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/fb/2f82be859249429b5e15d23e19cd42/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/79/db656108731ba2de3a43e386ace28f/FFPE_HD789_01_RNA_13_B23MVV7LT4_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/79/db656108731ba2de3a43e386ace28f/FFPE_HD789_01_RNA_13_B23MVV7LT4_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/fb/2f82be859249429b5e15d23e19cd42/.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 FFPE_HD789_01_RNA_13_B23MVV7LT4_1
+ all_qc -bam FFPE_HD789_01_RNA_13_B23MVV7LT4_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 FFPE_HD789_01_RNA_13_B23MVV7LT4_1 -reference ref_genome.fa -region chr20
mkdir -p FFPE_HD789_01_RNA_13_B23MVV7LT4_1/FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md/
cat Twist_rna_exome_AND_fusion_hg38.bed | cut -f 1-3 | bedtools sort -g ref_genome.fa.fai | bedtools merge > FFPE_HD789_01_RNA_13_B23MVV7LT4_1/FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md/full_bed.bed
seqtool depth -bam FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bam -bed FFPE_HD789_01_RNA_13_B23MVV7LT4_1/FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md/full_bed.bed -threads 4 -bam_threads 2 | bgzip -c > FFPE_HD789_01_RNA_13_B23MVV7LT4_1/FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md/FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.depth.gz
saturation_plot -bams FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bam -region chr20 -output FFPE_HD789_01_RNA_13_B23MVV7LT4_1/FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md/saturation_plot.png -threads 1
seqtool saturation_metric -at 1000000 -region chr20 -bam_threads 1 FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bam > FFPE_HD789_01_RNA_13_B23MVV7LT4_1/FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md/saturation_qc.tsv
fragment_size -bams FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bam -region chr20 -output_prefix FFPE_HD789_01_RNA_13_B23MVV7LT4_1/FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md/fragsize -threads 1
samtools mpileup -B --min-MQ 60 --min-BQ 30 -f ref_genome.fa -l dbsnp_hg38_contam_sites.bed FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bam > FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.mpileup && contamination -input FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.mpileup -dbsnp_vcf Homo_sapiens_assembly38.dbsnp138.vcf.gz > FFPE_HD789_01_RNA_13_B23MVV7LT4_1/FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md/contamination.tsv
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
[mpileup] 1 samples in 1 input files
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_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: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
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[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
tabix -s 1 -b 2 -e 2 FFPE_HD789_01_RNA_13_B23MVV7LT4_1/FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md/FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.depth.gz
seqtool depth_hist -nbins 500 FFPE_HD789_01_RNA_13_B23MVV7LT4_1/FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md/FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.depth.gz > FFPE_HD789_01_RNA_13_B23MVV7LT4_1/FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md/FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.depth_hist.tsv
cat FFPE_HD789_01_RNA_13_B23MVV7LT4_1/FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md/FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.depth_hist.tsv | plot -x 0 -xlabel Depth -ylabel "Number of Sites" -xlim 0 2000 -title FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md -output FFPE_HD789_01_RNA_13_B23MVV7LT4_1/FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md/FFPE_HD789_01_RNA_13_B23MVV7LT4_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 FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bam > FFPE_HD789_01_RNA_13_B23MVV7LT4_1/FFPE_HD789_01_RNA_13_B23MVV7LT4_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 FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bam > FFPE_HD789_01_RNA_13_B23MVV7LT4_1/FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md/reads_per_target.Twist_rna_exome_AND_fusion_hg38.bed.tsv
seqtool depth_stats -bed Twist_rna_exome_AND_fusion_hg38.bed FFPE_HD789_01_RNA_13_B23MVV7LT4_1/FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md/FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.depth.gz> FFPE_HD789_01_RNA_13_B23MVV7LT4_1/FFPE_HD789_01_RNA_13_B23MVV7LT4_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 FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bam > FFPE_HD789_01_RNA_13_B23MVV7LT4_1/FFPE_HD789_01_RNA_13_B23MVV7LT4_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: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
[W::hts_idx_load3] The index file is older than the data file: FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md.bai
cat FFPE_HD789_01_RNA_13_B23MVV7LT4_1/FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md/gc_bias_qc.Twist_rna_exome_AND_fusion_hg38.bed.tsv | plot -x 0 -header infer -ylim 0 2 -title "FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md" -suptitle "Twist_rna_exome_AND_fusion_hg38.bed" -output "FFPE_HD789_01_RNA_13_B23MVV7LT4_1/FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md/gc_bias.Twist_rna_exome_AND_fusion_hg38.bed.png" -ylabel "Fold enrichment / depletion" -xlabel "GC Quantile"
echo `date` > FFPE_HD789_01_RNA_13_B23MVV7LT4_1/FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md/qc_complete.txt
+ merge_qc -folders FFPE_HD789_01_RNA_13_B23MVV7LT4_1/FFPE_HD789_01_RNA_13_B23MVV7LT4_1.md -output FFPE_HD789_01_RNA_13_B23MVV7LT4_1/FFPE_HD789_01_RNA_13_B23MVV7LT4_1_full_basic_stats.tsv
+ head -n1 FFPE_HD789_01_RNA_13_B23MVV7LT4_1/FFPE_HD789_01_RNA_13_B23MVV7LT4_1_full_basic_stats.tsv
++ basename Twist_rna_exome_AND_fusion_hg38.bed
+ grep -e Twist_rna_exome_AND_fusion_hg38.bed FFPE_HD789_01_RNA_13_B23MVV7LT4_1/FFPE_HD789_01_RNA_13_B23MVV7LT4_1_full_basic_stats.tsv