Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/71/47a2e7d44667dfa9a332c3230b79ff/aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md.bam 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/6d/3c113421fc77583ac2e1225df59f29/.command.sh 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/6d/3c113421fc77583ac2e1225df59f29/.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-rnd-pltf-dev-nextflow-scratch-01/work/71/47a2e7d44667dfa9a332c3230b79ff/aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md.bai 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-3377ac-R1_A23YTGFLT4_1 + all_qc -bam aih-tih-sc-3377ac-R1_A23YTGFLT4_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-3377ac-R1_A23YTGFLT4_1 -reference ref_genome.fa -region chr20 mkdir -p aih-tih-sc-3377ac-R1_A23YTGFLT4_1/aih-tih-sc-3377ac-R1_A23YTGFLT4_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-3377ac-R1_A23YTGFLT4_1/aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md/full_bed.bed seqtool depth -bam aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md.bam -bed aih-tih-sc-3377ac-R1_A23YTGFLT4_1/aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-3377ac-R1_A23YTGFLT4_1/aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md/aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md.depth.gz saturation_plot -bams aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md.bam -region chr20 -output aih-tih-sc-3377ac-R1_A23YTGFLT4_1/aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-3377ac-R1_A23YTGFLT4_1/aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md/saturation_qc.tsv fragment_size -bams aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-3377ac-R1_A23YTGFLT4_1/aih-tih-sc-3377ac-R1_A23YTGFLT4_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-3377ac-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md.mpileup && contamination -input aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-3377ac-R1_A23YTGFLT4_1/aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3377ac-R1_A23YTGFLT4_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-3377ac-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3377ac-R1_A23YTGFLT4_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-3377ac-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md.bai 0it [00:00, ?it/s] 142391it [00:00, 1423795.94it/s] 304992it [00:00, 1542513.03it/s] 474651it [00:00, 1612828.23it/s] 640909it [00:00, 1632438.15it/s] 810650it [00:00, 1655835.37it/s] 980820it [00:00, 1671395.26it/s] 1149442it [00:00, 1676212.06it/s] 1320692it [00:00, 1687645.29it/s] 1492314it [00:00, 1696548.90it/s] 1661969it [00:01, 1691042.36it/s] 1831084it [00:01, 1690780.31it/s] 2000165it [00:01, 1670981.88it/s] 2171258it [00:01, 1682942.71it/s] 2347568it [00:01, 1706967.08it/s] 2518840it [00:01, 1708635.00it/s] 2689738it [00:01, 1708574.00it/s] 2860620it [00:01, 1546060.61it/s] 3032425it [00:01, 1594094.89it/s] 3195248it [00:01, 1603645.11it/s] 3357354it [00:02, 1574692.08it/s] 3528008it [00:02, 1612657.65it/s] 3690313it [00:02, 1590108.47it/s] 3858194it [00:02, 1615864.31it/s] 4027526it [00:02, 1638545.48it/s] 4193042it [00:02, 1643407.66it/s] 4360097it [00:02, 1651208.28it/s] 4527434it [00:02, 1657761.46it/s] 4698770it [00:02, 1674307.18it/s] 4871661it [00:02, 1690583.91it/s] 5040819it [00:03, 1645255.78it/s] 5212905it [00:03, 1667427.15it/s] 5387472it [00:03, 1690397.23it/s] 5560684it [00:03, 1702751.46it/s] 5732719it [00:03, 1707956.40it/s] 5906280it [00:03, 1716177.17it/s] 6077989it [00:03, 1709600.89it/s] 6249017it [00:03, 1704072.07it/s] 6419473it [00:03, 1631991.73it/s] 6583320it [00:03, 1591299.87it/s] 6743013it [00:04, 1589955.54it/s] 6903161it [00:04, 1593285.25it/s] 7062772it [00:04, 1586765.05it/s] 7233388it [00:04, 1621884.70it/s] 7404733it [00:04, 1648838.61it/s] 7575480it [00:04, 1666192.86it/s] 7744128it [00:04, 1672144.22it/s] 7916152it [00:04, 1686479.59it/s] 8087212it [00:04, 1693664.65it/s] 8257209it [00:04, 1695483.39it/s] 8426798it [00:05, 1695005.32it/s] 8596327it [00:05, 1692301.34it/s] 8765578it [00:05, 1680635.39it/s] 8933672it [00:05, 1672529.48it/s] 9105328it [00:05, 1685561.06it/s] 9277147it [00:05, 1695269.38it/s] 9449751it [00:05, 1704312.04it/s] 9620204it [00:05, 1697011.22it/s] 9795581it [00:05, 1713927.62it/s] 9968910it [00:05, 1719590.22it/s] 10140887it [00:06, 1714802.11it/s] 10312382it [00:06, 1694824.10it/s] 10481921it [00:06, 1683498.15it/s] 10650316it [00:06, 1658335.88it/s] 10816238it [00:06, 1640958.86it/s] 10981784it [00:06, 1645191.07it/s] 11151465it [00:06, 1660372.94it/s] 11320567it [00:06, 1669450.70it/s] 11490740it [00:06, 1679043.94it/s] 11663420it [00:07, 1693277.20it/s] 11832787it [00:07, 1692024.03it/s] 12005689it [00:07, 1703048.89it/s] 12177001it [00:07, 1706039.76it/s] 12347622it [00:07, 1701674.99it/s] 12517803it [00:07, 1638651.07it/s] 12682165it [00:07, 1625526.21it/s] 12834070it [00:07, 1659699.49it/s] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md.bai tabix -s 1 -b 2 -e 2 aih-tih-sc-3377ac-R1_A23YTGFLT4_1/aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md/aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md.depth.gz seqtool depth_hist -nbins 500 aih-tih-sc-3377ac-R1_A23YTGFLT4_1/aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md/aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md.depth.gz > aih-tih-sc-3377ac-R1_A23YTGFLT4_1/aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md/aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md.depth_hist.tsv cat aih-tih-sc-3377ac-R1_A23YTGFLT4_1/aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md/aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md -output aih-tih-sc-3377ac-R1_A23YTGFLT4_1/aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md/aih-tih-sc-3377ac-R1_A23YTGFLT4_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-3377ac-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-3377ac-R1_A23YTGFLT4_1/aih-tih-sc-3377ac-R1_A23YTGFLT4_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-3377ac-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-3377ac-R1_A23YTGFLT4_1/aih-tih-sc-3377ac-R1_A23YTGFLT4_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-3377ac-R1_A23YTGFLT4_1/aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md/aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md.depth.gz> aih-tih-sc-3377ac-R1_A23YTGFLT4_1/aih-tih-sc-3377ac-R1_A23YTGFLT4_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-3377ac-R1_A23YTGFLT4_1.md.bam > aih-tih-sc-3377ac-R1_A23YTGFLT4_1/aih-tih-sc-3377ac-R1_A23YTGFLT4_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-3377ac-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md.bai cat aih-tih-sc-3377ac-R1_A23YTGFLT4_1/aih-tih-sc-3377ac-R1_A23YTGFLT4_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-3377ac-R1_A23YTGFLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "aih-tih-sc-3377ac-R1_A23YTGFLT4_1/aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile" echo `date` > aih-tih-sc-3377ac-R1_A23YTGFLT4_1/aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md/qc_complete.txt + merge_qc -folders aih-tih-sc-3377ac-R1_A23YTGFLT4_1/aih-tih-sc-3377ac-R1_A23YTGFLT4_1.md -output aih-tih-sc-3377ac-R1_A23YTGFLT4_1/aih-tih-sc-3377ac-R1_A23YTGFLT4_1_full_basic_stats.tsv + head -n1 aih-tih-sc-3377ac-R1_A23YTGFLT4_1/aih-tih-sc-3377ac-R1_A23YTGFLT4_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-3377ac-R1_A23YTGFLT4_1/aih-tih-sc-3377ac-R1_A23YTGFLT4_1_full_basic_stats.tsv