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/e1/d5f8007d0f89a4b198d1054bf1cdba/659_bhK-T1-TRNA-1_A23MVY2LT4_2.md.bai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f4/341abee910991c7b0f678cb93efbbc/.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/e1/d5f8007d0f89a4b198d1054bf1cdba/659_bhK-T1-TRNA-1_A23MVY2LT4_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/f4/341abee910991c7b0f678cb93efbbc/.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 659_bhK-T1-TRNA-1_A23MVY2LT4_2 + all_qc -bam 659_bhK-T1-TRNA-1_A23MVY2LT4_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 659_bhK-T1-TRNA-1_A23MVY2LT4_2 -reference ref_genome.fa -region chr20 mkdir -p 659_bhK-T1-TRNA-1_A23MVY2LT4_2/659_bhK-T1-TRNA-1_A23MVY2LT4_2.md/ cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > 659_bhK-T1-TRNA-1_A23MVY2LT4_2/659_bhK-T1-TRNA-1_A23MVY2LT4_2.md/full_bed.bed seqtool depth -bam 659_bhK-T1-TRNA-1_A23MVY2LT4_2.md.bam -bed 659_bhK-T1-TRNA-1_A23MVY2LT4_2/659_bhK-T1-TRNA-1_A23MVY2LT4_2.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > 659_bhK-T1-TRNA-1_A23MVY2LT4_2/659_bhK-T1-TRNA-1_A23MVY2LT4_2.md/659_bhK-T1-TRNA-1_A23MVY2LT4_2.md.depth.gz saturation_plot -bams 659_bhK-T1-TRNA-1_A23MVY2LT4_2.md.bam -region chr20 -output 659_bhK-T1-TRNA-1_A23MVY2LT4_2/659_bhK-T1-TRNA-1_A23MVY2LT4_2.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 659_bhK-T1-TRNA-1_A23MVY2LT4_2.md.bam > 659_bhK-T1-TRNA-1_A23MVY2LT4_2/659_bhK-T1-TRNA-1_A23MVY2LT4_2.md/saturation_qc.tsv fragment_size -bams 659_bhK-T1-TRNA-1_A23MVY2LT4_2.md.bam -region chr20 -output_prefix 659_bhK-T1-TRNA-1_A23MVY2LT4_2/659_bhK-T1-TRNA-1_A23MVY2LT4_2.md/fragsize -threads 1 samtools mpileup -B --min-MQ 60 --min-BQ 30 -f ref_genome.fa -l dbsnp_hg38_contam_sites.bed 659_bhK-T1-TRNA-1_A23MVY2LT4_2.md.bam > 659_bhK-T1-TRNA-1_A23MVY2LT4_2.md.mpileup && contamination -input 659_bhK-T1-TRNA-1_A23MVY2LT4_2.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > 659_bhK-T1-TRNA-1_A23MVY2LT4_2/659_bhK-T1-TRNA-1_A23MVY2LT4_2.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_2.md.bai [mpileup] 1 samples in 1 input files [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_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: 659_bhK-T1-TRNA-1_A23MVY2LT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_2.md.bai 0it [00:00, ?it/s] 143306it [00:00, 1432948.62it/s] 306672it [00:00, 1550326.36it/s] 470650it [00:00, 1591135.25it/s] 639211it [00:00, 1628405.80it/s] 805432it [00:00, 1640408.86it/s] 969473it [00:00, 1637641.01it/s] 1137109it [00:00, 1650263.45it/s] 1302663it [00:00, 1651922.28it/s] 1467872it [00:00, 1651955.48it/s] 1636383it [00:01, 1662050.21it/s] 1806695it [00:01, 1674538.86it/s] 1976389it [00:01, 1681331.42it/s] 2144523it [00:01, 1677385.81it/s] 2318416it [00:01, 1695927.93it/s] 2490368it [00:01, 1703013.80it/s] 2661237it [00:01, 1704705.44it/s] 2831711it [00:01, 1700943.25it/s] 3003973it [00:01, 1707261.35it/s] 3175508it [00:01, 1709671.75it/s] 3346479it [00:02, 1682110.58it/s] 3514790it [00:02, 1682045.90it/s] 3685988it [00:02, 1690937.09it/s] 3855162it [00:02, 1691161.42it/s] 4024318it [00:02, 1689770.33it/s] 4193323it [00:02, 1683388.30it/s] 4363569it [00:02, 1689059.42it/s] 4532494it [00:02, 1681803.01it/s] 4700693it [00:02, 1676560.92it/s] 4871621it [00:02, 1686239.41it/s] 5040261it [00:03, 1684197.22it/s] 5208692it [00:03, 1673417.48it/s] 5380204it [00:03, 1685820.47it/s] 5552439it [00:03, 1696701.30it/s] 5726881it [00:03, 1710951.75it/s] 5900117it [00:03, 1717343.93it/s] 6072224it [00:03, 1718444.33it/s] 6244080it [00:03, 1713454.79it/s] 6416530it [00:03, 1716743.27it/s] 6588213it [00:03, 1716293.17it/s] 6759849it [00:04, 1701162.88it/s] 6935144it [00:04, 1716534.40it/s] 7106832it [00:04, 1715724.84it/s] 7282374it [00:04, 1727548.19it/s] 7456767it [00:04, 1732413.57it/s] 7630038it [00:04, 1732468.19it/s] 7803297it [00:04, 1730549.75it/s] 7976361it [00:04, 1721585.74it/s] 8148535it [00:04, 1704522.26it/s] 8319029it [00:04, 1704220.94it/s] 8489480it [00:05, 1682762.55it/s] 8657823it [00:05, 1679791.77it/s] 8828682it [00:05, 1688314.49it/s] 9002261it [00:05, 1702425.96it/s] 9175123it [00:05, 1710210.69it/s] 9347071it [00:05, 1712906.69it/s] 9522624it [00:05, 1725640.39it/s] 9695342it [00:05, 1726084.62it/s] 9867965it [00:05, 1721976.29it/s] 10040175it [00:05, 1705607.50it/s] 10211006it [00:06, 1706396.08it/s] 10381674it [00:06, 1703374.90it/s] 10552031it [00:06, 1683691.09it/s] 10722281it [00:06, 1689250.03it/s][W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_2.md.bai 10891716it [00:06, 1690644.13it/s] 11060814it [00:06, 1688251.66it/s] 11229662it [00:06, 1678177.77it/s] 11398252it [00:06, 1680461.22it/s] 11568151it [00:06, 1685974.08it/s] 11739050it [00:06, 1692828.47it/s] 11909607it [00:07, 1696627.69it/s] 12079536it [00:07, 1697409.58it/s] 12226374it [00:07, 1691598.15it/s] [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_2.md.bai tabix -s 1 -b 2 -e 2 659_bhK-T1-TRNA-1_A23MVY2LT4_2/659_bhK-T1-TRNA-1_A23MVY2LT4_2.md/659_bhK-T1-TRNA-1_A23MVY2LT4_2.md.depth.gz seqtool depth_hist -nbins 500 659_bhK-T1-TRNA-1_A23MVY2LT4_2/659_bhK-T1-TRNA-1_A23MVY2LT4_2.md/659_bhK-T1-TRNA-1_A23MVY2LT4_2.md.depth.gz > 659_bhK-T1-TRNA-1_A23MVY2LT4_2/659_bhK-T1-TRNA-1_A23MVY2LT4_2.md/659_bhK-T1-TRNA-1_A23MVY2LT4_2.md.depth_hist.tsv cat 659_bhK-T1-TRNA-1_A23MVY2LT4_2/659_bhK-T1-TRNA-1_A23MVY2LT4_2.md/659_bhK-T1-TRNA-1_A23MVY2LT4_2.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title 659_bhK-T1-TRNA-1_A23MVY2LT4_2.md -output 659_bhK-T1-TRNA-1_A23MVY2LT4_2/659_bhK-T1-TRNA-1_A23MVY2LT4_2.md/659_bhK-T1-TRNA-1_A23MVY2LT4_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 2 659_bhK-T1-TRNA-1_A23MVY2LT4_2.md.bam > 659_bhK-T1-TRNA-1_A23MVY2LT4_2/659_bhK-T1-TRNA-1_A23MVY2LT4_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 2 659_bhK-T1-TRNA-1_A23MVY2LT4_2.md.bam > 659_bhK-T1-TRNA-1_A23MVY2LT4_2/659_bhK-T1-TRNA-1_A23MVY2LT4_2.md/reads_per_target.Twist_rna_exome_AND_fusion_hg38.bed.tsv seqtool depth_stats -bed Twist_rna_exome_AND_fusion_hg38.bed 659_bhK-T1-TRNA-1_A23MVY2LT4_2/659_bhK-T1-TRNA-1_A23MVY2LT4_2.md/659_bhK-T1-TRNA-1_A23MVY2LT4_2.md.depth.gz> 659_bhK-T1-TRNA-1_A23MVY2LT4_2/659_bhK-T1-TRNA-1_A23MVY2LT4_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 2 659_bhK-T1-TRNA-1_A23MVY2LT4_2.md.bam > 659_bhK-T1-TRNA-1_A23MVY2LT4_2/659_bhK-T1-TRNA-1_A23MVY2LT4_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: 659_bhK-T1-TRNA-1_A23MVY2LT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_2.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_A23MVY2LT4_2.md.bai cat 659_bhK-T1-TRNA-1_A23MVY2LT4_2/659_bhK-T1-TRNA-1_A23MVY2LT4_2.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "659_bhK-T1-TRNA-1_A23MVY2LT4_2.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "659_bhK-T1-TRNA-1_A23MVY2LT4_2/659_bhK-T1-TRNA-1_A23MVY2LT4_2.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > 659_bhK-T1-TRNA-1_A23MVY2LT4_2/659_bhK-T1-TRNA-1_A23MVY2LT4_2.md/qc_complete.txt + merge_qc -folders 659_bhK-T1-TRNA-1_A23MVY2LT4_2/659_bhK-T1-TRNA-1_A23MVY2LT4_2.md -output 659_bhK-T1-TRNA-1_A23MVY2LT4_2/659_bhK-T1-TRNA-1_A23MVY2LT4_2_full_basic_stats.tsv + head -n1 659_bhK-T1-TRNA-1_A23MVY2LT4_2/659_bhK-T1-TRNA-1_A23MVY2LT4_2_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed 659_bhK-T1-TRNA-1_A23MVY2LT4_2/659_bhK-T1-TRNA-1_A23MVY2LT4_2_full_basic_stats.tsv