Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e4/ce7f360b0dfc2e97188385b240195c/aih-tih-sc-f14fdc-R1_B23WHYVLT4_1.md.bai 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/df/deac541659f851723f585e27d33fd7/.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/df/deac541659f851723f585e27d33fd7/.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/e4/ce7f360b0dfc2e97188385b240195c/aih-tih-sc-f14fdc-R1_B23WHYVLT4_1.md.bam 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-f14fdc-R1_B23WHYVLT4_1 + all_qc -bam aih-tih-sc-f14fdc-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-f14fdc-R1_B23WHYVLT4_1 -reference ref_genome.fa -region chr20 mkdir -p aih-tih-sc-f14fdc-R1_B23WHYVLT4_1/aih-tih-sc-f14fdc-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-f14fdc-R1_B23WHYVLT4_1/aih-tih-sc-f14fdc-R1_B23WHYVLT4_1.md/full_bed.bed seqtool depth -bam aih-tih-sc-f14fdc-R1_B23WHYVLT4_1.md.bam -bed aih-tih-sc-f14fdc-R1_B23WHYVLT4_1/aih-tih-sc-f14fdc-R1_B23WHYVLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-f14fdc-R1_B23WHYVLT4_1/aih-tih-sc-f14fdc-R1_B23WHYVLT4_1.md/aih-tih-sc-f14fdc-R1_B23WHYVLT4_1.md.depth.gz saturation_plot -bams aih-tih-sc-f14fdc-R1_B23WHYVLT4_1.md.bam -region chr20 -output aih-tih-sc-f14fdc-R1_B23WHYVLT4_1/aih-tih-sc-f14fdc-R1_B23WHYVLT4_1.md/saturation_plot.png -threads 1 seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-f14fdc-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-f14fdc-R1_B23WHYVLT4_1/aih-tih-sc-f14fdc-R1_B23WHYVLT4_1.md/saturation_qc.tsv fragment_size -bams aih-tih-sc-f14fdc-R1_B23WHYVLT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-f14fdc-R1_B23WHYVLT4_1/aih-tih-sc-f14fdc-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-f14fdc-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-f14fdc-R1_B23WHYVLT4_1.md.mpileup && contamination -input aih-tih-sc-f14fdc-R1_B23WHYVLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-f14fdc-R1_B23WHYVLT4_1/aih-tih-sc-f14fdc-R1_B23WHYVLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f14fdc-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-f14fdc-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f14fdc-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f14fdc-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f14fdc-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f14fdc-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-f14fdc-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f14fdc-R1_B23WHYVLT4_1.md.bai 0it [00:00, ?it/s] 145127it [00:00, 1451036.14it/s] 297278it [00:00, 1492437.11it/s] 454229it [00:00, 1525544.74it/s] 616488it [00:00, 1563739.50it/s] 772862it [00:00, 1552241.80it/s] 939711it [00:00, 1591529.78it/s] 1105279it [00:00, 1612306.55it/s] 1272744it [00:00, 1632082.87it/s] 1440542it [00:00, 1646384.89it/s] 1607356it [00:01, 1653072.95it/s] 1772677it [00:01, 1652290.16it/s] 1940608it [00:01, 1660483.48it/s] 2106664it [00:01, 1647866.21it/s] 2274201it [00:01, 1656102.42it/s] 2448452it [00:01, 1682005.87it/s] 2616680it [00:01, 1680868.97it/s] 2784786it [00:01, 1680805.35it/s] 2952880it [00:01, 1678246.66it/s] 3121500it [00:01, 1680601.45it/s] 3289568it [00:02, 1649215.74it/s] 3457076it [00:02, 1656846.58it/s] 3624523it [00:02, 1662060.56it/s] 3794297it [00:02, 1672545.93it/s] 3961613it [00:02, 1669766.70it/s] 4128766it [00:02, 1670197.40it/s] 4298157it [00:02, 1677264.40it/s] 4465907it [00:02, 1673216.05it/s] 4633809it [00:02, 1674849.22it/s] 4802567it [00:02, 1678641.88it/s] 4971680it [00:03, 1682358.49it/s] 5139924it [00:03, 1677348.08it/s] 5308543it [00:03, 1679968.22it/s] 5476547it [00:03, 1664313.88it/s] 5643014it [00:03, 1634077.55it/s] 5812166it [00:03, 1650971.75it/s] 5984002it [00:03, 1670900.82it/s] 6155055it [00:03, 1682611.33it/s] 6323404it [00:03, 1619602.90it/s] 6485901it [00:03, 1609086.22it/s] 6647927it [00:04, 1612261.57it/s] 6815130it [00:04, 1629822.63it/s] 6983578it [00:04, 1645896.69it/s] 7148342it [00:04, 1646015.19it/s] 7315573it [00:04, 1653821.78it/s] 7484941it [00:04, 1665695.94it/s] 7652086it [00:04, 1667300.30it/s] 7818865it [00:04, 1661849.34it/s] 7985354it [00:04, 1662734.63it/s] 8151654it [00:04, 1661722.94it/s] 8317845it [00:05, 1661091.99it/s] 8484204it [00:05, 1661811.89it/s] 8652018it [00:05, 1666680.04it/s] 8818694it [00:05, 1657556.27it/s] 8984466it [00:05, 1654561.55it/s] 9153903it [00:05, 1666428.61it/s] 9320650it [00:05, 1666719.13it/s] 9492065it [00:05, 1680780.65it/s] 9664164it [00:05, 1692796.76it/s] 9833453it [00:05, 1689309.44it/s] 10002965it [00:06, 1691006.93it/s] 10172072it [00:06, 1690530.13it/s] 10341129it [00:06, 1669221.07it/s] 10509534it [00:06, 1673604.19it/s] 10679997it [00:06, 1682828.08it/s] 10848320it [00:06, 1676704.28it/s] 11016819it [00:06, 1679154.11it/s] 11184757it [00:06, 1673794.17it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f14fdc-R1_B23WHYVLT4_1.md.bai 11353074it [00:06, 1676573.67it/s] 11520746it [00:06, 1672029.21it/s] 11687960it [00:07, 1631738.42it/s] 11851341it [00:07, 1619938.29it/s] 12015131it [00:07, 1625110.74it/s] 12177752it [00:07, 1488177.57it/s] 12342298it [00:07, 1531916.11it/s] 12508302it [00:07, 1568361.50it/s] 12674186it [00:07, 1594516.57it/s] 12834787it [00:07, 1514790.22it/s] 12898142it [00:07, 1640637.20it/s] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f14fdc-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f14fdc-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f14fdc-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f14fdc-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f14fdc-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f14fdc-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f14fdc-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f14fdc-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f14fdc-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f14fdc-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f14fdc-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f14fdc-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f14fdc-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f14fdc-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f14fdc-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f14fdc-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f14fdc-R1_B23WHYVLT4_1.md.bai