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/2c/52a8bbd0928a71f22facd49ea7e5b8/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/40/f75e2719d3e9d36bc6490dbb4a8d62/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bam
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/40/f75e2719d3e9d36bc6490dbb4a8d62/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai
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/2c/52a8bbd0928a71f22facd49ea7e5b8/.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 BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1
+ all_qc -bam BreastNP_FFPE_L03_RNA_01_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 BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1 -reference ref_genome.fa -region chr20
mkdir -p BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md/
cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md/full_bed.bed
saturation_plot -bams BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bam -region chr20 -output BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md/saturation_plot.png -threads 1
seqtool depth -bam BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bam -bed BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.depth.gz
seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bam > BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md/saturation_qc.tsv
fragment_size -bams BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bam -region chr20 -output_prefix BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L03_RNA_01_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 BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bam > BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.mpileup && contamination -input BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md/contamination.tsv
[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai
[mpileup] 1 samples in 1 input files
[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L03_RNA_01_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: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai
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[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai
237603it [00:00, 1159253.98it/s][W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai
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[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai
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[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai
tabix -s 1 -b 2 -e 2 BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.depth.gz
seqtool depth_hist -nbins 500 BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.depth.gz > BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.depth_hist.tsv
cat BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md -output BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md/BreastNP_FFPE_L03_RNA_01_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 BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bam > BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L03_RNA_01_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 BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bam > BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L03_RNA_01_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 BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.depth.gz> BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L03_RNA_01_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 BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bam > BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L03_RNA_01_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: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bai
cat BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile"
echo `date` > BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md/qc_complete.txt
+ merge_qc -folders BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md -output BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1_full_basic_stats.tsv
+ head -n1 BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1_full_basic_stats.tsv
++ basename Twist_rna_exome_AND_fusion_hg38.bed
+ grep -e Twist_rna_exome_AND_fusion_hg38.bed BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1_full_basic_stats.tsv