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/d0/b0fafbe56e71edb27e272dedb60c39/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f0/c69779d10a7c55a6db7f981583392e/659_bQZ-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/f0/c69779d10a7c55a6db7f981583392e/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d0/b0fafbe56e71edb27e272dedb60c39/.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_bQZ-T1-TRNA-1_B23MHV2LT4_1 + all_qc -bam 659_bQZ-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_bQZ-T1-TRNA-1_B23MHV2LT4_1 -reference ref_genome.fa -region chr20 mkdir -p 659_bQZ-T1-TRNA-1_B23MHV2LT4_1/659_bQZ-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_bQZ-T1-TRNA-1_B23MHV2LT4_1/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md/full_bed.bed seqtool depth -bam 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bam -bed 659_bQZ-T1-TRNA-1_B23MHV2LT4_1/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > 659_bQZ-T1-TRNA-1_B23MHV2LT4_1/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz saturation_plot -bams 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bam -region chr20 -output 659_bQZ-T1-TRNA-1_B23MHV2LT4_1/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bQZ-T1-TRNA-1_B23MHV2LT4_1/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md/saturation_qc.tsv fragment_size -bams 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bam -region chr20 -output_prefix 659_bQZ-T1-TRNA-1_B23MHV2LT4_1/659_bQZ-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_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.mpileup && contamination -input 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > 659_bQZ-T1-TRNA-1_B23MHV2LT4_1/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-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_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-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_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai 0it [00:00, ?it/s] 146425it [00:00, 1464160.63it/s] 297851it [00:00, 1493442.45it/s] 458248it [00:00, 1543866.17it/s] 619505it [00:00, 1570963.34it/s] 788856it [00:00, 1615127.82it/s] 957331it [00:00, 1638778.97it/s] 1124645it [00:00, 1649994.48it/s] 1295663it [00:00, 1669136.83it/s] 1464342it [00:00, 1674637.09it/s] 1634341it [00:01, 1682445.75it/s] 1803368it [00:01, 1684821.14it/s] 1972204it [00:01, 1685873.70it/s] 2141082it [00:01, 1686732.66it/s] 2309756it [00:01, 1673120.59it/s] 2483741it [00:01, 1693068.07it/s] 2660885it [00:01, 1716544.70it/s] 2834772it [00:01, 1723219.87it/s] 3007117it [00:01, 1708919.88it/s] 3178050it [00:01, 1706003.38it/s] 3348678it [00:02, 1689433.03it/s] 3519604it [00:02, 1695298.75it/s] 3689173it [00:02, 1688570.10it/s] 3859538it [00:02, 1693039.89it/s] 4029863it [00:02, 1696069.09it/s] 4199489it [00:02, 1689548.78it/s] 4371319it [00:02, 1698092.04it/s] 4541145it [00:02, 1665693.94it/s] 4707853it [00:02, 1546074.51it/s] 4864145it [00:02, 1493103.35it/s] 5014772it [00:03, 1479564.62it/s] 5178596it [00:03, 1524380.47it/s] 5337437it [00:03, 1542760.96it/s] 5505610it [00:03, 1583201.09it/s] 5677552it [00:03, 1623056.05it/s] 5847730it [00:03, 1646300.38it/s] 6018826it [00:03, 1665470.05it/s] 6188716it [00:03, 1675355.27it/s] 6358690it [00:03, 1682601.34it/s] 6527103it [00:03, 1673561.24it/s] 6696426it [00:04, 1679350.13it/s] 6865982it [00:04, 1684170.94it/s] 7034461it [00:04, 1684318.11it/s] 7202936it [00:04, 1649675.04it/s] 7372609it [00:04, 1663550.45it/s] 7543521it [00:04, 1677048.95it/s] 7715460it [00:04, 1689354.39it/s] 7885259it [00:04, 1691910.29it/s] 8054518it [00:04, 1689886.75it/s] 8223554it [00:04, 1689592.84it/s] 8394063it [00:05, 1694213.75it/s] 8563509it [00:05, 1690975.68it/s] 8732625it [00:05, 1689374.40it/s] 8901575it [00:05, 1679678.95it/s] 9070069it [00:05, 1681231.75it/s] 9242879it [00:05, 1695210.66it/s] 9414887it [00:05, 1702636.98it/s] 9586955it [00:05, 1708024.73it/s] 9757878it [00:05, 1708372.86it/s] 9928723it [00:05, 1704926.95it/s] 10099223it [00:06, 1697764.82it/s] 10269010it [00:06, 1684008.90it/s] 10439151it [00:06, 1689074.80it/s] 10608082it [00:06, 1676485.25it/s] 10775761it [00:06, 1666803.32it/s] 10942467it [00:06, 1664925.71it/s] 11108976it [00:06, 1656712.43it/s] 11279872it [00:06, 1672224.88it/s] 11447654it [00:06, 1673879.76it/s] 11617682it [00:06, 1681749.32it/s] 11785874it [00:07, 1674542.31it/s] 11956010it [00:07, 1682531.12it/s] 12126521it [00:07, 1689268.04it/s] 12295462it [00:07, 1686959.44it/s] 12464168it [00:07, 1683204.68it/s] 12633679it [00:07, 1686749.71it/s] 12685388it [00:07, 1664700.77it/s] [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai tabix -s 1 -b 2 -e 2 659_bQZ-T1-TRNA-1_B23MHV2LT4_1/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz seqtool depth_hist -nbins 500 659_bQZ-T1-TRNA-1_B23MHV2LT4_1/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz > 659_bQZ-T1-TRNA-1_B23MHV2LT4_1/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.depth_hist.tsv cat 659_bQZ-T1-TRNA-1_B23MHV2LT4_1/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md -output 659_bQZ-T1-TRNA-1_B23MHV2LT4_1/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md/659_bQZ-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_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bQZ-T1-TRNA-1_B23MHV2LT4_1/659_bQZ-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_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bQZ-T1-TRNA-1_B23MHV2LT4_1/659_bQZ-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_bQZ-T1-TRNA-1_B23MHV2LT4_1/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.depth.gz> 659_bQZ-T1-TRNA-1_B23MHV2LT4_1/659_bQZ-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_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bam > 659_bQZ-T1-TRNA-1_B23MHV2LT4_1/659_bQZ-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_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md.bai cat 659_bQZ-T1-TRNA-1_B23MHV2LT4_1/659_bQZ-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_bQZ-T1-TRNA-1_B23MHV2LT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "659_bQZ-T1-TRNA-1_B23MHV2LT4_1/659_bQZ-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_bQZ-T1-TRNA-1_B23MHV2LT4_1/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md/qc_complete.txt + merge_qc -folders 659_bQZ-T1-TRNA-1_B23MHV2LT4_1/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.md -output 659_bQZ-T1-TRNA-1_B23MHV2LT4_1/659_bQZ-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv + head -n1 659_bQZ-T1-TRNA-1_B23MHV2LT4_1/659_bQZ-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_bQZ-T1-TRNA-1_B23MHV2LT4_1/659_bQZ-T1-TRNA-1_B23MHV2LT4_1_full_basic_stats.tsv