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/74/8ce7518973843aab83f1e931eda422/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/be/e00579205bef1349cfdef3d2c930f0/aih-tih-sc-f39d87-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-rnd-pltf-dev-nextflow-scratch-01/work/be/e00579205bef1349cfdef3d2c930f0/aih-tih-sc-f39d87-R1_B23WHYVLT4_1.md.bam 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/74/8ce7518973843aab83f1e931eda422/.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-f39d87-R1_B23WHYVLT4_1 + all_qc -bam aih-tih-sc-f39d87-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-f39d87-R1_B23WHYVLT4_1 -reference ref_genome.fa -region chr20 mkdir -p aih-tih-sc-f39d87-R1_B23WHYVLT4_1/aih-tih-sc-f39d87-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-f39d87-R1_B23WHYVLT4_1/aih-tih-sc-f39d87-R1_B23WHYVLT4_1.md/full_bed.bed seqtool depth -bam aih-tih-sc-f39d87-R1_B23WHYVLT4_1.md.bam -bed aih-tih-sc-f39d87-R1_B23WHYVLT4_1/aih-tih-sc-f39d87-R1_B23WHYVLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > aih-tih-sc-f39d87-R1_B23WHYVLT4_1/aih-tih-sc-f39d87-R1_B23WHYVLT4_1.md/aih-tih-sc-f39d87-R1_B23WHYVLT4_1.md.depth.gz seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 aih-tih-sc-f39d87-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-f39d87-R1_B23WHYVLT4_1/aih-tih-sc-f39d87-R1_B23WHYVLT4_1.md/saturation_qc.tsv saturation_plot -bams aih-tih-sc-f39d87-R1_B23WHYVLT4_1.md.bam -region chr20 -output aih-tih-sc-f39d87-R1_B23WHYVLT4_1/aih-tih-sc-f39d87-R1_B23WHYVLT4_1.md/saturation_plot.png -threads 1 fragment_size -bams aih-tih-sc-f39d87-R1_B23WHYVLT4_1.md.bam -region chr20 -output_prefix aih-tih-sc-f39d87-R1_B23WHYVLT4_1/aih-tih-sc-f39d87-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-f39d87-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-f39d87-R1_B23WHYVLT4_1.md.mpileup && contamination -input aih-tih-sc-f39d87-R1_B23WHYVLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > aih-tih-sc-f39d87-R1_B23WHYVLT4_1/aih-tih-sc-f39d87-R1_B23WHYVLT4_1.md/contamination.tsv [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f39d87-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-f39d87-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f39d87-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f39d87-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f39d87-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f39d87-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-f39d87-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f39d87-R1_B23WHYVLT4_1.md.bai 0it [00:00, ?it/s] 127118it [00:00, 1270675.28it/s] 273435it [00:00, 1383625.87it/s] 411798it [00:00, 1347797.74it/s] 557415it [00:00, 1389853.66it/s] 696533it [00:00, 1377668.02it/s] 842866it [00:00, 1406373.10it/s] 983602it [00:00, 1397862.50it/s] 1123458it [00:00, 1387905.10it/s] 1264985it [00:00, 1396315.07it/s] 1421001it [00:01, 1446433.14it/s] 1581492it [00:01, 1494540.56it/s] 1737760it [00:01, 1514840.66it/s] 1889307it [00:01, 1509710.98it/s] 2040325it [00:01, 1488524.33it/s] 2200782it [00:01, 1523002.36it/s] 2356980it [00:01, 1534568.15it/s] 2510524it [00:01, 1496965.34it/s] 2660464it [00:01, 1465236.82it/s] 2817899it [00:01, 1489386.80it/s] 2967203it [00:02, 1490408.69it/s] 3119523it [00:02, 1500024.96it/s] 3269656it [00:02, 1405840.41it/s] 3411454it [00:02, 1311394.75it/s] 3544396it [00:02, 1257443.83it/s] 3685233it [00:02, 1298476.91it/s] 3837109it [00:02, 1360112.51it/s] 3993446it [00:02, 1418149.29it/s] 4148824it [00:02, 1457424.41it/s] 4300081it [00:03, 1473504.04it/s] 4448193it [00:03, 1469547.63it/s] 4603148it [00:03, 1493132.64it/s] 4756864it [00:03, 1506151.93it/s] 4907778it [00:03, 1500793.84it/s] 5067426it [00:03, 1529233.83it/s] 5220520it [00:03, 1476184.78it/s] 5368634it [00:03, 1473190.29it/s] 5516293it [00:03, 1388228.13it/s] 5656230it [00:03, 1308708.94it/s] 5812059it [00:04, 1377421.78it/s] 5958667it [00:04, 1402368.65it/s] 6104913it [00:04, 1419609.08it/s] 6251303it [00:04, 1432466.12it/s] 6409969it [00:04, 1477712.69it/s] 6571965it [00:04, 1519715.45it/s] 6734295it [00:04, 1550429.67it/s] 6893319it [00:04, 1562214.51it/s] 7056155it [00:04, 1581915.22it/s] 7218153it [00:04, 1593247.99it/s] 7381299it [00:05, 1604577.17it/s] 7541859it [00:05, 1596325.02it/s] 7706488it [00:05, 1611189.07it/s] 7867671it [00:05, 1554162.94it/s] 8029007it [00:05, 1571394.53it/s] 8188105it [00:05, 1576993.58it/s] 8349802it [00:05, 1588781.25it/s] 8509292it [00:05, 1590556.69it/s] 8668495it [00:05, 1568871.55it/s] 8825540it [00:05, 1532655.98it/s] 8979056it [00:06, 1517427.46it/s] 9133954it [00:06, 1526608.18it/s] 9286760it [00:06, 1505101.91it/s] 9437405it [00:06, 1478564.89it/s] 9585406it [00:06, 1449449.22it/s] 9730505it [00:06, 1398928.45it/s] 9871056it [00:06, 1400753.87it/s] 10011382it [00:06, 1387415.13it/s] 10171709it [00:06, 1450029.70it/s] 10324576it [00:07, 1473057.21it/s] 10475396it [00:07, 1483304.46it/s] 10630778it [00:07, 1504134.31it/s] 10781360it [00:07, 1481072.09it/s] 10943628it [00:07, 1522598.86it/s] 11104860it [00:07, 1549133.68it/s] 11265163it [00:07, 1565054.09it/s] 11424697it [00:07, 1573918.21it/s] 11582186it [00:07, 1539344.67it/s] 11736345it [00:07, 1510569.20it/s] 11887634it [00:08, 1497930.77it/s] 12037582it [00:08, 1436371.84it/s] 12181746it [00:08, 1346856.49it/s] 12317645it [00:08, 1276451.45it/s] 12446503it [00:08, 1249215.11it/s] 12572175it [00:08, 1217870.22it/s] 12694428it [00:08, 1203923.54it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f39d87-R1_B23WHYVLT4_1.md.bai 12815077it [00:08, 1202059.33it/s] 12935794it [00:08, 1203486.69it/s] 13056268it [00:09, 1203104.43it/s] 13176665it [00:09, 1199085.78it/s] 13296628it [00:09, 1193904.39it/s] 13416052it [00:09, 1183794.51it/s] 13534501it [00:09, 1183964.01it/s] 13654779it [00:09, 1189500.47it/s] 13775191it [00:09, 1193811.48it/s][W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f39d87-R1_B23WHYVLT4_1.md.bai 13894868it [00:09, 1194656.49it/s] 14014347it [00:09, 1194566.55it/s] 14133813it [00:09, 1192657.71it/s] 14253086it [00:10, 1182545.18it/s] 14371362it [00:10, 1175121.75it/s] 14434914it [00:10, 1415344.52it/s] [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f39d87-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f39d87-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f39d87-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f39d87-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f39d87-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f39d87-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f39d87-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f39d87-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f39d87-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f39d87-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f39d87-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f39d87-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f39d87-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f39d87-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f39d87-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f39d87-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f39d87-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f39d87-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f39d87-R1_B23WHYVLT4_1.md.bai tabix -s 1 -b 2 -e 2 aih-tih-sc-f39d87-R1_B23WHYVLT4_1/aih-tih-sc-f39d87-R1_B23WHYVLT4_1.md/aih-tih-sc-f39d87-R1_B23WHYVLT4_1.md.depth.gz seqtool depth_hist -nbins 500 aih-tih-sc-f39d87-R1_B23WHYVLT4_1/aih-tih-sc-f39d87-R1_B23WHYVLT4_1.md/aih-tih-sc-f39d87-R1_B23WHYVLT4_1.md.depth.gz > aih-tih-sc-f39d87-R1_B23WHYVLT4_1/aih-tih-sc-f39d87-R1_B23WHYVLT4_1.md/aih-tih-sc-f39d87-R1_B23WHYVLT4_1.md.depth_hist.tsv cat aih-tih-sc-f39d87-R1_B23WHYVLT4_1/aih-tih-sc-f39d87-R1_B23WHYVLT4_1.md/aih-tih-sc-f39d87-R1_B23WHYVLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title aih-tih-sc-f39d87-R1_B23WHYVLT4_1.md -output aih-tih-sc-f39d87-R1_B23WHYVLT4_1/aih-tih-sc-f39d87-R1_B23WHYVLT4_1.md/aih-tih-sc-f39d87-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-f39d87-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-f39d87-R1_B23WHYVLT4_1/aih-tih-sc-f39d87-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-f39d87-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-f39d87-R1_B23WHYVLT4_1/aih-tih-sc-f39d87-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-f39d87-R1_B23WHYVLT4_1/aih-tih-sc-f39d87-R1_B23WHYVLT4_1.md/aih-tih-sc-f39d87-R1_B23WHYVLT4_1.md.depth.gz> aih-tih-sc-f39d87-R1_B23WHYVLT4_1/aih-tih-sc-f39d87-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-f39d87-R1_B23WHYVLT4_1.md.bam > aih-tih-sc-f39d87-R1_B23WHYVLT4_1/aih-tih-sc-f39d87-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-f39d87-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f39d87-R1_B23WHYVLT4_1.md.bai [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f39d87-R1_B23WHYVLT4_1.md.bai cat aih-tih-sc-f39d87-R1_B23WHYVLT4_1/aih-tih-sc-f39d87-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-f39d87-R1_B23WHYVLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "aih-tih-sc-f39d87-R1_B23WHYVLT4_1/aih-tih-sc-f39d87-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-f39d87-R1_B23WHYVLT4_1/aih-tih-sc-f39d87-R1_B23WHYVLT4_1.md/qc_complete.txt + merge_qc -folders aih-tih-sc-f39d87-R1_B23WHYVLT4_1/aih-tih-sc-f39d87-R1_B23WHYVLT4_1.md -output aih-tih-sc-f39d87-R1_B23WHYVLT4_1/aih-tih-sc-f39d87-R1_B23WHYVLT4_1_full_basic_stats.tsv + head -n1 aih-tih-sc-f39d87-R1_B23WHYVLT4_1/aih-tih-sc-f39d87-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-f39d87-R1_B23WHYVLT4_1/aih-tih-sc-f39d87-R1_B23WHYVLT4_1_full_basic_stats.tsv