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/dc/96019a9be1d45008d18f704e0cba15/.command.sh
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/24/ca2ff9c0b35c112a28875b9a8b2f5f/BT-20_FFPE_RNA_0001_B23LG7FLT4_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/dc/96019a9be1d45008d18f704e0cba15/.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/24/ca2ff9c0b35c112a28875b9a8b2f5f/BT-20_FFPE_RNA_0001_B23LG7FLT4_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 BT-20_FFPE_RNA_0001_B23LG7FLT4_1
+ all_qc -bam BT-20_FFPE_RNA_0001_B23LG7FLT4_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 BT-20_FFPE_RNA_0001_B23LG7FLT4_1 -reference ref_genome.fa -region chr20
mkdir -p BT-20_FFPE_RNA_0001_B23LG7FLT4_1/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md/
cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > BT-20_FFPE_RNA_0001_B23LG7FLT4_1/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md/full_bed.bed
seqtool depth -bam BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bam -bed BT-20_FFPE_RNA_0001_B23LG7FLT4_1/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > BT-20_FFPE_RNA_0001_B23LG7FLT4_1/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.depth.gz
saturation_plot -bams BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bam -region chr20 -output BT-20_FFPE_RNA_0001_B23LG7FLT4_1/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md/saturation_plot.png -threads 1
seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bam > BT-20_FFPE_RNA_0001_B23LG7FLT4_1/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md/saturation_qc.tsv
fragment_size -bams BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bam -region chr20 -output_prefix BT-20_FFPE_RNA_0001_B23LG7FLT4_1/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md/fragsize -threads 1
samtools mpileup -B --min-MQ 60 --min-BQ 30 -f ref_genome.fa -l dbsnp_hg38_contam_sites.bed BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bam > BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.mpileup && contamination -input BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > BT-20_FFPE_RNA_0001_B23LG7FLT4_1/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md/contamination.tsv
[W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[mpileup] 1 samples in 1 input files
[W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_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: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
0it [00:00, ?it/s][W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
93111it [00:00, 930837.91it/s]
186195it [00:00, 920256.52it/s]
278229it [00:00, 889869.78it/s]
367319it [00:00, 883736.84it/s]
465064it [00:00, 916786.19it/s]
558594it [00:00, 922958.10it/s]
650966it [00:00, 920016.91it/s]
750392it [00:00, 943428.41it/s]
845403it [00:00, 945324.36it/s]
941317it [00:01, 949552.93it/s]
1036301it [00:01, 947719.20it/s]
1136346it [00:01, 963688.39it/s]
1233513it [00:01, 966083.99it/s]
1332646it [00:01, 973677.85it/s]
1430025it [00:01, 910422.36it/s]
1521898it [00:01, 793026.01it/s]
1604232it [00:01, 729008.45it/s]
1679799it [00:01, 690435.96it/s]
1750707it [00:02, 665435.02it/s]
1818432it [00:02, 647127.40it/s]
1883852it [00:02, 633936.33it/s]
1947646it [00:02, 624061.21it/s]
2010266it [00:02, 616163.56it/s]
2071986it [00:02, 610908.86it/s]
2133122it [00:02, 606872.69it/s]
2193823it [00:02, 604895.37it/s]
2254315it [00:02, 601490.45it/s]
2314458it [00:03, 599588.53it/s]
2374409it [00:03, 598378.92it/s]
2434637it [00:03, 599514.67it/s]
2494585it [00:03, 599406.72it/s][W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
2554862it [00:03, 600393.18it/s]
2614901it [00:03, 599925.37it/s]
2674893it [00:03, 598257.53it/s]
2734719it [00:03, 583607.73it/s]
2833773it [00:03, 703114.76it/s]
2933236it [00:03, 789261.54it/s][W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
3032059it [00:04, 848316.14it/s]
3130425it [00:04, 888603.69it/s][W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
3230216it [00:04, 921206.16it/s]
3328736it [00:04, 940316.27it/s]
3422905it [00:04, 930541.09it/s]
3516077it [00:04, 924157.03it/s]
3608776it [00:04, 924975.71it/s]
3701336it [00:04, 916334.15it/s]
3793025it [00:04, 904242.55it/s]
3883865it [00:04, 905447.77it/s]
3989241it [00:05, 949227.32it/s]
4095419it [00:05, 982667.24it/s]
4196600it [00:05, 991331.37it/s]
4296026it [00:05, 992189.34it/s]
4374251it [00:05, 807935.67it/s]
[W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
tabix -s 1 -b 2 -e 2 BT-20_FFPE_RNA_0001_B23LG7FLT4_1/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.depth.gz
seqtool depth_hist -nbins 500 BT-20_FFPE_RNA_0001_B23LG7FLT4_1/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.depth.gz > BT-20_FFPE_RNA_0001_B23LG7FLT4_1/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.depth_hist.tsv
cat BT-20_FFPE_RNA_0001_B23LG7FLT4_1/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md -output BT-20_FFPE_RNA_0001_B23LG7FLT4_1/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md/BT-20_FFPE_RNA_0001_B23LG7FLT4_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 BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bam > BT-20_FFPE_RNA_0001_B23LG7FLT4_1/BT-20_FFPE_RNA_0001_B23LG7FLT4_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 BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bam > BT-20_FFPE_RNA_0001_B23LG7FLT4_1/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md/reads_per_target.Twist_rna_exome_AND_fusion_hg38.bed.tsv
seqtool depth_stats -bed Twist_rna_exome_AND_fusion_hg38.bed BT-20_FFPE_RNA_0001_B23LG7FLT4_1/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.depth.gz> BT-20_FFPE_RNA_0001_B23LG7FLT4_1/BT-20_FFPE_RNA_0001_B23LG7FLT4_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 BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bam > BT-20_FFPE_RNA_0001_B23LG7FLT4_1/BT-20_FFPE_RNA_0001_B23LG7FLT4_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: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bai
cat BT-20_FFPE_RNA_0001_B23LG7FLT4_1/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "BT-20_FFPE_RNA_0001_B23LG7FLT4_1/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile"
echo `date` > BT-20_FFPE_RNA_0001_B23LG7FLT4_1/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md/qc_complete.txt
+ merge_qc -folders BT-20_FFPE_RNA_0001_B23LG7FLT4_1/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md -output BT-20_FFPE_RNA_0001_B23LG7FLT4_1/BT-20_FFPE_RNA_0001_B23LG7FLT4_1_full_basic_stats.tsv
+ head -n1 BT-20_FFPE_RNA_0001_B23LG7FLT4_1/BT-20_FFPE_RNA_0001_B23LG7FLT4_1_full_basic_stats.tsv
++ basename Twist_rna_exome_AND_fusion_hg38.bed
+ grep -e Twist_rna_exome_AND_fusion_hg38.bed BT-20_FFPE_RNA_0001_B23LG7FLT4_1/BT-20_FFPE_RNA_0001_B23LG7FLT4_1_full_basic_stats.tsv