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/52/2cc9a96ff7228408be08be25c40b24/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/66/5005a8f9b8eb652fec779f90fd6059/659_bhK-T1-TRNA-1_B23WHTKLT4_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/66/5005a8f9b8eb652fec779f90fd6059/659_bhK-T1-TRNA-1_B23WHTKLT4_1.md.bai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/52/2cc9a96ff7228408be08be25c40b24/.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_B23WHTKLT4_1 + all_qc -bam 659_bhK-T1-TRNA-1_B23WHTKLT4_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_bhK-T1-TRNA-1_B23WHTKLT4_1 -reference ref_genome.fa -region chr20 mkdir -p 659_bhK-T1-TRNA-1_B23WHTKLT4_1/659_bhK-T1-TRNA-1_B23WHTKLT4_1.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_B23WHTKLT4_1/659_bhK-T1-TRNA-1_B23WHTKLT4_1.md/full_bed.bed seqtool depth -bam 659_bhK-T1-TRNA-1_B23WHTKLT4_1.md.bam -bed 659_bhK-T1-TRNA-1_B23WHTKLT4_1/659_bhK-T1-TRNA-1_B23WHTKLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > 659_bhK-T1-TRNA-1_B23WHTKLT4_1/659_bhK-T1-TRNA-1_B23WHTKLT4_1.md/659_bhK-T1-TRNA-1_B23WHTKLT4_1.md.depth.gz saturation_plot -bams 659_bhK-T1-TRNA-1_B23WHTKLT4_1.md.bam -region chr20 -output 659_bhK-T1-TRNA-1_B23WHTKLT4_1/659_bhK-T1-TRNA-1_B23WHTKLT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 659_bhK-T1-TRNA-1_B23WHTKLT4_1.md.bam > 659_bhK-T1-TRNA-1_B23WHTKLT4_1/659_bhK-T1-TRNA-1_B23WHTKLT4_1.md/saturation_qc.tsv fragment_size -bams 659_bhK-T1-TRNA-1_B23WHTKLT4_1.md.bam -region chr20 -output_prefix 659_bhK-T1-TRNA-1_B23WHTKLT4_1/659_bhK-T1-TRNA-1_B23WHTKLT4_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_bhK-T1-TRNA-1_B23WHTKLT4_1.md.bam > 659_bhK-T1-TRNA-1_B23WHTKLT4_1.md.mpileup && contamination -input 659_bhK-T1-TRNA-1_B23WHTKLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > 659_bhK-T1-TRNA-1_B23WHTKLT4_1/659_bhK-T1-TRNA-1_B23WHTKLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23WHTKLT4_1.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_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23WHTKLT4_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_bhK-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23WHTKLT4_1.md.bai 0it [00:00, ?it/s] 148042it [00:00, 1480019.15it/s] 309007it [00:00, 1556236.59it/s] 472822it [00:00, 1593618.96it/s] 642868it [00:00, 1635778.66it/s] 814470it [00:00, 1664693.69it/s] 985049it [00:00, 1678579.46it/s] 1152908it [00:00, 1675124.91it/s] 1324689it [00:00, 1688680.62it/s] 1493561it [00:00, 1684374.07it/s] 1664361it [00:01, 1691635.54it/s] 1835783it [00:01, 1698428.56it/s] 2005631it [00:01, 1695716.47it/s] 2175207it [00:01, 1678783.81it/s] 2347724it [00:01, 1692666.96it/s] 2523233it [00:01, 1711358.58it/s] 2694407it [00:01, 1707814.19it/s] 2865215it [00:01, 1688238.80it/s] 3037136it [00:01, 1697422.99it/s] 3206932it [00:01, 1692069.15it/s] 3376177it [00:02, 1659630.58it/s] 3542283it [00:02, 1651396.68it/s] 3711456it [00:02, 1663279.08it/s] 3881949it [00:02, 1675468.00it/s] 4052162it [00:02, 1683383.09it/s] 4220848it [00:02, 1684402.62it/s] 4389331it [00:02, 1679902.11it/s] 4560509it [00:02, 1689280.76it/s] 4732114it [00:02, 1697264.08it/s] 4903951it [00:02, 1703566.59it/s] 5074324it [00:03, 1677905.76it/s] 5242210it [00:03, 1666685.39it/s] 5412813it [00:03, 1678320.84it/s] 5585405it [00:03, 1692454.30it/s] 5758917it [00:03, 1705158.55it/s] 5934039it [00:03, 1718898.94it/s] 6106394it [00:03, 1720276.82it/s] 6278451it [00:03, 1713039.71it/s] 6449781it [00:03, 1711222.11it/s] 6622530it [00:03, 1715949.16it/s] 6794140it [00:04, 1706898.26it/s] 6964849it [00:04, 1700132.96it/s] 7137796it [00:04, 1708808.05it/s] 7308694it [00:04, 1704960.44it/s] 7479202it [00:04, 1703997.30it/s] 7652793it [00:04, 1713447.77it/s] 7825197it [00:04, 1716603.70it/s] 7996865it [00:04, 1714229.73it/s] 8168294it [00:04, 1713016.09it/s] 8339600it [00:04, 1710648.90it/s] 8510668it [00:05, 1702784.80it/s] 8680955it [00:05, 1695225.36it/s][W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23WHTKLT4_1.md.bai 8850488it [00:05, 1694872.86it/s] 9019983it [00:05, 1681040.61it/s] 9188112it [00:05, 1662644.61it/s] 9357758it [00:05, 1672638.83it/s] 9531267it [00:05, 1691159.51it/s] 9705303it [00:05, 1705805.41it/s] 9879799it [00:05, 1717483.93it/s] 10052012it [00:05, 1718773.00it/s] 10223917it [00:06, 1710269.19it/s] 10394971it [00:06, 1702479.04it/s] 10568372it [00:06, 1711799.65it/s] 10739575it [00:06, 1708166.64it/s] 10910408it [00:06, 1707181.86it/s] 11081137it [00:06, 1705423.61it/s] 11251687it [00:06, 1699706.66it/s] 11421666it [00:06, 1693333.80it/s] 11592715it [00:06, 1698440.73it/s] 11762926it [00:06, 1699526.49it/s] 11933566it [00:07, 1701562.33it/s] 12105934it [00:07, 1708119.76it/s] 12277631it [00:07, 1710759.18it/s] 12450434it [00:07, 1715923.28it/s] 12622030it [00:07, 1705384.04it/s] 12704825it [00:07, 1693598.56it/s] [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23WHTKLT4_1.md.bai tabix -s 1 -b 2 -e 2 659_bhK-T1-TRNA-1_B23WHTKLT4_1/659_bhK-T1-TRNA-1_B23WHTKLT4_1.md/659_bhK-T1-TRNA-1_B23WHTKLT4_1.md.depth.gz seqtool depth_hist -nbins 500 659_bhK-T1-TRNA-1_B23WHTKLT4_1/659_bhK-T1-TRNA-1_B23WHTKLT4_1.md/659_bhK-T1-TRNA-1_B23WHTKLT4_1.md.depth.gz > 659_bhK-T1-TRNA-1_B23WHTKLT4_1/659_bhK-T1-TRNA-1_B23WHTKLT4_1.md/659_bhK-T1-TRNA-1_B23WHTKLT4_1.md.depth_hist.tsv cat 659_bhK-T1-TRNA-1_B23WHTKLT4_1/659_bhK-T1-TRNA-1_B23WHTKLT4_1.md/659_bhK-T1-TRNA-1_B23WHTKLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title 659_bhK-T1-TRNA-1_B23WHTKLT4_1.md -output 659_bhK-T1-TRNA-1_B23WHTKLT4_1/659_bhK-T1-TRNA-1_B23WHTKLT4_1.md/659_bhK-T1-TRNA-1_B23WHTKLT4_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_bhK-T1-TRNA-1_B23WHTKLT4_1.md.bam > 659_bhK-T1-TRNA-1_B23WHTKLT4_1/659_bhK-T1-TRNA-1_B23WHTKLT4_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_bhK-T1-TRNA-1_B23WHTKLT4_1.md.bam > 659_bhK-T1-TRNA-1_B23WHTKLT4_1/659_bhK-T1-TRNA-1_B23WHTKLT4_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_bhK-T1-TRNA-1_B23WHTKLT4_1/659_bhK-T1-TRNA-1_B23WHTKLT4_1.md/659_bhK-T1-TRNA-1_B23WHTKLT4_1.md.depth.gz> 659_bhK-T1-TRNA-1_B23WHTKLT4_1/659_bhK-T1-TRNA-1_B23WHTKLT4_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_bhK-T1-TRNA-1_B23WHTKLT4_1.md.bam > 659_bhK-T1-TRNA-1_B23WHTKLT4_1/659_bhK-T1-TRNA-1_B23WHTKLT4_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_bhK-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23WHTKLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23WHTKLT4_1.md.bai cat 659_bhK-T1-TRNA-1_B23WHTKLT4_1/659_bhK-T1-TRNA-1_B23WHTKLT4_1.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_B23WHTKLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "659_bhK-T1-TRNA-1_B23WHTKLT4_1/659_bhK-T1-TRNA-1_B23WHTKLT4_1.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_B23WHTKLT4_1/659_bhK-T1-TRNA-1_B23WHTKLT4_1.md/qc_complete.txt + merge_qc -folders 659_bhK-T1-TRNA-1_B23WHTKLT4_1/659_bhK-T1-TRNA-1_B23WHTKLT4_1.md -output 659_bhK-T1-TRNA-1_B23WHTKLT4_1/659_bhK-T1-TRNA-1_B23WHTKLT4_1_full_basic_stats.tsv + head -n1 659_bhK-T1-TRNA-1_B23WHTKLT4_1/659_bhK-T1-TRNA-1_B23WHTKLT4_1_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_B23WHTKLT4_1/659_bhK-T1-TRNA-1_B23WHTKLT4_1_full_basic_stats.tsv