00:06, 1479462.67it/s] 10085175it [00:06, 1542452.98it/s] 10259424it [00:06, 1599834.49it/s] 10433117it [00:06, 1639669.92it/s] 10606428it [00:06, 1667072.52it/s] 10780108it [00:06, 1687649.49it/s] 10954212it [00:06, 1703476.98it/s] 11125974it [00:06, 1707667.50it/s] 11299874it [00:06, 1716830.64it/s] 11476005it [00:06, 1729932.89it/s] 11650129it [00:07, 1733290.21it/s] 11826506it [00:07, 1742390.78it/s] 12003017it [00:07, 1749170.22it/s] 12177984it [00:07, 1746217.28it/s] 12352939it [00:07, 1747092.20it/s] 12527674it [00:07, 1742959.60it/s] 12702168it [00:07, 1743527.76it/s] 12710005it [00:07, 1670097.47it/s] [W::hts_idx_load3] The index file is older than the data file: 659_bR4-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bR4-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bR4-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bR4-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bR4-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bR4-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bR4-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bR4-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bR4-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bR4-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bR4-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bR4-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bR4-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bR4-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bR4-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bR4-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bR4-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bR4-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bR4-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bR4-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bR4-T1-TRNA-1_B23MHV2LT4_1.md.bai tabix -s 1 -b 2 -e 2 659_bR4-T1-TRNA-1_B23MHV2LT4_1/659_bR4-T1-TRNA-1_B23MHV2LT4_1.md/659_bR4-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz seqtool depth_hist -nbins 500 659_bR4-T1-TRNA-1_B23MHV2LT4_1/659_bR4-T1-TRNA-1_B23MHV2LT4_1.md/659_bR4-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz > 659_bR4-T1-TRNA-1_B23MHV2LT4_1/659_bR4-T1-TRNA-1_B23MHV2LT4_1.md/659_bR4-T1-TRNA-1_B23MHV2LT4_1.md.depth_hist.tsv cat 659_bR4-T1-TRNA-1_B23MHV2LT4_1/659_bR4-T1-TRNA-1_B23MHV2LT4_1.md/659_bR4-T1-TRNA-1_B23MHV2LT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title 659_bR4-T1-TRNA-1_B23MHV2LT4_1.md -output 659_bR4-T1-TRNA-1_B23MHV2LT4_1/659_bR4-T1-TRNA-1_B23MHV2LT4_1.md/659_bR4-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_bR4-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bR4-T1-TRNA-1_B23MHV2LT4_1/659_bR4-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_bR4-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bR4-T1-TRNA-1_B23MHV2LT4_1/659_bR4-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_bR4-T1-TRNA-1_B23MHV2LT4_1/659_bR4-T1-TRNA-1_B23MHV2LT4_1.md/659_bR4-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz> 659_bR4-T1-TRNA-1_B23MHV2LT4_1/659_bR4-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_bR4-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bR4-T1-TRNA-1_B23MHV2LT4_1/659_bR4-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_bR4-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bR4-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bR4-T1-TRNA-1_B23MHV2LT4_1.md.bai cat 659_bR4-T1-TRNA-1_B23MHV2LT4_1/659_bR4-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_bR4-T1-TRNA-1_B23MHV2LT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "659_bR4-T1-TRNA-1_B23MHV2LT4_1/659_bR4-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_bR4-T1-TRNA-1_B23MHV2LT4_1/659_bR4-T1-TRNA-1_B23MHV2LT4_1.md/qc_complete.txt + merge_qc -folders 659_bR4-T1-TRNA-1_B23MHV2LT4_1/659_bR4-T1-TRNA-1_B23MHV2LT4_1.md -output 659_bR4-T1-TRNA-1_B23MHV2LT4_1/659_bR4-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv + head -n1 659_bR4-T1-TRNA-1_B23MHV2LT4_1/659_bR4-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_bR4-T1-TRNA-1_B23MHV2LT4_1/659_bR4-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv