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/ce/777741159a8ad1b119f8cfd5faf368/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c1/69359b6b8de1390cf1d07b10b23d02/aih-tih-sc-79f487-R1_B23WHYVLT4_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/c1/69359b6b8de1390cf1d07b10b23d02/aih-tih-sc-79f487-R1_B23WHYVLT4_1.md.bam Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ce/777741159a8ad1b119f8cfd5faf368/.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 aih-tih-sc-79f487-R1_B23WHYVLT4_1 + all_qc -bam aih-tih-sc-79f487-R1_B23WHYVLT4_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 aih-tih-sc-79f487-R1_B23WHYVLT4_1 -reference ref_genome.fa -region chr20 mkdir -p aih-tih-sc-79f487-R1_B23WHYVLT4_1/aih-tih-sc-79f487-R1_B23WHYVLT4_1.md/ cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > aih-tih-sc-79f487-R1_B23WHYVLT4_1/aih-tih-sc-79f487-R1_B23WHYVLT4_1.md/full_bed.bed seqtool depth -bam aih-tih-sc-79f487-R1_B23WHYVLT4_1.md.bam -bed aih-tih-sc-79f487-R1_B23WHYVLT4_1/aih-tih-sc-79f487-R1_B23WHYVLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-79f487-R1_B23WHYVLT4_1/aih-tih-sc-79f487-R1_B23WHYVLT4_1.md/aih-tih-sc-79f487-R1_B23WHYVLT4_1.md.depth.gz saturation_plot -bams aih-tih-sc-79f487-R1_B23WHYVLT4_1.md.bam -region chr20 -output aih-tih-sc-79f487-R1_B23WHYVLT4_1/aih-tih-sc-79f487-R1_B23WHYVLT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-79f487-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-79f487-R1_B23WHYVLT4_1/aih-tih-sc-79f487-R1_B23WHYVLT4_1.md/saturation_qc.tsv fragment_size -bams aih-tih-sc-79f487-R1_B23WHYVLT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-79f487-R1_B23WHYVLT4_1/aih-tih-sc-79f487-R1_B23WHYVLT4_1.md/fragsize -threads 1 samtools mpileup -B --min-MQ 60 --min-BQ 30 -f ref_genome.fa -l dbsnp_hg38_contam_sites.bed aih-tih-sc-79f487-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-79f487-R1_B23WHYVLT4_1.md.mpileup && contamination -input aih-tih-sc-79f487-R1_B23WHYVLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-79f487-R1_B23WHYVLT4_1/aih-tih-sc-79f487-R1_B23WHYVLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-79f487-R1_B23WHYVLT4_1.md.bai [mpileup] 1 samples in 1 input files [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-79f487-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-79f487-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-79f487-R1_B23WHYVLT4_1.md.bai The index file is older than the data file: aih-tih-sc-79f487-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-79f487-R1_B23WHYVLT4_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: aih-tih-sc-79f487-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-79f487-R1_B23WHYVLT4_1.md.bai 0it [00:00, ?it/s] 144142it [00:00, 1441115.58it/s] 298832it [00:00, 1503303.41it/s] 451300it [00:00, 1512931.09it/s] 606785it [00:00, 1529459.16it/s] 763645it [00:00, 1543553.34it/s] 919524it [00:00, 1548716.48it/s] 1077770it [00:00, 1559734.68it/s] 1234388it [00:00, 1561770.37it/s] 1390912it [00:00, 1562840.32it/s] 1547197it [00:01, 1561406.07it/s] 1703338it [00:01, 1558552.83it/s] 1861348it [00:01, 1565083.23it/s] 2019924it [00:01, 1571326.20it/s] 2177073it [00:01, 1571359.13it/s] 2338001it [00:01, 1582768.44it/s] 2500784it [00:01, 1596311.75it/s] 2660417it [00:01, 1586876.79it/s] 2819119it [00:01, 1578004.27it/s] 2976937it [00:01, 1577960.64it/s] 3134746it [00:02, 1569676.84it/s] 3291729it [00:02, 1568775.46it/s] 3450500it [00:02, 1574409.67it/s] 3614185it [00:02, 1593057.62it/s] 3778159it [00:02, 1606891.45it/s] 3944128it [00:02, 1622583.55it/s] 4110492it [00:02, 1634867.23it/s] 4273989it [00:02, 1628537.50it/s] 4436855it [00:02, 1623137.66it/s] 4603990it [00:02, 1637502.36it/s] 4772670it [00:03, 1652226.70it/s] 4939776it [00:03, 1657846.28it/s] 5107512it [00:03, 1663587.94it/s] 5273880it [00:03, 1641680.64it/s] 5442944it [00:03, 1656204.24it/s] 5608747it [00:03, 1656730.90it/s] 5774465it [00:03, 1655266.83it/s] 5941672it [00:03, 1660274.24it/s] 6110997it [00:03, 1670123.01it/s] 6278919it [00:03, 1672725.19it/s] 6446206it [00:04, 1665574.73it/s] 6613173it [00:04, 1666783.37it/s] 6779863it [00:04, 1662991.27it/s] 6946172it [00:04, 1638099.93it/s] 7110065it [00:04, 1630247.76it/s] 7273147it [00:04, 1628847.50it/s] 7441127it [00:04, 1643972.83it/s] 7607188it [00:04, 1648914.61it/s] 7774398it [00:04, 1655664.70it/s] 7941374it [00:04, 1659864.13it/s] 8108529it [00:05, 1663236.26it/s] 8276522it [00:05, 1668099.31it/s] 8445647it [00:05, 1675020.71it/s] 8613873it [00:05, 1677175.47it/s] 8785007it [00:05, 1687405.62it/s] 8954686it [00:05, 1690121.09it/s] 9123702it [00:05, 1687506.53it/s] 9292456it [00:05, 1686085.04it/s] 9461067it [00:05, 1661643.74it/s] 9629416it [00:05, 1667974.49it/s] 9798472it [00:06, 1674682.36it/s] 9965989it [00:06, 1672258.02it/s] 10133249it [00:06, 1663336.73it/s] 10300971it [00:06, 1667460.03it/s] 10467742it [00:06, 1646221.72it/s] 10635814it [00:06, 1656427.79it/s] 10801518it [00:06, 1651399.28it/s] 10966940it [00:06, 1652156.84it/s] 11132186it [00:06, 1643441.73it/s] 11299686it [00:06, 1652817.49it/s] 11466039it [00:07, 1655964.46it/s] 11531263it [00:07, 1629155.01it/s] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-79f487-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-79f487-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-79f487-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-79f487-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-79f487-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-79f487-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-79f487-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-79f487-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-79f487-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-79f487-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-79f487-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-79f487-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-79f487-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-79f487-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-79f487-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-79f487-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-79f487-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-79f487-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-79f487-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-79f487-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-79f487-R1_B23WHYVLT4_1.md.bai tabix -s 1 -b 2 -e 2 aih-tih-sc-79f487-R1_B23WHYVLT4_1/aih-tih-sc-79f487-R1_B23WHYVLT4_1.md/aih-tih-sc-79f487-R1_B23WHYVLT4_1.md.depth.gz seqtool depth_hist -nbins 500 aih-tih-sc-79f487-R1_B23WHYVLT4_1/aih-tih-sc-79f487-R1_B23WHYVLT4_1.md/aih-tih-sc-79f487-R1_B23WHYVLT4_1.md.depth.gz > aih-tih-sc-79f487-R1_B23WHYVLT4_1/aih-tih-sc-79f487-R1_B23WHYVLT4_1.md/aih-tih-sc-79f487-R1_B23WHYVLT4_1.md.depth_hist.tsv cat aih-tih-sc-79f487-R1_B23WHYVLT4_1/aih-tih-sc-79f487-R1_B23WHYVLT4_1.md/aih-tih-sc-79f487-R1_B23WHYVLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-79f487-R1_B23WHYVLT4_1.md -output aih-tih-sc-79f487-R1_B23WHYVLT4_1/aih-tih-sc-79f487-R1_B23WHYVLT4_1.md/aih-tih-sc-79f487-R1_B23WHYVLT4_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 aih-tih-sc-79f487-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-79f487-R1_B23WHYVLT4_1/aih-tih-sc-79f487-R1_B23WHYVLT4_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 aih-tih-sc-79f487-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-79f487-R1_B23WHYVLT4_1/aih-tih-sc-79f487-R1_B23WHYVLT4_1.md/reads_per_target.Twist_rna_exome_AND_fusion_hg38.bed.tsv seqtool depth_stats -bed Twist_rna_exome_AND_fusion_hg38.bed aih-tih-sc-79f487-R1_B23WHYVLT4_1/aih-tih-sc-79f487-R1_B23WHYVLT4_1.md/aih-tih-sc-79f487-R1_B23WHYVLT4_1.md.depth.gz> aih-tih-sc-79f487-R1_B23WHYVLT4_1/aih-tih-sc-79f487-R1_B23WHYVLT4_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 aih-tih-sc-79f487-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-79f487-R1_B23WHYVLT4_1/aih-tih-sc-79f487-R1_B23WHYVLT4_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: aih-tih-sc-79f487-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-79f487-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-79f487-R1_B23WHYVLT4_1.md.bai cat aih-tih-sc-79f487-R1_B23WHYVLT4_1/aih-tih-sc-79f487-R1_B23WHYVLT4_1.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "aih-tih-sc-79f487-R1_B23WHYVLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "aih-tih-sc-79f487-R1_B23WHYVLT4_1/aih-tih-sc-79f487-R1_B23WHYVLT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > aih-tih-sc-79f487-R1_B23WHYVLT4_1/aih-tih-sc-79f487-R1_B23WHYVLT4_1.md/qc_complete.txt + merge_qc -folders aih-tih-sc-79f487-R1_B23WHYVLT4_1/aih-tih-sc-79f487-R1_B23WHYVLT4_1.md -output aih-tih-sc-79f487-R1_B23WHYVLT4_1/aih-tih-sc-79f487-R1_B23WHYVLT4_1_full_basic_stats.tsv + head -n1 aih-tih-sc-79f487-R1_B23WHYVLT4_1/aih-tih-sc-79f487-R1_B23WHYVLT4_1_full_basic_stats.tsv ++ basename Twist_rna_exome_AND_fusion_hg38.bed + grep -e Twist_rna_exome_AND_fusion_hg38.bed aih-tih-sc-79f487-R1_B23WHYVLT4_1/aih-tih-sc-79f487-R1_B23WHYVLT4_1_full_basic_stats.tsv